=> Building biology/cufflinks Started : Wednesday, 24 JUL 2019 at 16:49:25 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.6-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.6-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/construction/biology/cufflinks XDG_CONFIG_HOME=/construction/biology/cufflinks HOME=/construction/biology/cufflinks TMPDIR="/tmp" PATH=/construction/biology/cufflinks/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/cufflinks XDG_CONFIG_HOME=/construction/biology/cufflinks HOME=/construction/biology/cufflinks TMPDIR="/tmp" PATH=/construction/biology/cufflinks/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS=" -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -I/usr/local/include/eigen3 " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/cufflinks/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PYTHON_INCLUDEDIR=include/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=dragonfly5 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=5.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/cufflinks" EXAMPLESDIR="share/examples/cufflinks" DATADIR="share/cufflinks" WWWDIR="www/cufflinks" ETCDIR="etc/cufflinks" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cufflinks DOCSDIR=/usr/local/share/doc/cufflinks EXAMPLESDIR=/usr/local/share/examples/cufflinks WWWDIR=/usr/local/www/cufflinks ETCDIR=/usr/local/etc/cufflinks -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.6 USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500601 OSVERSION=9999999 OSREL=5.6 _OSRELEASE=5.6-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSL accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> cufflinks-2.2.1.83 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> cufflinks-2.2.1.83 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cufflinks-2.2.1.83 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.83 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.83 for building => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.83 for building ===> Extracting for cufflinks-2.2.1.83 => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for cufflinks-2.2.1.83 ===> Applying ports patches for cufflinks-2.2.1.83 ===> Applying dragonfly patches for cufflinks-2.2.1.83 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> cufflinks-2.2.1.83 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_2.txz Installing autoconf-2.69_2... `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: .......... done `-- Installing indexinfo-0.3.1... `-- Extracting indexinfo-0.3.1: .... done `-- Installing m4-1.4.18_1,1... `-- Extracting m4-1.4.18_1,1: .......... done `-- Installing perl5-5.28.2... `-- Extracting perl5-5.28.2: .......... done Extracting autoconf-2.69_2: .......... done Message from perl5-5.28.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> cufflinks-2.2.1.83 depends on package: autoconf>=2.69 - found ===> Returning to build of cufflinks-2.2.1.83 ===> cufflinks-2.2.1.83 depends on package: automake>=1.16.1 - not found ===> Installing existing package /packages/All/automake-1.16.1_1.txz Installing automake-1.16.1_1... Extracting automake-1.16.1_1: .......... done ===> cufflinks-2.2.1.83 depends on package: automake>=1.16.1 - found ===> Returning to build of cufflinks-2.2.1.83 ===> cufflinks-2.2.1.83 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.3.7.txz Installing eigen-3.3.7... Extracting eigen-3.3.7: .......... done ===> cufflinks-2.2.1.83 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of cufflinks-2.2.1.83 ===> cufflinks-2.2.1.83 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... `-- Installing gettext-runtime-0.20.1... `-- Extracting gettext-runtime-0.20.1: .......... done Extracting gmake-4.2.1_3: .......... done ===> cufflinks-2.2.1.83 depends on executable: gmake - found ===> Returning to build of cufflinks-2.2.1.83 ===> cufflinks-2.2.1.83 depends on file: /usr/local/bin/python3.6 - not found ===> Installing existing package /packages/All/python36-3.6.9.txz Installing python36-3.6.9... `-- Installing expat-2.2.6_1... `-- Extracting expat-2.2.6_1: .......... done `-- Installing libffi-3.2.1_3... `-- Extracting libffi-3.2.1_3: .......... done `-- Installing libressl-2.9.2... `-- Extracting libressl-2.9.2: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done `-- Installing readline-8.0.0... `-- Extracting readline-8.0.0: .......... done Extracting python36-3.6.9: .......... done Message from python36-3.6.9: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== ===> cufflinks-2.2.1.83 depends on file: /usr/local/bin/python3.6 - found ===> Returning to build of cufflinks-2.2.1.83 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> cufflinks-2.2.1.83 depends on shared library: libboost_system.so - not found ===> Installing existing package /packages/All/boost-libs-1.70.0_2.txz Installing boost-libs-1.70.0_2... `-- Installing icu-64.2,1... `-- Extracting icu-64.2,1: .......... done Extracting boost-libs-1.70.0_2: .......... done Message from boost-libs-1.70.0_2: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> cufflinks-2.2.1.83 depends on shared library: libboost_system.so - found (/usr/local/lib/libboost_system.so) ===> Returning to build of cufflinks-2.2.1.83 ===> cufflinks-2.2.1.83 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.9.txz Installing htslib-1.9... `-- Installing curl-7.65.1_1... | `-- Installing ca_root_nss-3.45... | `-- Extracting ca_root_nss-3.45: ........ done | `-- Installing libnghttp2-1.39.1... | `-- Extracting libnghttp2-1.39.1: .......... done `-- Extracting curl-7.65.1_1: .......... done Extracting htslib-1.9: .......... done Message from ca_root_nss-3.45: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> cufflinks-2.2.1.83 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of cufflinks-2.2.1.83 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for cufflinks-2.2.1.83 sh: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:42: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:42: the top level sh: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:42: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:42: the top level sh: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:42: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:42: the top level sh: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:42: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:42: the top level sh: svnversion: not found configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_system.m4:33: AX_BOOST_SYSTEM is expanded from... configure.ac:39: the top level configure.ac:40: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_serialization.m4:33: AX_BOOST_SERIALIZATION is expanded from... configure.ac:40: the top level configure.ac:42: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from... ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from... ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from... ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from... ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from... ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from... ax_boost_thread.m4:33: AX_BOOST_THREAD is expanded from... configure.ac:42: the top level configure.ac:35: installing 'build-aux/ar-lib' configure.ac:31: installing 'build-aux/compile' configure.ac:39: installing 'build-aux/config.guess' configure.ac:39: installing 'build-aux/config.sub' configure.ac:16: installing 'build-aux/install-sh' configure.ac:16: installing 'build-aux/missing' src/Makefile.am:113: warning: source file 'locfit/adap.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled automake: warning: possible forward-incompatibility. automake: At least a source file is in a subdirectory, but the 'subdir-objects' automake: automake option hasn't been enabled. For now, the corresponding output automake: object file(s) will be placed in the top-level directory. However, automake: this behaviour will change in future Automake versions: they will automake: unconditionally cause object files to be placed in the same subdirectory automake: of the corresponding sources. automake: You are advised to start using 'subdir-objects' option throughout your automake: project, to avoid future incompatibilities. src/Makefile.am:113: warning: source file 'locfit/ar_funs.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/arith.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/band.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_args.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/c_plot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/cmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_haz.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_int.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dens_odi.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/density.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/dist.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_atree.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_interp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_kdtre.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_main.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/ev_trian.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/family.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/fitted.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/frend.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/help.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_dercor.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_fitfun.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_robust.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lf_vari.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/lfstr.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/linalg.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/locfit.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_chol.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_eigen.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_jacob.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/m_max.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/makecmd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/math.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/minmax.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/nbhd.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pcomp.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/pout.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/preplot.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/random.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/readfile.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/scb_cons.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/simul.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/solve.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/startlf.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/strings.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/vari.cpp' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/wdiag.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am:113: warning: source file 'locfit/weight.c' is in a subdirectory, src/Makefile.am:113: but option 'subdir-objects' is disabled src/Makefile.am: installing 'build-aux/depcomp' configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking for gawk... (cached) /usr/bin/awk checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking whether gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking whether gmake sets $(MAKE)... (cached) yes checking for ranlib... ranlib checking for ar... ar checking the archiver (ar) interface... ar checking whether /usr/local/bin/python3.6 version is >= 2.4... yes checking for /usr/local/bin/python3.6 version... 3.6 checking for /usr/local/bin/python3.6 platform... dragonfly5 checking for /usr/local/bin/python3.6 script directory... ${prefix}/lib/python3.6/site-packages checking for /usr/local/bin/python3.6 extension module directory... ${exec_prefix}/lib/python3.6/site-packages checking for boostlib >= 1.47.0... yes checking for htslib or bamlib... yes checking build system type... x86_64-portbld-dragonfly5.6 checking whether the Boost::System library is available... yes checking for exit in -lboost_system... yes checking for exit in -lboost_system... (cached) yes checking whether the Boost::Serialization library is available... yes checking for exit in -lboost_serialization... yes checking for exit in -lboost_serialization... (cached) yes checking whether the Boost::Filesystem library is available... yes checking for exit in -lboost_filesystem... yes checking whether the Boost::Thread library is available... yes checking for exit in -lboost_thread... yes checking for exit in -lboost_system... (cached) yes checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking if zlib is wanted... yes checking for inflateEnd in -lz... yes checking for zlib.h... (cached) yes checking for inflateEnd in -lz... (cached) yes checking zlib in /usr... ok ./configure: AX_EIGEN: not found checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for inline... inline checking for pid_t... (cached) yes checking for size_t... (cached) yes checking for ptrdiff_t... (cached) yes checking host system type... x86_64-portbld-dragonfly5.6 checking if gcc accepts -m64... checking for struct sysinfo.totalram... no checking whether sysctl is declared... yes checking whether CTL_HW is declared... yes checking whether HW_PHYSMEM is declared... yes checking how to create a pax tar archive... gnutar checking dependency style of cc... (cached) gcc3 checking dependency style of c++... (cached) gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- cufflinks 2.2.2 Configuration Results -- C++ compiler: c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib GCC version: cc 8.3 [DragonFly] Release/2019-02-22 Host System type: x86_64-portbld-dragonfly5.6 Install prefix: /usr/local Install eprefix: ${prefix} See config.h for further configuration information. Email with questions and bug reports. -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for cufflinks-2.2.1.83 gmake[1]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' gmake all-recursive gmake[2]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' Making all in src gmake[3]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050/src' c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT cufflinks.o -MD -MP -MF .deps/cufflinks.Tpo -c -o cufflinks.o cufflinks.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT clustering.o -MD -MP -MF .deps/clustering.Tpo -c -o clustering.o clustering.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT differential.o -MD -MP -MF .deps/differential.Tpo -c -o differential.o differential.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT common.o -MD -MP -MF .deps/common.Tpo -c -o common.o common.cpp c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT assemble.o -MD -MP -MF .deps/assemble.Tpo -c -o assemble.o assemble.cpp In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: ./lemon/error.h:93:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr<_Type> ptr; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: ./lemon/error.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr buf; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from assemble.cpp:19: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from assemble.cpp:19: ./lemon/topology.h: In function 'bool lemon::stronglyConnected(const Graph&)': ./lemon/topology.h:249:34: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::Node Node; ^~~~ ./lemon/topology.h: In function 'int lemon::countStronglyConnectedComponents(const Graph&)': ./lemon/topology.h:311:34: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::Edge Edge; ^~~~ ./lemon/topology.h:313:36: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::EdgeIt EdgeIt; ^~~~~~ ./lemon/topology.h: In function 'void lemon::topologicalSort(const Graph&, NodeMap&)': ./lemon/topology.h:1213:34: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::Node Node; ^~~~ ./lemon/topology.h:1215:34: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::Edge Edge; ^~~~ ./lemon/topology.h: In function 'bool lemon::bipartite(const UGraph&)': ./lemon/topology.h:1470:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs] typedef typename UGraph::EdgeIt EdgeIt; ^~~~~~ ./lemon/topology.h: In function 'bool lemon::bipartitePartitions(const UGraph&, NodeMap&)': ./lemon/topology.h:1514:35: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs] typedef typename UGraph::Node Node; ^~~~ ./lemon/topology.h:1516:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs] typedef typename UGraph::EdgeIt EdgeIt; ^~~~~~ In file included from hits.h:23, from bundles.h:22, from replicates.h:10, from common.cpp:28: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from bundles.h:22, from replicates.h:10, from common.cpp:28: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from bundles.h:22, from replicates.h:10, from common.cpp:28: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hits.h:23, from cufflinks.cpp:15: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from cufflinks.cpp:15: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from cufflinks.cpp:15: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cufflinks.cpp:19: update_check.h: In function 'bool get_current_version(char*)': update_check.h:81:22: warning: argument to 'sizeof' in 'void bzero(void*, size_t)' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~~~~~~~~~ In file included from common.cpp:28: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ In file included from hits.h:23, from abundances.h:23, from differential.cpp:20: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from assemble.cpp:44: transitive_closure.h: In function 'void transitive_closure(const Graph&, GraphTC&, G_to_TC_VertexMap, VertexIndexMap)': transitive_closure.h:85:62: warning: typedef 'edge' locally defined but not used [-Wunused-local-typedefs] typedef typename graph_traits < Graph >::edge_descriptor edge; ^~~~ transitive_closure.h:226:66: warning: typedef 'tc_vertex' locally defined but not used [-Wunused-local-typedefs] typedef typename graph_traits < GraphTC >::vertex_descriptor tc_vertex; ^~~~~~~~~ transitive_closure.h: In function 'void warshall_transitive_closure(G&)': transitive_closure.h:323:60: warning: typedef 'vertex' locally defined but not used [-Wunused-local-typedefs] typedef typename graph_traits < G >::vertex_descriptor vertex; ^~~~~~ transitive_closure.h: In function 'void warren_transitive_closure(G&)': transitive_closure.h:349:60: warning: typedef 'vertex' locally defined but not used [-Wunused-local-typedefs] typedef typename graph_traits < G >::vertex_descriptor vertex; ^~~~~~ In file included from assemble.cpp:45: transitive_reduction.h: In function 'boost::ccheck_aux::unaryfunptr_arg_type::type boost::transitive_reduction(const Graph&, GraphTR&, G_to_TR_VertexMap, VertexIndexMap)': transitive_reduction.h:53:63: warning: typedef 'VertexIterator' locally defined but not used [-Wunused-local-typedefs] typedef typename graph_traits::vertex_iterator VertexIterator; ^~~~~~~~~~~~~~ In file included from hits.h:23, from abundances.h:23, from clustering.h:38, from clustering.cpp:10: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from replicates.h:10, from common.cpp:28: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from replicates.h:10, from common.cpp:28: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from /usr/local/include/boost/utility.hpp:21, from /usr/local/include/boost/range/size.hpp:25, from /usr/local/include/boost/range/functions.hpp:20, from /usr/local/include/boost/range/iterator_range_core.hpp:38, from /usr/local/include/boost/lexical_cast.hpp:30, from /usr/local/include/boost/math/tools/convert_from_string.hpp:15, from /usr/local/include/boost/math/constants/constants.hpp:13, from /usr/local/include/boost/math/special_functions/gamma.hpp:24, from /usr/local/include/boost/math/special_functions/erf.hpp:15, from /usr/local/include/boost/math/distributions/normal.hpp:19, from common.h:27, from common.cpp:27: /usr/local/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = PoissonDispersionModel]': /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = PoissonDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = const MassDispersionModel; Y = PoissonDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = PoissonDispersionModel; T = const MassDispersionModel]' common.cpp:487:105: required from here /usr/local/include/boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'PoissonDispersionModel' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from replicates.h:10, from common.cpp:28: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from replicates.h:10, from common.cpp:28: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from replicates.h:10, from common.cpp:28: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from replicates.h:10, from common.cpp:28: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from hits.h:23, from bundles.h:22, from assemble.h:21, from assemble.cpp:48: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from bundles.h:22, from assemble.h:21, from assemble.cpp:48: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from bundles.h:22, from assemble.h:21, from assemble.cpp:48: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from abundances.h:23, from differential.cpp:20: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from abundances.h:23, from differential.cpp:20: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from abundances.h:23, from clustering.h:38, from clustering.cpp:10: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from abundances.h:23, from clustering.h:38, from clustering.cpp:10: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cufflinks.cpp:28: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ cufflinks.cpp: In function 'bool scaffolds_for_bundle(const HitBundle&, std::vector >&, std::vector >*, BundleStats*)': cufflinks.cpp:690:30: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (bundle.hits().size() >= max_frags_per_bundle) ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:690:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (bundle.hits().size() >= max_frags_per_bundle) ^~ cufflinks.cpp:693:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' bool ref_guided = (ref_scaffs != NULL); ^~~~ cufflinks.cpp: In function 'void quantitate_transcript_cluster(AbundanceGroup&, double, std::vector&, bool)': cufflinks.cpp:980:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < N; ++j) ~~^~~ cufflinks.cpp:988:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < N; ++j) ~~^~~ cufflinks.cpp: In function 'void assemble_bundle(const RefSequenceTable&, HitBundle*, boost::shared_ptr, boost::shared_ptr, FILE*, FILE*, FILE*, FILE*)': cufflinks.cpp:1264:55: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool bundle_too_large = bundle_ptr->hits().size() >= max_frags_per_bundle; ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ cufflinks.cpp:1275:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (allow_junk_filtering) ^~ cufflinks.cpp:1279:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' if (!final_est_run && bundle_mode==REF_DRIVEN) // Bias needs to be learned ^~ cufflinks.cpp:1176:17: warning: unused variable 'map_mass' [-Wunused-variable] long double map_mass = rg_props->normalized_map_mass(); ^~~~~~~~ cufflinks.cpp: In function 'bool assemble_hits(BundleFactory&, boost::shared_ptr)': cufflinks.cpp:1491:38: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] if (bundle.right() - bundle.left() > max_gene_length) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ assemble.cpp: In function 'void create_reachability_bp_graph(DAG&, ReachGraph&, std::vector::BNode, std::allocator::BNode> >, DagToBp&, const boost::adjacency_list<>&, const std::vector&)': assemble.cpp:188:21: warning: variable 'a_for_b' set but not used [-Wunused-but-set-variable] ReachGraph::ANode a_for_b = b_to_a[b_id]; ^~~~~~~ assemble.cpp:123:17: warning: variable 'hits_for_node' set but not used [-Wunused-but-set-variable] HitsForNodeMap hits_for_node = get(vertex_name, dag); ^~~~~~~~~~~~~ assemble.cpp: In function 'void add_weights_to_reachability_bp_graph(ReachGraph&, const HitsForNodeMap&, const std::vector&, const std::vector&, lemon::BpUGraphExtender >::UEdgeMap&)': assemble.cpp:262:21: warning: variable 'a_for_b' set but not used [-Wunused-but-set-variable] ReachGraph::ANode a_for_b = bp.nodeFromANodeId(a_id_for_b); ^~~~~~~ In file included from differential.h:29, from differential.cpp:21: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ In file included from differential.cpp:21: differential.h: In constructor 'TrackingDataWriter::TrackingDataWriter(int, Outfiles*, Tracking*, const std::vector >&, std::vector >, ProgressBar*, boost::shared_ptr)': differential.h:230:20: warning: 'TrackingDataWriter::sample_labels' will be initialized after [-Wreorder] vector sample_labels; ^~~~~~~~~~~~~ differential.h:228:10: warning: 'bool TrackingDataWriter::headers_written' [-Wreorder] bool headers_written; // this flag records whether we've written out the file headers yet. ^~~~~~~~~~~~~~~ differential.h:204:5: warning: when initialized here [-Wreorder] TrackingDataWriter(int num_samples, ^~~~~~~~~~~~~~~~~~ In file included from differential.cpp:21: differential.h: In member function 'void TrackingDataWriter::print_FPKM_tracking(const string&, FILE*, const FPKMTrackingTable&)': differential.h:325:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ differential.h: In member function 'void TrackingDataWriter::print_count_tracking(const string&, FILE*, const FPKMTrackingTable&)': differential.h:407:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ differential.h: In member function 'void TrackingDataWriter::print_read_group_simple_table_info(FILE*, const std::vector >&)': differential.h:614:27: warning: format '%lg' expects a matching 'double' argument [-Wformat=] fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from clustering.h:38, from clustering.cpp:10: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from differential.cpp:24: sampling.h: In function 'double boost::numeric::ublas::cholesky_factorize(M&)': sampling.h:50:13: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef M matrix_type; ^~~~~~~~~~~ In file included from differential.cpp:24: sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression&)': sampling.h:113:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:114:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs] typedef vector vector_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression&)': sampling.h:120:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:121:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef matrix matrix_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression&, const M&)': sampling.h:127:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:128:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs] typedef vector vector_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression&, const M&)': sampling.h:134:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:135:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef matrix matrix_type; ^~~~~~~~~~~ differential.cpp: In member function 'virtual void TestLauncher::perform_testing(std::vector >)': differential.cpp:134:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^~ differential.cpp: In member function 'void TestLauncher::record_tracking_data(std::vector >&)': differential.cpp:163:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^~ differential.cpp: In function 'SampleDifference test_diffexp(const FPKMContext&, const FPKMContext&)': differential.cpp:350:61: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (next_sample_idx >= 0 && next_sample_idx < prev.fpkm_samples.size()) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:358:61: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (next_sample_idx >= 0 && next_sample_idx < prev.fpkm_samples.size()) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:380:61: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (next_sample_idx >= 0 && next_sample_idx < curr.fpkm_samples.size()) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:388:61: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (next_sample_idx >= 0 && next_sample_idx < curr.fpkm_samples.size()) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp: In function 'bool test_js(const AbundanceGroup&, const AbundanceGroup&, double&, double&)': differential.cpp:632:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (next_sample_idx >= 0 && next_sample_idx < prev_abundance.member_fpkm_samples().size()) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:644:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (next_sample_idx >= 0 && next_sample_idx < prev_abundance.member_fpkm_samples().size()) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:670:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (next_sample_idx >= 0 && next_sample_idx < curr_abundance.member_fpkm_samples().size()) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:682:57: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (next_sample_idx >= 0 && next_sample_idx < curr_abundance.member_fpkm_samples().size()) ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ differential.cpp: In function 'void test_differential(const string&, const std::vector >&, const std::vector >&, Tests&, Tracking&)': differential.cpp:1400:76: warning: comparison of integer expressions of different signedness: 'std::map, double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1401:76: warning: comparison of integer expressions of different signedness: 'std::map, double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1439:77: warning: comparison of integer expressions of different signedness: 'std::map, double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1440:77: warning: comparison of integer expressions of different signedness: 'std::map, double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1477:76: warning: comparison of integer expressions of different signedness: 'std::map, double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] bool enough_reads = (curr_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test && ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ differential.cpp:1478:76: warning: comparison of integer expressions of different signedness: 'std::map, double>::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] prev_abundance.FPKM_by_replicate().size() >= min_reps_for_js_test); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from differential.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from differential.cpp:20: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ mv -f .deps/common.Tpo .deps/common.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT tokenize.o -MD -MP -MF .deps/tokenize.Tpo -c -o tokenize.o tokenize.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from differential.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from differential.cpp:20: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from differential.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from differential.cpp:20: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from assemble.h:21, from assemble.cpp:48: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ mv -f .deps/tokenize.Tpo .deps/tokenize.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT abundances.o -MD -MP -MF .deps/abundances.Tpo -c -o abundances.o abundances.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from assemble.h:21, from assemble.cpp:48: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from assemble.h:21, from assemble.cpp:48: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from assemble.h:21, from assemble.cpp:48: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ mv -f .deps/clustering.Tpo .deps/clustering.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT scaffolds.o -MD -MP -MF .deps/scaffolds.Tpo -c -o scaffolds.o scaffolds.cpp In file included from hits.h:23, from abundances.h:23, from abundances.cpp:16: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from bundles.h:25, from abundances.h:25, from differential.cpp:20: progressbar.h: In member function 'virtual std::vector > > TestLauncher::test_finished_loci()': progressbar.h:70:26: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ progressbar.h:70:26: note: directive argument in the range [-2147483648, 99] progressbar.h:70:11: note: 'snprintf' output between 54 and 89 bytes into a destination of size 82 snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from abundances.h:23, from abundances.cpp:16: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from abundances.h:23, from abundances.cpp:16: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hits.h:23, from scaffolds.h:20, from scaffolds.cpp:14: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from /usr/local/include/boost/graph/detail/adjacency_list.hpp:34, from /usr/local/include/boost/graph/adjacency_list.hpp:223, from assemble.cpp:28: /usr/local/include/boost/graph/detail/adj_list_edge_iterator.hpp: In function 'void create_reachability_bp_graph(DAG&, ReachGraph&, std::vector::BNode, std::allocator::BNode> >, DagToBp&, const boost::adjacency_list<>&, const std::vector&)': /usr/local/include/boost/graph/detail/adj_list_edge_iterator.hpp:70:9: warning: '*((void*)& i +48)' may be used uninitialized in this function [-Wmaybe-uninitialized] if (edges BOOST_GRAPH_MEMBER first == edges BOOST_GRAPH_MEMBER second) ^~ assemble.cpp:150:51: note: '*((void*)& i +48)' was declared here graph_traits < adjacency_list<> >::edge_iterator i, end; ^ assemble.cpp:150:51: warning: '*((void*)(& i)+32).__gnu_cxx::__normal_iterator*, std::vector, std::allocator > > >::_M_current' may be used uninitialized in this function [-Wmaybe-uninitialized] In file included from scaffolds.h:20, from scaffolds.cpp:14: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from scaffolds.h:20, from scaffolds.cpp:14: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ scaffolds.cpp: In member function 'void Scaffold::fill_gaps(int)': scaffolds.cpp:835:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (filled_gap_size <= 0) ^~ scaffolds.cpp:838:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' const vector& orig_ops = augmented_ops(); ^~~~~ scaffolds.cpp: In member function 'void Scaffold::fill_gaps(const std::vector&)': scaffolds.cpp:933:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (overlapping.empty()) ^~ scaffolds.cpp:936:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' AugmentedCuffOp::merge_ops(overlapping, _augmented_ops, true); ^~~~~~~~~~~~~~~ In file included from bundles.h:25, from abundances.h:25, from clustering.h:38, from cufflinks.cpp:20: progressbar.h:70:26: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ progressbar.h:70:26: note: directive argument in the range [-2147483648, 99] progressbar.h:70:11: note: 'snprintf' output between 54 and 89 bytes into a destination of size 82 snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ progressbar.h:92:26: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size between 5 and 32 [-Wformat-truncation=] snprintf(line_buf, 81, "\r> %-44s %s %3d%%", msg_buff, _bar_buf, percent); ^~~~~~~~~~~~~~~~~~~~ progressbar.h:92:26: note: directive argument in the range [-2147483648, 99] progressbar.h:92:11: note: 'snprintf' output between 54 and 89 bytes into a destination of size 81 snprintf(line_buf, 81, "\r> %-44s %s %3d%%", msg_buff, _bar_buf, percent); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void ProgressBar::update(const char*, double)', inlined from 'bool assemble_hits(BundleFactory&, boost::shared_ptr)' at cufflinks.cpp:1515:15: progressbar.h:59:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 27 bytes from a string of length 2047 [-Wstringop-truncation] strncpy(bundle_buf, bundle_label_buf, 27); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from abundances.cpp:43: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ In file included from abundances.cpp:44: sampling.h: In function 'double boost::numeric::ublas::cholesky_factorize(M&)': sampling.h:50:13: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef M matrix_type; ^~~~~~~~~~~ In file included from abundances.cpp:44: sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression&)': sampling.h:113:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:114:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs] typedef vector vector_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression&)': sampling.h:120:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:121:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef matrix matrix_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression&, const M&)': sampling.h:127:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:128:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs] typedef vector vector_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression&, const M&)': sampling.h:134:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:135:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef matrix matrix_type; ^~~~~~~~~~~ mv -f .deps/differential.Tpo .deps/differential.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT hits.o -MD -MP -MF .deps/hits.Tpo -c -o hits.o hits.cpp abundances.cpp: In constructor 'AbundanceGroup::AbundanceGroup(const std::vector >&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const boost::numeric::ublas::matrix&, const std::set >&)': abundances.cpp:518:58: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test) ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function 'virtual AbundanceStatus AbundanceGroup::status() const': abundances.cpp:549:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (has_ok_member == false) ^~ abundances.cpp:552:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' return NUMERIC_OK; ^~~~~~ abundances.cpp:526:10: warning: variable 'has_lowdata_member' set but not used [-Wunused-but-set-variable] bool has_lowdata_member = false; ^~~~~~~~~~~~~~~~~~ abundances.cpp: In member function 'void AbundanceGroup::collect_per_replicate_mass(const std::vector&, std::vector >&)': abundances.cpp:1043:20: warning: unused variable 'curr_mass' [-Wunused-variable] double curr_mass = inserted.first->second; ^~~~~~~~~ abundances.cpp: In function 'void collapse_equivalent_hits(const std::vector&, std::vector >&, std::vector&, std::vector&, bool)': abundances.cpp:1160:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < N; ++j) ~~^~~ abundances.cpp:1347:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] for(int i = 0 ; i < nr_alignments.size(); ++i) ~~^~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In function 'bool generate_count_assignment_samples(int, const std::vector&, const boost::numeric::ublas::matrix&, std::vector > > >&)': abundances.cpp:1495:44: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t assign_idx = 0; assign_idx < num_draws; ++assign_idx) ~~~~~~~~~~~^~~~~~~~~~~ abundances.cpp: In function 'void calculate_gamma_mle_covariance(const std::map, boost::shared_ptr >&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&)': abundances.cpp:1562:27: warning: comparison of integer expressions of different signedness: 'int' and 'boost::numeric::ublas::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0; j < all_assigned_count_samples[i].size(); ++j) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1577:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t i = 0; i < num_transcripts; ++i) ~~^~~~~~~~~~~~~~~~~ abundances.cpp:1579:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < num_transcripts; ++j) ~~^~~~~~~~~~~~~~~~~ abundances.cpp: In function 'void calculate_fragment_assignment_distribution(const std::map, boost::shared_ptr >&, boost::numeric::ublas::vector > >&, boost::numeric::ublas::matrix&, std::vector > > >&)': abundances.cpp:1672:27: warning: comparison of integer expressions of different signedness: 'int' and 'boost::numeric::ublas::vector > >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int j = 0; j < all_assigned_count_samples[i].size(); ++j) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:1687:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t i = 0; i < num_transcripts; ++i) ~~^~~~~~~~~~~~~~~~~ abundances.cpp:1689:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < num_transcripts; ++j) ~~^~~~~~~~~~~~~~~~~ abundances.cpp: In member function 'void AbundanceGroup::calculate_abundance_group_variance(const std::vector >&, const std::map, boost::shared_ptr >&)': abundances.cpp:1770:62: warning: comparison of integer expressions of different signedness: 'std::set >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (no_js_tests == false && _read_group_props.size() >= min_reps_for_js_test) ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function 'void AbundanceGroup::aggregate_replicate_abundances(const std::map, boost::shared_ptr >&)': abundances.cpp:1872:58: warning: unused variable 'sc_ab' [-Wunused-variable] const vector >& sc_ab = itr->second->abundances(); ^~~~~ abundances.cpp: In function 'bool estimate_count_variance(long double&, double, double, double, double, double)': abundances.cpp:2079:17: warning: variable 'bnb_mean' set but not used [-Wunused-but-set-variable] long double bnb_mean = 0.0; ^~~~~~~~ abundances.cpp: In member function 'void AbundanceGroup::generate_fpkm_samples()': abundances.cpp:2470:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase >::Index' {aka 'long int'} [-Wsign-compare] for (size_t j = 0; j < sample.size(); ++j) ~~^~~~~~~~~~~~~~~ abundances.cpp: In member function 'void AbundanceGroup::calculate_FPKM_covariance()': abundances.cpp:2585:42: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses] if (length_i > 0 && length_j > 0 & M > 0) ~~~~~~~~~^~~ abundances.cpp:2598:24: warning: unused variable 'fpkm' [-Wunused-variable] double fpkm = _abundances[i]->FPKM(); ^~~~ abundances.cpp: In member function 'void AbundanceGroup::calculate_conf_intervals()': abundances.cpp:2722:34: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < N; ++j) ~~^~~ abundances.cpp:2741:34: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t j = 0; j < N; ++j) ~~^~~ abundances.cpp: In function 'void calculate_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)': abundances.cpp:3154:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase >::Index' {aka 'long int'} [-Wsign-compare] for (size_t i = 0; i < alignment_multiplicities.size(); ++i) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In function 'void calculate_average_assignment_probs(const VectorXd&, const MatrixXd&, const VectorXd&, Eigen::MatrixXd&)': abundances.cpp:3180:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase >::Index' {aka 'long int'} [-Wsign-compare] for (size_t i = 0; i < alignment_multiplicities.size(); ++i) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:3195:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase >::Index' {aka 'long int'} [-Wsign-compare] for (size_t i = 0; i < alignment_multiplicities.size(); ++i) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:3197:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase >::Index' {aka 'long int'} [-Wsign-compare] for (size_t j = 0; j < proposed_gammas.size(); ++j) ~~^~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp:3210:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase >::Index' {aka 'long int'} [-Wsign-compare] for (size_t j = 0; j < proposed_gammas.size(); ++j) ~~^~~~~~~~~~~~~~~~~~~~~~~~ abundances.cpp: In member function 'AbundanceStatus AbundanceGroup::calculate_per_replicate_abundances(std::vector >&, const std::map, std::vector >&, std::map, boost::shared_ptr >&, bool)': abundances.cpp:3868:94: warning: variable 'al_itr' set but not used [-Wunused-but-set-variable] map, vector >::const_iterator al_itr = ^~~~~~ abundances.cpp: In function 'bool is_identifiable(M&, PM&)': abundances.cpp:4056:15: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef M matrix_type; ^~~~~~~~~~~ abundances.cpp: In function 'AbundanceStatus gamma_mle(const std::vector >&, const std::vector&, const std::vector&, std::vector&, bool)': abundances.cpp:4124:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare] for (size_t j = 0; j < cond_probs.rows(); ++j) ~~^~~~~~~~~~~~~~~~~~~ abundances.cpp:4126:34: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::Index' {aka 'long int'} [-Wsign-compare] for (size_t i = 0; i < cond_probs.cols(); ++i) ~~^~~~~~~~~~~~~~~~~~~ abundances.cpp:4120:10: warning: variable 'logL' set but not used [-Wunused-but-set-variable] double logL; ^~~~ mv -f .deps/assemble.Tpo .deps/assemble.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT genes.o -MD -MP -MF .deps/genes.Tpo -c -o genes.o genes.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from abundances.cpp:16: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from abundances.cpp:16: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ cufflinks.cpp: In function 'void assemble_bundle(const RefSequenceTable&, HitBundle*, boost::shared_ptr, boost::shared_ptr, FILE*, FILE*, FILE*, FILE*)': cufflinks.cpp:1352:11: warning: 'status' may be used uninitialized in this function [-Wmaybe-uninitialized] fprintf(ftrans_abundances,"%s\t%c\t%s\t%s\t%s\t%s\t%s:%d-%d\t%d\t%lg\t%lg\t%lg\t%lg\t%s\n", ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iso.trans_id().c_str(), ~~~~~~~~~~~~~~~~~~~~~~~ (iso.scaffold().nearest_ref_classcode() == 0 ? '-' : iso.scaffold().nearest_ref_classcode()), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (iso.scaffold().nearest_ref_id() == "" ? "-" : iso.scaffold().nearest_ref_id().c_str()), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gene.gene_id().c_str(), ~~~~~~~~~~~~~~~~~~~~~~~ (iso.scaffold().annotated_gene_name() == "" ? "-" : iso.scaffold().annotated_gene_name().c_str()), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (iso.scaffold().annotated_tss_id() == "" ? "-" : iso.scaffold().annotated_tss_id().c_str()), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ rt.get_name(bundle.ref_id()), ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ iso.scaffold().left(), ~~~~~~~~~~~~~~~~~~~~~~ iso.scaffold().right(), ~~~~~~~~~~~~~~~~~~~~~~~ iso.scaffold().length(), ~~~~~~~~~~~~~~~~~~~~~~~~ iso.coverage(), ~~~~~~~~~~~~~~~ iso.FPKM(), ~~~~~~~~~~~ iso.confidence().low, ~~~~~~~~~~~~~~~~~~~~~ iso.confidence().high, ~~~~~~~~~~~~~~~~~~~~~~ status); ~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from abundances.cpp:16: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from abundances.cpp:16: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from abundances.cpp:16: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from abundances.cpp:16: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from hits.h:23, from hits.cpp:22: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ mv -f .deps/cufflinks.Tpo .deps/cufflinks.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT bundles.o -MD -MP -MF .deps/bundles.Tpo -c -o bundles.o bundles.cpp In file included from hits.cpp:22: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from hits.cpp:22: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/scaffolds.Tpo .deps/scaffolds.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT filters.o -MD -MP -MF .deps/filters.Tpo -c -o filters.o filters.cpp In file included from hits.h:23, from scaffolds.h:20, from genes.h:17, from genes.cpp:10: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from scaffolds.h:20, from genes.h:17, from genes.cpp:10: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from scaffolds.h:20, from genes.h:17, from genes.cpp:10: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bundles.cpp:674:23: warning: integer constant is so large that it is unsigned if (tmp.ref_id() == 12638153115695167477) // corresponds to SAM "*" under FNV hash. unaligned read record ^~~~~~~~~~~~~~~~~~~~ hits.cpp: In member function 'void ReadHit::trim(int)': hits.cpp:40:9: warning: variable 'new_left' set but not used [-Wunused-but-set-variable] int new_left = 0; ^~~~~~~~ hits.cpp: In member function 'bool BAMHitFactory::get_hit_from_bam1t(const bam1_t*, const bam_hdr_t*, ReadHit&)': hits.cpp:461:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uint32_t' {aka 'const unsigned int'} [-Wsign-compare] for (int i = 0; i < hit_buf->core.n_cigar; ++i) ~~^~~~~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from hits.cpp:25: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from hits.cpp:25: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from hits.cpp:25: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from hits.cpp:25: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from hits.cpp:25: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from hits.cpp:25: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from genes.h:18, from genes.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from genes.h:18, from genes.cpp:10: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from genes.h:18, from genes.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from genes.h:18, from genes.cpp:10: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from genes.h:18, from genes.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from genes.h:18, from genes.cpp:10: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from hits.h:23, from bundles.h:22, from bundles.cpp:17: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from bundles.h:22, from bundles.cpp:17: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from bundles.h:22, from bundles.cpp:17: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from hits.h:23, from scaffolds.h:20, from filters.h:17, from filters.cpp:10: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from scaffolds.h:20, from filters.h:17, from filters.cpp:10: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from scaffolds.h:20, from filters.h:17, from filters.cpp:10: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ bundles.cpp: In function 'void load_ref_rnas(FILE*, RefSequenceTable&, std::vector >&, boost::crc_32_type&, bool, bool)': bundles.cpp:87:5: warning: this 'else' clause does not guard... [-Wmisleading-indentation] else ^~~~ bundles.cpp:90:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'else' GList ref_rnas; ^~~~~ bundles.cpp: In member function 'bool HitBundle::add_open_hit(boost::shared_ptr, const ReadHit*, bool)': bundles.cpp:300:34: warning: comparison of integer expressions of different signedness: 'int' and 'uint32_t' {aka 'unsigned int'} [-Wsign-compare] if (m.right() - m.left() > max_gene_length) ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ bundles.cpp: In member function 'double BundleFactory::next_valid_alignment(const ReadHit*&)': bundles.cpp:728:18: warning: variable 'found_scaff' set but not used [-Wunused-but-set-variable] bool found_scaff = false; ^~~~~~~~~~~ bundles.cpp: In member function 'bool BundleFactory::next_bundle_hit_driven(HitBundle&)': bundles.cpp:804:34: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (bundle.hits().size() >= max_frags_per_bundle) ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bundles.cpp: In member function 'bool BundleFactory::next_bundle_ref_driven(HitBundle&)': bundles.cpp:846:38: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (bundle.hits().size() < max_frags_per_bundle) ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ bundles.cpp:897:34: warning: comparison of integer expressions of different signedness: 'std::vector::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare] if (bundle.hits().size() >= max_frags_per_bundle) ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ bundles.cpp:886:8: warning: variable 'last_hit_ref_id_seen' set but not used [-Wunused-but-set-variable] RefID last_hit_ref_id_seen = 0; ^~~~~~~~~~~~~~~~~~~~ bundles.cpp:887:6: warning: variable 'last_hit_pos_seen' set but not used [-Wunused-but-set-variable] int last_hit_pos_seen = 0; ^~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from bundles.cpp:17: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from bundles.cpp:17: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ filters.cpp: In function 'void clip_by_3_prime_dropoff(std::vector&)': filters.cpp:880:63: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'const int' [-Wsign-compare] if (avg_cov >= trim_3_avgcov_thresh && min_cost_x < exon_3->genomic_length) ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ filters.cpp:806:20: warning: variable 'mean_to_keep' set but not used [-Wunused-but-set-variable] double mean_to_keep = 0.0; ^~~~~~~~~~~~ filters.cpp:807:20: warning: variable 'mean_to_trim' set but not used [-Wunused-but-set-variable] double mean_to_trim = 0.0; ^~~~~~~~~~~~ filters.cpp:934:36: warning: variable 'exon_3' set but not used [-Wunused-but-set-variable] const AugmentedCuffOp* exon_3 = NULL; ^~~~~~ filters.cpp:935:17: warning: variable 'mult' set but not used [-Wunused-but-set-variable] int mult; ^~~~ filters.cpp:936:17: warning: variable 'offset' set but not used [-Wunused-but-set-variable] int offset; ^~~~~~ mv -f .deps/genes.Tpo .deps/genes.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT scaffold_graph.o -MD -MP -MF .deps/scaffold_graph.Tpo -c -o scaffold_graph.o scaffold_graph.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from bundles.cpp:17: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from bundles.cpp:17: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from bundles.cpp:17: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from bundles.cpp:17: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from genes.h:18, from filters.h:18, from filters.cpp:10: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from hits.h:23, from scaffolds.h:20, from scaffold_graph.cpp:12: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from scaffolds.h:20, from scaffold_graph.cpp:12: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from scaffolds.h:20, from scaffold_graph.cpp:12: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/hits.Tpo .deps/hits.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT matching_merge.o -MD -MP -MF .deps/matching_merge.Tpo -c -o matching_merge.o matching_merge.cpp In file included from ./lemon/bits/base_extender.h:23, from ./lemon/smart_graph.h:30, from matching_merge.h:16, from matching_merge.cpp:10: ./lemon/error.h:93:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr<_Type> ptr; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/smart_graph.h:30, from matching_merge.h:16, from matching_merge.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/smart_graph.h:30, from matching_merge.h:16, from matching_merge.cpp:10: ./lemon/error.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr buf; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from ./lemon/error.h:31, from ./lemon/bits/base_extender.h:23, from ./lemon/smart_graph.h:30, from matching_merge.h:16, from matching_merge.cpp:10: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ mv -f .deps/filters.Tpo .deps/filters.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT graph_optimize.o -MD -MP -MF .deps/graph_optimize.Tpo -c -o graph_optimize.o graph_optimize.cpp In file included from hits.h:23, from scaffolds.h:20, from matching_merge.h:20, from matching_merge.cpp:10: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from scaffolds.h:20, from matching_merge.h:20, from matching_merge.cpp:10: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from scaffolds.h:20, from matching_merge.h:20, from matching_merge.cpp:10: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:25, from bundles.cpp:17: progressbar.h: In function 'void inspect_map(boost::shared_ptr, BadIntronTable*, std::vector&, std::vector&, IdToLocusMap&, bool, bool)': progressbar.h:70:26: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ progressbar.h:70:26: note: directive argument in the range [-2147483648, 99] progressbar.h:70:11: note: 'snprintf' output between 54 and 89 bytes into a destination of size 82 snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void ProgressBar::update(const char*, double)', inlined from 'void inspect_map(boost::shared_ptr, BadIntronTable*, std::vector&, std::vector&, IdToLocusMap&, bool, bool)' at bundles.cpp:1745:16: progressbar.h:59:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 27 bytes from a string of length 2047 [-Wstringop-truncation] strncpy(bundle_buf, bundle_label_buf, 27); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/bundles.Tpo .deps/bundles.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT biascorrection.o -MD -MP -MF .deps/biascorrection.Tpo -c -o biascorrection.o biascorrection.cpp In file included from hits.h:23, from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from bundles.h:22, from graph_optimize.h:17, from graph_optimize.cpp:13: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/scaffold_graph.Tpo .deps/scaffold_graph.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT sampling.o -MD -MP -MF .deps/sampling.Tpo -c -o sampling.o sampling.cpp In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from graph_optimize.cpp:16: ./lemon/error.h: At global scope: ./lemon/error.h:93:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr<_Type> ptr; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from /usr/local/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/property_map/vector_property_map.hpp:14, from /usr/local/include/boost/property_map/property_map.hpp:602, from /usr/local/include/boost/graph/graph_concepts.hpp:17, from /usr/local/include/boost/graph/depth_first_search.hpp:18, from graph_optimize.h:14, from graph_optimize.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from ./lemon/bits/base_extender.h:23, from ./lemon/list_graph.h:26, from ./lemon/dfs.h:26, from ./lemon/topology.h:22, from graph_optimize.cpp:16: ./lemon/error.h:108:10: warning: 'template class std::auto_ptr' is deprecated [-Wdeprecated-declarations] std::auto_ptr buf; ^~~~~~~~ In file included from /usr/include/c++/8.0/memory:80, from /usr/local/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/property_map/vector_property_map.hpp:14, from /usr/local/include/boost/property_map/property_map.hpp:602, from /usr/local/include/boost/graph/graph_concepts.hpp:17, from /usr/local/include/boost/graph/depth_first_search.hpp:18, from graph_optimize.h:14, from graph_optimize.cpp:13: /usr/include/c++/8.0/bits/unique_ptr.h:53:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from graph_optimize.cpp:16: ./lemon/topology.h: In function 'bool lemon::stronglyConnected(const Graph&)': ./lemon/topology.h:249:34: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::Node Node; ^~~~ ./lemon/topology.h: In function 'int lemon::countStronglyConnectedComponents(const Graph&)': ./lemon/topology.h:311:34: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::Edge Edge; ^~~~ ./lemon/topology.h:313:36: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::EdgeIt EdgeIt; ^~~~~~ ./lemon/topology.h: In function 'void lemon::topologicalSort(const Graph&, NodeMap&)': ./lemon/topology.h:1213:34: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::Node Node; ^~~~ ./lemon/topology.h:1215:34: warning: typedef 'Edge' locally defined but not used [-Wunused-local-typedefs] typedef typename Graph::Edge Edge; ^~~~ ./lemon/topology.h: In function 'bool lemon::bipartite(const UGraph&)': ./lemon/topology.h:1470:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs] typedef typename UGraph::EdgeIt EdgeIt; ^~~~~~ ./lemon/topology.h: In function 'bool lemon::bipartitePartitions(const UGraph&, NodeMap&)': ./lemon/topology.h:1514:35: warning: typedef 'Node' locally defined but not used [-Wunused-local-typedefs] typedef typename UGraph::Node Node; ^~~~ ./lemon/topology.h:1516:37: warning: typedef 'EdgeIt' locally defined but not used [-Wunused-local-typedefs] typedef typename UGraph::EdgeIt EdgeIt; ^~~~~~ mv -f .deps/matching_merge.Tpo .deps/matching_merge.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT adap.o -MD -MP -MF .deps/adap.Tpo -c -o adap.o `test -f 'locfit/adap.c' || echo './'`locfit/adap.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/adap.c: In function 'mmse': locfit/adap.c:29:17: warning: variable 'p' set but not used [-Wunused-but-set-variable] { int i, ii, j, p, p1; ^ locfit/adap.c: In function 'aband3': locfit/adap.c:157:17: warning: variable 'n' set but not used [-Wunused-but-set-variable] INT i, i0, d, n; ^ locfit/adap.c:157:14: warning: variable 'd' set but not used [-Wunused-but-set-variable] INT i, i0, d, n; ^ graph_optimize.cpp: In function 'bool collapse_contained_transfrags(std::vector&, uint32_t)': graph_optimize.cpp:264:30: warning: variable 'e' set but not used [-Wunused-but-set-variable] ContainmentGraph::UEdge e = containment.addEdge(nj.first, ^ graph_optimize.cpp: In function 'bool collapse_equivalent_transfrags(std::vector&, uint32_t)': graph_optimize.cpp:342:31: warning: typedef 'ContainmentGraph' locally defined but not used [-Wunused-local-typedefs] typedef lemon::SmartBpUGraph ContainmentGraph; ^~~~~~~~~~~~~~~~ mv -f .deps/adap.Tpo .deps/adap.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT ar_funs.o -MD -MP -MF .deps/ar_funs.Tpo -c -o ar_funs.o `test -f 'locfit/ar_funs.c' || echo './'`locfit/ar_funs.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/ar_funs.Tpo .deps/ar_funs.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT arith.o -MD -MP -MF .deps/arith.Tpo -c -o arith.o `test -f 'locfit/arith.c' || echo './'`locfit/arith.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/arith.Tpo .deps/arith.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT band.o -MD -MP -MF .deps/band.Tpo -c -o band.o `test -f 'locfit/band.c' || echo './'`locfit/band.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/band.Tpo .deps/band.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT c_args.o -MD -MP -MF .deps/c_args.Tpo -c -o c_args.o `test -f 'locfit/c_args.c' || echo './'`locfit/c_args.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/c_args.c: In function 'readilist': locfit/c_args.c:58:13: warning: variable 'nd' set but not used [-Wunused-but-set-variable] { int i, n, nd; ^~ mv -f .deps/c_args.Tpo .deps/c_args.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT c_plot.o -MD -MP -MF .deps/c_plot.Tpo -c -o c_plot.o `test -f 'locfit/c_plot.c' || echo './'`locfit/c_plot.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/c_plot.c: In function 'plotfit': locfit/c_plot.c:228:13: warning: variable 'sd' set but not used [-Wunused-but-set-variable] double c, sd, xl[2*MXDIM], xll[2]; ^~ locfit/c_plot.c:226:36: warning: variable 'sef' set but not used [-Wunused-but-set-variable] { INT add, d, dp, i = 0, j = 0, n, sef; ^~~ locfit/c_plot.c: In function 'setplot': locfit/c_plot.c:470:14: warning: passing argument 1 of 'setvarname' from incompatible pointer type [-Wincompatible-pointer-types] setvarname(curstr,tname); ^~~~~~ In file included from locfit/lffuns.h:214, from locfit/local.h:106, from locfit/c_plot.c:6: locfit/vari.hpp:16:27: note: expected 'vari *' {aka 'struct *'} but argument is of type 'char *' void setvarname(vari* v, varname name); ~~~~~~^ locfit/c_plot.c: In function 'plotfit': locfit/c_plot.c:282:21: warning: 'iy' may be used uninitialized in this function [-Wmaybe-uninitialized] mg[ix] = mg[iy] = 50; ~~~~~~~^~~~ locfit/c_plot.c:280:12: warning: 'ix' may be used uninitialized in this function [-Wmaybe-uninitialized] mg[ix] = 100; ~~~~~~~^~~~~ mv -f .deps/c_plot.Tpo .deps/c_plot.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT cmd.o -MD -MP -MF .deps/cmd.Tpo -c -o cmd.o `test -f 'locfit/cmd.c' || echo './'`locfit/cmd.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/cmd.c: In function 'ckap': locfit/cmd.c:101:10: warning: variable 'nd' set but not used [-Wunused-but-set-variable] { INT i, nd; ^~ locfit/cmd.c: In function 'predict': locfit/cmd.c:197:13: warning: variable 'data' set but not used [-Wunused-but-set-variable] double *data[MXDIM]; ^~~~ locfit/cmd.c: In function 'table': locfit/cmd.c:539:7: warning: this 'if' clause does not guard... [-Wmisleading-indentation] { if (my>0) ^~ locfit/cmd.c:542:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' for (i=0; i<=mx; i++) ^~~ locfit/cmd.c: In function 'cmdint': locfit/cmd.c:675:19: warning: variable 'nr' set but not used [-Wunused-but-set-variable] INT i, j, mn, nr; ^~ mv -f .deps/abundances.Tpo .deps/abundances.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT dens_haz.o -MD -MP -MF .deps/dens_haz.Tpo -c -o dens_haz.o `test -f 'locfit/dens_haz.c' || echo './'`locfit/dens_haz.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/dens_haz.Tpo .deps/dens_haz.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT dens_int.o -MD -MP -MF .deps/dens_int.Tpo -c -o dens_int.o `test -f 'locfit/dens_int.c' || echo './'`locfit/dens_int.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/dens_int.Tpo .deps/dens_int.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT dens_odi.o -MD -MP -MF .deps/dens_odi.Tpo -c -o dens_odi.o `test -f 'locfit/dens_odi.c' || echo './'`locfit/dens_odi.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/cmd.c: In function 'table': locfit/cmd.c:528:24: warning: 'iy' may be used uninitialized in this function [-Wmaybe-uninitialized] count[ix*(my+1)+iy]++; ~~~~~~~~~^~~ locfit/cmd.c:528:17: warning: 'ix' may be used uninitialized in this function [-Wmaybe-uninitialized] count[ix*(my+1)+iy]++; ~~^~~~~~~ locfit/cmd.c: In function 'setuplf': locfit/cmd.c:796:28: warning: '%s' directive writing up to 99 bytes into a region of size 96 [-Wformat-overflow=] { sprintf(command,"run %s",filename); ^~ ~~~~~~~~ locfit/cmd.c:796:7: note: 'sprintf' output between 5 and 104 bytes into a destination of size 100 { sprintf(command,"run %s",filename); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/cmd.Tpo .deps/cmd.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT density.o -MD -MP -MF .deps/density.Tpo -c -o density.o `test -f 'locfit/density.c' || echo './'`locfit/density.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/dens_odi.Tpo .deps/dens_odi.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT dist.o -MD -MP -MF .deps/dist.Tpo -c -o dist.o `test -f 'locfit/dist.c' || echo './'`locfit/dist.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/dist.Tpo .deps/dist.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT ev_atree.o -MD -MP -MF .deps/ev_atree.Tpo -c -o ev_atree.o `test -f 'locfit/ev_atree.c' || echo './'`locfit/ev_atree.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/ev_atree.c: In function 'atree_int': locfit/ev_atree.c:203:10: warning: 'nc' may be used uninitialized in this function [-Wmaybe-uninitialized] return(rectcell_interp(x,vdptr(tr->xxev),vv,ll,ur,d,nc)); ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/ev_atree.Tpo .deps/ev_atree.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT ev_interp.o -MD -MP -MF .deps/ev_interp.Tpo -c -o ev_interp.o `test -f 'locfit/ev_interp.c' || echo './'`locfit/ev_interp.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/density.Tpo .deps/density.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT ev_kdtre.o -MD -MP -MF .deps/ev_kdtre.Tpo -c -o ev_kdtre.o `test -f 'locfit/ev_kdtre.c' || echo './'`locfit/ev_kdtre.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/ev_interp.Tpo .deps/ev_interp.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT ev_main.o -MD -MP -MF .deps/ev_main.Tpo -c -o ev_main.o `test -f 'locfit/ev_main.c' || echo './'`locfit/ev_main.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/ev_main.Tpo .deps/ev_main.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT ev_trian.o -MD -MP -MF .deps/ev_trian.Tpo -c -o ev_trian.o `test -f 'locfit/ev_trian.c' || echo './'`locfit/ev_trian.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/ev_kdtre.Tpo .deps/ev_kdtre.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT family.o -MD -MP -MF .deps/family.Tpo -c -o family.o `test -f 'locfit/family.c' || echo './'`locfit/family.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C In file included from hits.h:23, from scaffolds.h:20, from biascorrection.cpp:11: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ locfit/ev_trian.c: In function 'triang_grow': locfit/ev_trian.c:77:13: warning: 'jm' may be used uninitialized in this function [-Wmaybe-uninitialized] nce[jm] = pv[0]; triang_grow(des,tr,nce,ct,term); ~~~~~~~~^~~~~~~ locfit/ev_trian.c:74:31: warning: 'im' may be used uninitialized in this function [-Wmaybe-uninitialized] pv[0] = newsplit(des,tr,ce[im],ce[jm],0); ^ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from graph_optimize.h:17, from graph_optimize.cpp:13: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from graph_optimize.h:17, from graph_optimize.cpp:13: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from scaffolds.h:20, from biascorrection.cpp:11: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from scaffolds.h:20, from biascorrection.cpp:11: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/family.Tpo .deps/family.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT fitted.o -MD -MP -MF .deps/fitted.Tpo -c -o fitted.o `test -f 'locfit/fitted.c' || echo './'`locfit/fitted.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/ev_trian.Tpo .deps/ev_trian.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT frend.o -MD -MP -MF .deps/frend.Tpo -c -o frend.o `test -f 'locfit/frend.c' || echo './'`locfit/frend.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/frend.c: In function 'procvvord': locfit/frend.c:205:39: warning: variable 'ip' set but not used [-Wunused-but-set-variable] INT i, j, k = 0, d1, *mi, i0, p1, ip; ^~ locfit/frend.c:204:48: warning: variable 't2' set but not used [-Wunused-but-set-variable] double tr[6], gcv, g0, ap, coef[x_1][y_1], t2[4], th, md = 0.0; ^~ locfit/frend.c: In function 'ressumm': locfit/frend.c:380:15: warning: this 'for' clause does not guard... [-Wmisleading-indentation] { for (j=0; jmi[MN]; i++) ^~~ locfit/frend.c:403:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' *df = lf->mi[MN]-lf->mi[MP]; ^ mv -f .deps/fitted.Tpo .deps/fitted.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT help.o -MD -MP -MF .deps/help.Tpo -c -o help.o `test -f 'locfit/help.c' || echo './'`locfit/help.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/help.Tpo .deps/help.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT lf_dercor.o -MD -MP -MF .deps/lf_dercor.Tpo -c -o lf_dercor.o `test -f 'locfit/lf_dercor.c' || echo './'`locfit/lf_dercor.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/lf_dercor.Tpo .deps/lf_dercor.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT lf_fitfun.o -MD -MP -MF .deps/lf_fitfun.Tpo -c -o lf_fitfun.o `test -f 'locfit/lf_fitfun.c' || echo './'`locfit/lf_fitfun.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/lf_fitfun.c: In function 'fitfun': locfit/lf_fitfun.c:182:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation] { for (j=1; j<=deg; j++) ^~~ locfit/lf_fitfun.c:185:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for' return; ^~~~~~ mv -f .deps/frend.Tpo .deps/frend.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT lf_robust.o -MD -MP -MF .deps/lf_robust.Tpo -c -o lf_robust.o `test -f 'locfit/lf_robust.c' || echo './'`locfit/lf_robust.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/lf_robust.Tpo .deps/lf_robust.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT lf_vari.o -MD -MP -MF .deps/lf_vari.Tpo -c -o lf_vari.o `test -f 'locfit/lf_vari.c' || echo './'`locfit/lf_vari.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from graph_optimize.h:17, from graph_optimize.cpp:13: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from graph_optimize.h:17, from graph_optimize.cpp:13: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from graph_optimize.h:17, from graph_optimize.cpp:13: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from graph_optimize.h:17, from graph_optimize.cpp:13: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ mv -f .deps/lf_fitfun.Tpo .deps/lf_fitfun.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT lfd.o -MD -MP -MF .deps/lfd.Tpo -c -o lfd.o `test -f 'locfit/lfd.c' || echo './'`locfit/lfd.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/lfd.c: In function 'setfilename': locfit/lfd.c:60:20: warning: zero-length gnu_printf format string [-Wformat-zero-length] sprintf(subp,""); ^~ mv -f .deps/lf_vari.Tpo .deps/lf_vari.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT lfstr.o -MD -MP -MF .deps/lfstr.Tpo -c -o lfstr.o `test -f 'locfit/lfstr.c' || echo './'`locfit/lfstr.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/lfstr.Tpo .deps/lfstr.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT linalg.o -MD -MP -MF .deps/linalg.Tpo -c -o linalg.o `test -f 'locfit/linalg.c' || echo './'`locfit/linalg.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/lfd.Tpo .deps/lfd.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT locfit.o -MD -MP -MF .deps/locfit.Tpo -c -o locfit.o `test -f 'locfit/locfit.c' || echo './'`locfit/locfit.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/locfit.Tpo .deps/locfit.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT m_chol.o -MD -MP -MF .deps/m_chol.Tpo -c -o m_chol.o `test -f 'locfit/m_chol.c' || echo './'`locfit/m_chol.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/m_chol.Tpo .deps/m_chol.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT m_eigen.o -MD -MP -MF .deps/m_eigen.Tpo -c -o m_eigen.o `test -f 'locfit/m_eigen.c' || echo './'`locfit/m_eigen.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/linalg.Tpo .deps/linalg.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT m_jacob.o -MD -MP -MF .deps/m_jacob.Tpo -c -o m_jacob.o `test -f 'locfit/m_jacob.c' || echo './'`locfit/m_jacob.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/m_jacob.Tpo .deps/m_jacob.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT m_max.o -MD -MP -MF .deps/m_max.Tpo -c -o m_max.o `test -f 'locfit/m_max.c' || echo './'`locfit/m_max.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/m_eigen.Tpo .deps/m_eigen.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT makecmd.o -MD -MP -MF .deps/makecmd.Tpo -c -o makecmd.o `test -f 'locfit/makecmd.c' || echo './'`locfit/makecmd.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/makecmd.c: In function 'makefields': locfit/makecmd.c:88:36: warning: suggest parentheses around '&&' within '||' [-Wparentheses] } while ((instr) || (*z !=' ') && (!isterminator(*z))); ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ In file included from sampling.cpp:9: sampling.h: In function 'double boost::numeric::ublas::cholesky_factorize(M&)': sampling.h:50:13: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef M matrix_type; ^~~~~~~~~~~ In file included from sampling.cpp:9: sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::vector_expression&)': sampling.h:113:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:114:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs] typedef vector vector_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute(const M&, boost::numeric::ublas::matrix_expression&)': sampling.h:120:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:121:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef matrix matrix_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::vector_expression&, const M&)': sampling.h:127:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:128:42: warning: typedef 'vector_type' locally defined but not used [-Wunused-local-typedefs] typedef vector vector_type; ^~~~~~~~~~~ sampling.h: In function 'void boost::numeric::ublas::cholesky_substitute_left(boost::numeric::ublas::matrix_expression&, const M&)': sampling.h:134:19: warning: typedef 'const_matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef const M const_matrix_type; ^~~~~~~~~~~~~~~~~ sampling.h:135:42: warning: typedef 'matrix_type' locally defined but not used [-Wunused-local-typedefs] typedef matrix matrix_type; ^~~~~~~~~~~ mv -f .deps/makecmd.Tpo .deps/makecmd.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT math.o -MD -MP -MF .deps/math.Tpo -c -o math.o `test -f 'locfit/math.c' || echo './'`locfit/math.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/m_max.Tpo .deps/m_max.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT minmax.o -MD -MP -MF .deps/minmax.Tpo -c -o minmax.o `test -f 'locfit/minmax.c' || echo './'`locfit/minmax.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/math.Tpo .deps/math.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT nbhd.o -MD -MP -MF .deps/nbhd.Tpo -c -o nbhd.o `test -f 'locfit/nbhd.c' || echo './'`locfit/nbhd.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/minmax.c: In function 'updatesd': locfit/minmax.c:94:21: warning: 'sd' may be used uninitialized in this function [-Wmaybe-uninitialized] if (des->xtwx.dg[sd]>0) ^ locfit/minmax.c: In function 'mmax': locfit/minmax.c:217:8: warning: 'sing' may be used uninitialized in this function [-Wmaybe-uninitialized] if (sing) printf("final singular\n"); ^ mv -f .deps/minmax.Tpo .deps/minmax.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT pcomp.o -MD -MP -MF .deps/pcomp.Tpo -c -o pcomp.o `test -f 'locfit/pcomp.c' || echo './'`locfit/pcomp.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/pcomp.Tpo .deps/pcomp.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT pout.o -MD -MP -MF .deps/pout.Tpo -c -o pout.o `test -f 'locfit/pout.c' || echo './'`locfit/pout.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/pout.c: In function 'plotxwin': locfit/pout.c:447:38: warning: variable 'vz' set but not used [-Wunused-but-set-variable] double z[3], z2[3], xx[2], vx, vy, vz; ^~ locfit/pout.c:447:34: warning: variable 'vy' set but not used [-Wunused-but-set-variable] double z[3], z2[3], xx[2], vx, vy, vz; ^~ locfit/pout.c:447:30: warning: variable 'vx' set but not used [-Wunused-but-set-variable] double z[3], z2[3], xx[2], vx, vy, vz; ^~ mv -f .deps/nbhd.Tpo .deps/nbhd.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT preplot.o -MD -MP -MF .deps/preplot.Tpo -c -o preplot.o `test -f 'locfit/preplot.c' || echo './'`locfit/preplot.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/preplot.Tpo .deps/preplot.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT random.o -MD -MP -MF .deps/random.Tpo -c -o random.o `test -f 'locfit/random.c' || echo './'`locfit/random.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/random.Tpo .deps/random.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT readfile.o -MD -MP -MF .deps/readfile.Tpo -c -o readfile.o `test -f 'locfit/readfile.c' || echo './'`locfit/readfile.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/readfile.Tpo .deps/readfile.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT scb.o -MD -MP -MF .deps/scb.Tpo -c -o scb.o `test -f 'locfit/scb.c' || echo './'`locfit/scb.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/scb.c: In function 'cumulant': locfit/scb.c:61:10: warning: variable 'b2i' set but not used [-Wunused-but-set-variable] { double b2i, b3i, b3j, b4i; ^~~ mv -f .deps/pout.Tpo .deps/pout.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT scb_cons.o -MD -MP -MF .deps/scb_cons.Tpo -c -o scb_cons.o `test -f 'locfit/scb_cons.c' || echo './'`locfit/scb_cons.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/scb.Tpo .deps/scb.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT simul.o -MD -MP -MF .deps/simul.Tpo -c -o simul.o `test -f 'locfit/simul.c' || echo './'`locfit/simul.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/simul.Tpo .deps/simul.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT solve.o -MD -MP -MF .deps/solve.Tpo -c -o solve.o `test -f 'locfit/solve.c' || echo './'`locfit/solve.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/solve.Tpo .deps/solve.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT startlf.o -MD -MP -MF .deps/startlf.Tpo -c -o startlf.o `test -f 'locfit/startlf.c' || echo './'`locfit/startlf.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/scb_cons.Tpo .deps/scb_cons.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT strings.o -MD -MP -MF .deps/strings.Tpo -c -o strings.o `test -f 'locfit/strings.c' || echo './'`locfit/strings.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C mv -f .deps/strings.Tpo .deps/strings.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT vari.o -MD -MP -MF .deps/vari.Tpo -c -o vari.o `test -f 'locfit/vari.cpp' || echo './'`locfit/vari.cpp mv -f .deps/startlf.Tpo .deps/startlf.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT wdiag.o -MD -MP -MF .deps/wdiag.Tpo -c -o wdiag.o `test -f 'locfit/wdiag.c' || echo './'`locfit/wdiag.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/wdiag.c: In function 'wdiag': locfit/wdiag.c:206:31: warning: 'lxdd' may be used uninitialized in this function [-Wmaybe-uninitialized] lxdd[(i*d+j)*m+k] += des->f1[l]*X[k*p+l]*des->w[k]; ^~ locfit/wdiag.c:193:22: warning: 'lxd' may be used uninitialized in this function [-Wmaybe-uninitialized] lxd[i*m+k] += des->f1[l]*X[k*p+l]*des->w[k]; ^~ mv -f .deps/wdiag.Tpo .deps/wdiag.Po cc -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -MT weight.o -MD -MP -MF .deps/weight.Tpo -c -o weight.o `test -f 'locfit/weight.c' || echo './'`locfit/weight.c cc1: warning: command line option '-ftemplate-depth=1024' is valid for C++/ObjC++ but not for C locfit/weight.c: In function 'weightdd': locfit/weight.c:162:10: warning: variable 'w' set but not used [-Wunused-but-set-variable] { double w; ^ mv -f .deps/weight.Tpo .deps/weight.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT replicates.o -MD -MP -MF .deps/replicates.Tpo -c -o replicates.o replicates.cpp mv -f .deps/vari.Tpo .deps/vari.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT multireads.o -MD -MP -MF .deps/multireads.Tpo -c -o multireads.o multireads.cpp biascorrection.cpp: In member function 'double BiasCorrectionHelper::get_cond_prob(const MateHit&)': biascorrection.cpp:794:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (isinf(cond_prob) || isnan(cond_prob)) ^~ biascorrection.cpp:797:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' return cond_prob; ^~~~~~ biascorrection.cpp: In member function 'double BiasCorrectionHelper::get_effective_length()': biascorrection.cpp:809:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (no_length_correction) ^~ biascorrection.cpp:812:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' double tot_mass = accumulate( _rg_masses.begin(), _rg_masses.end(), 0.0 ); ^~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from biascorrection.cpp:12: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from biascorrection.cpp:12: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from biascorrection.cpp:12: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from biascorrection.cpp:12: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from biascorrection.cpp:12: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from biascorrection.cpp:12: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from hits.h:23, from multireads.cpp:11: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ mv -f .deps/sampling.Tpo .deps/sampling.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT jensen_shannon.o -MD -MP -MF .deps/jensen_shannon.Tpo -c -o jensen_shannon.o jensen_shannon.cpp In file included from hits.h:23, from bundles.h:22, from replicates.h:10, from replicates.cpp:18: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from bundles.h:25, from abundances.h:25, from biascorrection.cpp:12: progressbar.h: In function 'void learn_bias(BundleFactory&, BiasLearner&, bool)': progressbar.h:70:26: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ progressbar.h:70:26: note: directive argument in the range [-2147483648, 99] progressbar.h:70:11: note: 'snprintf' output between 54 and 89 bytes into a destination of size 82 snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In member function 'void ProgressBar::update(const char*, double)', inlined from 'void learn_bias(BundleFactory&, BiasLearner&, bool)' at biascorrection.cpp:121:16: progressbar.h:59:10: warning: 'char* strncpy(char*, const char*, size_t)' output may be truncated copying 27 bytes from a string of length 2047 [-Wstringop-truncation] strncpy(bundle_buf, bundle_label_buf, 27); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:22, from replicates.h:10, from replicates.cpp:18: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from bundles.h:22, from replicates.h:10, from replicates.cpp:18: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from multireads.cpp:11: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from multireads.cpp:11: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from replicates.cpp:18: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ replicates.cpp: In member function 'virtual double MassDispersionModel::scale_mass_variance(double) const': replicates.cpp:146:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (d >= _scaled_compatible_mass_means.size()) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ replicates.cpp:150:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (d >= _scaled_mass_variances.size()) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ replicates.cpp: In member function 'virtual double MleErrorModel::scale_mle_variance(double) const': replicates.cpp:260:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (d >= _scaled_compatible_mass_means.size()) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ replicates.cpp:264:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (d >= _scaled_mle_variances.size()) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ replicates.cpp: In member function 'double SCVInterpolator::interpolate_scv(double)': replicates.cpp:542:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (d >= est_scvs.size()) ~~^~~~~~~~~~~~~~~~~~ replicates.cpp:546:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector::size_type' {aka 'long unsigned int'} [-Wsign-compare] if (d >= true_scvs.size()) ~~^~~~~~~~~~~~~~~~~~~ replicates.cpp: In function 'void build_scv_correction_fit(int, int, int, SCVInterpolator&)': replicates.cpp:620:30: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t i = 0; i < ngenes; ++i) ~~^~~~~~~~ replicates.cpp:623:46: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for (size_t rep_idx = 0; rep_idx < nreps; ++rep_idx) ~~~~~~~~^~~~~~~ replicates.cpp:721:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'INT' {aka 'int'} [-Wsign-compare] for (size_t i = 0; i < cp->n; ++i) ~~^~~~~~~ replicates.cpp: In function 'boost::shared_ptr fit_dispersion_model_helper(const string&, const std::vector&, const std::vector&)': replicates.cpp:845:26: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'INT' {aka 'int'} [-Wsign-compare] for (size_t i = 0; i < cp->n; ++i) ~~^~~~~~~ jensen_shannon.cpp: In function 'double entropy(const VectorXd&)': jensen_shannon.cpp:21:23: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase >::Index' {aka 'long int'} [-Wsign-compare] for (size_t i = 0; i < p.size(); ++i) ~~^~~~~~~~~~ jensen_shannon.cpp:29:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (e < 0) ^~ jensen_shannon.cpp:31:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' return e; ^~~~~~ jensen_shannon.cpp: In function 'double jensen_shannon_distance(std::vector >&)': jensen_shannon.cpp:65:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (js < 0) // can happen due to underflow or rounding errors. ^~ jensen_shannon.cpp:67:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' return sqrt(js); ^~~~~~ jensen_shannon.cpp: In function 'void jensen_shannon_gradient(std::vector >&, double, boost::numeric::ublas::vector&)': jensen_shannon.cpp:100:24: warning: comparison of integer expressions of different signedness: 'size_t' {aka 'long unsigned int'} and 'Eigen::EigenBase >::Index' {aka 'long int'} [-Wsign-compare] for (size_t j = 0; j < sample_kappas[i].size(); ++j) ~~^~~~~~~~~~~~~~~~~~~~~~~~~ jensen_shannon.cpp:132:24: warning: unused variable 'curr_grad' [-Wunused-variable] double curr_grad = gradient(i*kappa_length + k); ^~~~~~~~~ mv -f .deps/biascorrection.Tpo .deps/biascorrection.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT tracking.o -MD -MP -MF .deps/tracking.Tpo -c -o tracking.o tracking.cpp mv -f .deps/graph_optimize.Tpo .deps/graph_optimize.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT codons.o -MD -MP -MF .deps/codons.Tpo -c -o codons.o codons.cpp mv -f .deps/codons.Tpo .deps/codons.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT GArgs.o -MD -MP -MF .deps/GArgs.Tpo -c -o GArgs.o GArgs.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from replicates.h:10, from replicates.cpp:18: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from replicates.h:10, from replicates.cpp:18: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ mv -f .deps/GArgs.Tpo .deps/GArgs.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT GBase.o -MD -MP -MF .deps/GBase.Tpo -c -o GBase.o GBase.cpp mv -f .deps/GBase.Tpo .deps/GBase.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT gdna.o -MD -MP -MF .deps/gdna.Tpo -c -o gdna.o gdna.cpp mv -f .deps/gdna.Tpo .deps/gdna.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT GStr.o -MD -MP -MF .deps/GStr.Tpo -c -o GStr.o GStr.cpp mv -f .deps/jensen_shannon.Tpo .deps/jensen_shannon.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT GFaSeqGet.o -MD -MP -MF .deps/GFaSeqGet.Tpo -c -o GFaSeqGet.o GFaSeqGet.cpp mv -f .deps/GFaSeqGet.Tpo .deps/GFaSeqGet.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT GFastaIndex.o -MD -MP -MF .deps/GFastaIndex.Tpo -c -o GFastaIndex.o GFastaIndex.cpp In file included from /usr/local/include/boost/checked_delete.hpp:15, from /usr/local/include/boost/smart_ptr/shared_ptr.hpp:26, from /usr/local/include/boost/shared_ptr.hpp:17, from /usr/local/include/boost/date_time/time_clock.hpp:17, from /usr/local/include/boost/thread/thread_time.hpp:9, from /usr/local/include/boost/thread/lock_types.hpp:18, from /usr/local/include/boost/thread/pthread/thread_data.hpp:12, from /usr/local/include/boost/thread/thread_only.hpp:17, from /usr/local/include/boost/thread/thread.hpp:12, from /usr/local/include/boost/thread.hpp:13, from replicates.cpp:9: /usr/local/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = PoissonDispersionModel]': /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = PoissonDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = MassDispersionModel; Y = PoissonDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = PoissonDispersionModel; T = MassDispersionModel]' replicates.cpp:793:102: required from here /usr/local/include/boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'PoissonDispersionModel' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ /usr/local/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = MassDispersionModel]': /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = MassDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = MassDispersionModel; Y = MassDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = MassDispersionModel; T = MassDispersionModel]' replicates.cpp:871:149: required from here /usr/local/include/boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'MassDispersionModel' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from replicates.h:10, from replicates.cpp:18: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from replicates.h:10, from replicates.cpp:18: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from replicates.h:10, from replicates.cpp:18: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from replicates.h:10, from replicates.cpp:18: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ mv -f .deps/GFastaIndex.Tpo .deps/GFastaIndex.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT gff.o -MD -MP -MF .deps/gff.Tpo -c -o gff.o gff.cpp mv -f .deps/GStr.Tpo .deps/GStr.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT gff_utils.o -MD -MP -MF .deps/gff_utils.Tpo -c -o gff_utils.o gff_utils.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gff.cpp:1: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GffCDSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GffCDSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GffCDSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GffCDSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GffCDSeg]' gff.cpp:2119:22: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GffCDSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.cpp:1: gff.h:425:7: note: 'class GffCDSeg' declared here class GffCDSeg:public GSeg { ^~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gff_utils.h:3, from gff_utils.cpp:1: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gff_utils.h:321:31: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gff_utils.h:3, from gff_utils.cpp:1: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ mv -f .deps/multireads.Tpo .deps/multireads.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT gtf_tracking.o -MD -MP -MF .deps/gtf_tracking.Tpo -c -o gtf_tracking.o gtf_tracking.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from gtf_tracking.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gtf_tracking.cpp:10: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from gtf_tracking.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gtf_tracking.cpp:10: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from gtf_tracking.cpp:10: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from gtf_tracking.cpp:10: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ mv -f .deps/gff_utils.Tpo .deps/gff_utils.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT cuffcompare.o -MD -MP -MF .deps/cuffcompare.Tpo -c -o cuffcompare.o cuffcompare.cpp In file included from cuffcompare.cpp:14: update_check.h: In function 'bool get_current_version(char*)': update_check.h:81:22: warning: argument to 'sizeof' in 'void bzero(void*, size_t)' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~~~~~~~~~ In file included from hits.h:23, from abundances.h:23, from tracking.h:1, from tracking.cpp:1: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from cuffcompare.cpp:11: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffcompare.cpp:11: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from cuffcompare.cpp:11: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffcompare.cpp:11: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from cuffcompare.cpp:11: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from cuffcompare.cpp:11: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ mv -f .deps/gtf_tracking.Tpo .deps/gtf_tracking.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT cuffdiff.o -MD -MP -MF .deps/cuffdiff.Tpo -c -o cuffdiff.o cuffdiff.cpp mv -f .deps/gff.Tpo .deps/gff.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT gtf_to_sam.o -MD -MP -MF .deps/gtf_to_sam.Tpo -c -o gtf_to_sam.o gtf_to_sam.cpp In file included from abundances.h:23, from tracking.h:1, from tracking.cpp:1: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from abundances.h:23, from tracking.h:1, from tracking.cpp:1: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/replicates.Tpo .deps/replicates.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT compress_gtf.o -MD -MP -MF .deps/compress_gtf.Tpo -c -o compress_gtf.o compress_gtf.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from abundances.h:25, from tracking.h:1, from tracking.cpp:1: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ mv -f .deps/cuffcompare.Tpo .deps/cuffcompare.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT gffread.o -MD -MP -MF .deps/gffread.Tpo -c -o gffread.o gffread.cpp In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gff_utils.h:3, from gffread.cpp:2: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gff_utils.h:321:31: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gff_utils.h:3, from gffread.cpp:2: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from hits.h:23, from cuffdiff.cpp:18: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from cuffdiff.cpp:18: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from cuffdiff.cpp:18: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/gffread.Tpo .deps/gffread.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT cuffquant.o -MD -MP -MF .deps/cuffquant.Tpo -c -o cuffquant.o cuffquant.cpp In file included from hits.h:23, from gtf_to_sam.cpp:22: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from gtf_to_sam.cpp:22: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from gtf_to_sam.cpp:22: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffdiff.cpp:23: update_check.h: In function 'bool get_current_version(char*)': update_check.h:81:22: warning: argument to 'sizeof' in 'void bzero(void*, size_t)' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~~~~~~~~~ In file included from differential.h:29, from cuffdiff.cpp:36: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ In file included from cuffdiff.cpp:36: differential.h: In constructor 'TrackingDataWriter::TrackingDataWriter(int, Outfiles*, Tracking*, const std::vector >&, std::vector >, ProgressBar*, boost::shared_ptr)': differential.h:230:20: warning: 'TrackingDataWriter::sample_labels' will be initialized after [-Wreorder] vector sample_labels; ^~~~~~~~~~~~~ differential.h:228:10: warning: 'bool TrackingDataWriter::headers_written' [-Wreorder] bool headers_written; // this flag records whether we've written out the file headers yet. ^~~~~~~~~~~~~~~ differential.h:204:5: warning: when initialized here [-Wreorder] TrackingDataWriter(int num_samples, ^~~~~~~~~~~~~~~~~~ In file included from cuffdiff.cpp:36: differential.h: In member function 'void TrackingDataWriter::print_FPKM_tracking(const string&, FILE*, const FPKMTrackingTable&)': differential.h:325:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ differential.h: In member function 'void TrackingDataWriter::print_count_tracking(const string&, FILE*, const FPKMTrackingTable&)': differential.h:407:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ differential.h: In member function 'void TrackingDataWriter::print_read_group_simple_table_info(FILE*, const std::vector >&)': differential.h:614:27: warning: format '%lg' expects a matching 'double' argument [-Wformat=] fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp: In function 'void print_FPKM_tracking(FILE*, const FPKMTrackingTable&)': cuffdiff.cpp:628:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ cuffdiff.cpp: In function 'void print_count_tracking(FILE*, const FPKMTrackingTable&)': cuffdiff.cpp:719:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ mv -f .deps/tracking.Tpo .deps/tracking.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT cuffnorm.o -MD -MP -MF .deps/cuffnorm.Tpo -c -o cuffnorm.o cuffnorm.cpp cuffdiff.cpp: In function 'void driver(FILE*, FILE*, FILE*, FILE*, std::vector >&, Outfiles&)': cuffdiff.cpp:1660:9: warning: variable 'most_reps_idx' set but not used [-Wunused-but-set-variable] int most_reps_idx = 0; ^~~~~~~~~~~~~ cuffdiff.cpp:1662:10: warning: variable 'single_replicate_fac' set but not used [-Wunused-but-set-variable] bool single_replicate_fac = false; ^~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp: In function 'int main(int, char**)': cuffdiff.cpp:2327:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (random_seed == -1) ^~ cuffdiff.cpp:2332:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' srand48(random_seed); ^~~~~~~ gtf_to_sam.cpp: In function 'void print_scaff_as_sam(FILE*, const RefSequenceTable&, const Scaffold&)': gtf_to_sam.cpp:142:25: warning: format '%d' expects argument of type 'int', but argument 3 has type 'RefID' {aka 'long unsigned int'} [-Wformat=] fprintf(stderr, "Warning: Could not find contig name for ID %d, skipping\n", scaff.ref_id()); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~ In file included from hits.h:23, from compress_gtf.cpp:23: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from compress_gtf.cpp:23: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from compress_gtf.cpp:23: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from gtf_to_sam.cpp:23: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from gtf_to_sam.cpp:23: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from gtf_to_sam.cpp:23: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from gtf_to_sam.cpp:23: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from gtf_to_sam.cpp:23: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from gtf_to_sam.cpp:23: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffdiff.cpp:19: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from cuffdiff.cpp:19: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from /usr/local/include/boost/utility.hpp:21, from /usr/local/include/boost/range/size.hpp:25, from /usr/local/include/boost/range/functions.hpp:20, from /usr/local/include/boost/range/iterator_range_core.hpp:38, from /usr/local/include/boost/lexical_cast.hpp:30, from /usr/local/include/boost/math/tools/convert_from_string.hpp:15, from /usr/local/include/boost/math/constants/constants.hpp:13, from /usr/local/include/boost/math/special_functions/gamma.hpp:24, from /usr/local/include/boost/math/special_functions/erf.hpp:15, from /usr/local/include/boost/math/distributions/normal.hpp:19, from common.h:27, from cuffdiff.cpp:17: /usr/local/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = MassDispersionModel]': /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = MassDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = MassDispersionModel; Y = MassDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = MassDispersionModel; T = MassDispersionModel]' cuffdiff.cpp:1514:155: required from here /usr/local/include/boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'MassDispersionModel' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] delete x; ^~~~~~ /usr/local/include/boost/core/checked_delete.hpp: In instantiation of 'void boost::checked_delete(T*) [with T = PoissonDispersionModel]': /usr/local/include/boost/smart_ptr/detail/shared_count.hpp:149:34: required from 'boost::detail::shared_count::shared_count(Y*) [with Y = PoissonDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:285:20: required from 'void boost::detail::sp_pointer_construct(boost::shared_ptr*, Y*, boost::detail::shared_count&) [with T = MassDispersionModel; Y = PoissonDispersionModel]' /usr/local/include/boost/smart_ptr/shared_ptr.hpp:379:44: required from 'boost::shared_ptr::shared_ptr(Y*) [with Y = PoissonDispersionModel; T = MassDispersionModel]' cuffdiff.cpp:1541:129: required from here /usr/local/include/boost/core/checked_delete.hpp:36:5: warning: deleting object of polymorphic class type 'PoissonDispersionModel' which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffdiff.cpp:19: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from cuffdiff.cpp:19: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffdiff.cpp:19: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from cuffdiff.cpp:19: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from hits.h:23, from cuffquant.cpp:19: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from cuffquant.cpp:19: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from cuffquant.cpp:19: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from compress_gtf.cpp:24: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from compress_gtf.cpp:24: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from compress_gtf.cpp:24: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from compress_gtf.cpp:24: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from compress_gtf.cpp:24: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from compress_gtf.cpp:24: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ In file included from hits.h:23, from cuffnorm.cpp:18: /usr/local/include/htslib/hfile.h: In function 'ssize_t hwrite(hFILE*, const void*, size_t)': /usr/local/include/htslib/hfile.h:245:35: warning: comparison of integer expressions of different signedness: 'long int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare] if (fp->limit - fp->begin < nbytes){ ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from cuffnorm.cpp:18: hits.h: In constructor 'PrecomputedExpressionHitFactory::PrecomputedExpressionHitFactory(const string&, ReadTable&, RefSequenceTable&)': hits.h:1002:12: warning: 'PrecomputedExpressionHitFactory::_expression_file_name' will be initialized after [-Wreorder] string _expression_file_name; ^~~~~~~~~~~~~~~~~~~~~ hits.h:1001:19: warning: 'std::ifstream PrecomputedExpressionHitFactory::_ifs' [-Wreorder] std::ifstream _ifs; ^~~~ In file included from cuffnorm.cpp:18: hits.h:903:5: warning: when initialized here [-Wreorder] PrecomputedExpressionHitFactory(const string& expression_file_name, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from cuffquant.cpp:24: update_check.h: In function 'bool get_current_version(char*)': update_check.h:81:22: warning: argument to 'sizeof' in 'void bzero(void*, size_t)' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~~~~~~~~~ In file included from cuffquant.cpp:37: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ cuffquant.cpp: In function 'void print_FPKM_tracking(FILE*, const FPKMTrackingTable&)': cuffquant.cpp:418:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ cuffquant.cpp: In function 'void print_count_tracking(FILE*, const FPKMTrackingTable&)': cuffquant.cpp:509:25: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ cuffquant.cpp: In member function 'void AbundanceRecorder::record_tracking_data(int, std::vector >&)': cuffquant.cpp:742:31: warning: unused variable 's2' [-Wunused-variable] const AbundanceGroup& s2 = prev.transcripts; ^~ cuffquant.cpp:760:25: warning: unused variable 'ab_group' [-Wunused-variable] const AbundanceGroup& ab_group = abundances[i]->transcripts; ^~~~~~~~ cuffquant.cpp: In function 'void driver(const string&, const string&, FILE*, std::vector >&, Outfiles&)': cuffquant.cpp:1415:23: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector >::size_type' {aka 'long unsigned int'} [-Wsign-compare] for (int i = 0; i < single_sample_tracking.size(); ++i) ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffquant.cpp: In function 'int main(int, char**)': cuffquant.cpp:1531:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (random_seed == -1) ^~ cuffquant.cpp:1536:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' srand48(random_seed); ^~~~~~~ In file included from cuffnorm.cpp:23: update_check.h: In function 'bool get_current_version(char*)': update_check.h:81:22: warning: argument to 'sizeof' in 'void bzero(void*, size_t)' call is the same expression as the destination; did you mean to provide an explicit length? [-Wsizeof-pointer-memaccess] bzero(curr_version, sizeof(curr_version)); ^~~~~~~~~~~~~~~~~~~~ mv -f .deps/gtf_to_sam.Tpo .deps/gtf_to_sam.Po rm -f libcufflinks.a ar cru libcufflinks.a clustering.o differential.o common.o assemble.o tokenize.o abundances.o scaffolds.o hits.o genes.o bundles.o filters.o scaffold_graph.o matching_merge.o graph_optimize.o biascorrection.o sampling.o adap.o ar_funs.o arith.o band.o c_args.o c_plot.o cmd.o dens_haz.o dens_int.o dens_odi.o density.o dist.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_trian.o family.o fitted.o frend.o help.o lf_dercor.o lf_fitfun.o lf_robust.o lf_vari.o lfd.o lfstr.o linalg.o locfit.o m_chol.o m_eigen.o m_jacob.o m_max.o makecmd.o math.o minmax.o nbhd.o pcomp.o pout.o preplot.o random.o readfile.o scb.o scb_cons.o simul.o solve.o startlf.o strings.o vari.o wdiag.o weight.o replicates.o multireads.o jensen_shannon.o tracking.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libcufflinks.a In file included from differential.h:29, from cuffnorm.cpp:38: replicates.h: In member function 'bool ReplicatedBundleFactory::next_bundle(HitBundle&, bool)': replicates.h:224:57: warning: unused variable 's2' [-Wunused-variable] const vector >& s2 = bundles[i-1]->ref_scaffolds(); ^~ In file included from cuffnorm.cpp:38: differential.h: In constructor 'TrackingDataWriter::TrackingDataWriter(int, Outfiles*, Tracking*, const std::vector >&, std::vector >, ProgressBar*, boost::shared_ptr)': differential.h:230:20: warning: 'TrackingDataWriter::sample_labels' will be initialized after [-Wreorder] vector sample_labels; ^~~~~~~~~~~~~ differential.h:228:10: warning: 'bool TrackingDataWriter::headers_written' [-Wreorder] bool headers_written; // this flag records whether we've written out the file headers yet. ^~~~~~~~~~~~~~~ differential.h:204:5: warning: when initialized here [-Wreorder] TrackingDataWriter(int num_samples, ^~~~~~~~~~~~~~~~~~ rm -f libgc.a ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') ranlib libgc.a In file included from cuffnorm.cpp:38: differential.h: In member function 'void TrackingDataWriter::print_FPKM_tracking(const string&, FILE*, const FPKMTrackingTable&)': differential.h:325:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ differential.h: In member function 'void TrackingDataWriter::print_count_tracking(const string&, FILE*, const FPKMTrackingTable&)': differential.h:407:29: warning: variable 'status' set but not used [-Wunused-but-set-variable] AbundanceStatus status = NUMERIC_OK; ^~~~~~ c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib -L/usr/local/lib -L/usr/local/lib -L/usr/lib -o cufflinks cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz differential.h: In member function 'void TrackingDataWriter::print_read_group_simple_table_info(FILE*, const std::vector >&)': differential.h:614:27: warning: format '%lg' expects a matching 'double' argument [-Wformat=] fprintf(fout, "%s_%d\t%s\t%Lg\t%lg\t%lg\t%lg\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffnorm.cpp: In function 'int main(int, char**)': cuffnorm.cpp:1205:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation] if (random_seed == -1) ^~ cuffnorm.cpp:1210:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if' srand48(random_seed); ^~~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffquant.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from cuffquant.cpp:20: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib -o cuffcompare cuffcompare.o libgc.a -lz In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffquant.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from cuffquant.cpp:20: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib -L/usr/local/lib -L/usr/local/lib -L/usr/lib -o gtf_to_sam gtf_to_sam.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffquant.cpp:20: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from cuffquant.cpp:20: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib -o gffread gffread.o libgc.a -lz In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffnorm.cpp:19: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GISeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GISeg]' GVec.hh:83:42: required from 'void GVec::idxInsert(int, OBJ&) [with OBJ = GISeg]' gtf_tracking.h:210:29: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GISeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from cuffnorm.cpp:19: gtf_tracking.h:188:7: note: 'class GISeg' declared here class GISeg: public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffnorm.cpp:19: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GXSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GXSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GXSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GXSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GXSeg]' gtf_tracking.h:419:20: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GXSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from bundles.h:24, from cuffnorm.cpp:19: gtf_tracking.h:359:7: note: 'class GXSeg' declared here class GXSeg : public GSeg { ^~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:9, from gtf_tracking.h:12, from bundles.h:24, from cuffnorm.cpp:19: GVec.hh: In instantiation of 'void GVec::Grow(int, OBJ&) [with OBJ = GSeg]': GVec.hh:436:5: required from 'void GVec::Insert(int, OBJ*) [with OBJ = GSeg]' GVec.hh:81:38: required from 'void GVec::Insert(int, OBJ) [with OBJ = GSeg]' GList.hh:231:21: required from 'int GArray::Add(OBJ*) [with OBJ = GSeg]' GList.hh:51:42: required from 'int GArray::Add(OBJ&) [with OBJ = GSeg]' gtf_tracking.h:420:19: required from here GVec.hh:364:15: warning: 'void* memset(void*, int, size_t)' clearing an object of non-trivial type 'class GSeg'; use assignment or value-initialization instead [-Wclass-memaccess] memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:6, from gtf_tracking.h:12, from bundles.h:24, from cuffnorm.cpp:19: GBase.h:286:7: note: 'class GSeg' declared here class GSeg { ^~~~ mv -f .deps/compress_gtf.Tpo .deps/compress_gtf.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib -L/usr/local/lib -L/usr/local/lib -L/usr/lib -o compress_gtf compress_gtf.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz cuffdiff.cpp:2412:32: warning: 'isoform_exp.diff' directive writing 16 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] sprintf(iso_out_file_name, "%sisoform_exp.diff", out_file_prefix); ^~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2412:12: note: 'sprintf' output between 17 and 2064 bytes into a destination of size 2048 sprintf(iso_out_file_name, "%sisoform_exp.diff", out_file_prefix); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2422:34: warning: 'tss_group_exp.diff' directive writing 18 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] sprintf(group_out_file_name, "%stss_group_exp.diff", out_file_prefix); ^~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2422:12: note: 'sprintf' output between 19 and 2066 bytes into a destination of size 2048 sprintf(group_out_file_name, "%stss_group_exp.diff", out_file_prefix); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2432:33: warning: 'gene_exp.diff' directive writing 13 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] sprintf(gene_out_file_name, "%sgene_exp.diff", out_file_prefix); ^~~~~~~~~~~~~~~~~ cuffdiff.cpp:2432:12: note: 'sprintf' output between 14 and 2061 bytes into a destination of size 2048 sprintf(gene_out_file_name, "%sgene_exp.diff", out_file_prefix); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2442:32: warning: 'cds_exp.diff' directive writing 12 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] sprintf(cds_out_file_name, "%scds_exp.diff", out_file_prefix); ^~~~~~~~~~~~~~~~ cuffdiff.cpp:2442:12: note: 'sprintf' output between 13 and 2060 bytes into a destination of size 2048 sprintf(cds_out_file_name, "%scds_exp.diff", out_file_prefix); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2452:42: warning: 'splicing.diff' directive writing 13 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] sprintf(diff_splicing_out_file_name, "%ssplicing.diff", out_file_prefix); ^~~~~~~~~~~~~~~~~ cuffdiff.cpp:2452:12: note: 'sprintf' output between 14 and 2061 bytes into a destination of size 2048 sprintf(diff_splicing_out_file_name, "%ssplicing.diff", out_file_prefix); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2462:42: warning: 'promoters.diff' directive writing 14 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] sprintf(diff_promoter_out_file_name, "%spromoters.diff", out_file_prefix); ^~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2462:12: note: 'sprintf' output between 15 and 2062 bytes into a destination of size 2048 sprintf(diff_promoter_out_file_name, "%spromoters.diff", out_file_prefix); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cuffdiff.cpp:2472:37: warning: 'cds.diff' directive writing 8 bytes into a region of size between 1 and 2048 [-Wformat-overflow=] sprintf(diff_cds_out_file_name, "%scds.diff", out_file_prefix); ^~~~~~~~~~~~ cuffdiff.cpp:2472:12: note: 'sprintf' output between 9 and 2056 bytes into a destination of size 2048 sprintf(diff_cds_out_file_name, "%scds.diff", out_file_prefix); ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/cuffdiff.Tpo .deps/cuffdiff.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib -L/usr/local/lib -L/usr/local/lib -L/usr/lib -o cuffdiff cuffdiff.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz mv -f .deps/cuffnorm.Tpo .deps/cuffnorm.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib -L/usr/local/lib -L/usr/local/lib -L/usr/lib -o cuffnorm cuffnorm.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz In file included from bundles.h:25, from cuffquant.cpp:20: progressbar.h: In member function 'void AbundanceRecorder::record_finished_loci()': progressbar.h:70:26: warning: '%3d' directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ progressbar.h:70:26: note: directive argument in the range [-2147483648, 99] progressbar.h:70:11: note: 'snprintf' output between 54 and 89 bytes into a destination of size 82 snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/cuffquant.Tpo .deps/cuffquant.Po c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -pipe -I/usr/local/include/eigen3 -O2 -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -L/usr/lib -L/usr/local/lib -L/usr/local/lib -L/usr/lib -o cuffquant cuffquant.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz gmake[3]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050/src' gmake[3]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' gmake[2]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' gmake[1]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> cufflinks-2.2.1.83 depends on file: /usr/local/bin/python3.6 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for cufflinks-2.2.1.83 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' Making install in src gmake[2]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050/src' gmake[3]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050/src' /bin/mkdir -p '/construction/biology/cufflinks/stage/usr/local/bin' install -s -m 555 cufflinks cuffcompare cuffdiff gtf_to_sam compress_gtf gffread cuffquant cuffnorm '/construction/biology/cufflinks/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/cufflinks/stage/usr/local/bin' install -m 555 cuffmerge '/construction/biology/cufflinks/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050/src' gmake[2]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050/src' gmake[2]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' gmake[3]: Entering directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' gmake[2]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' gmake[1]: Leaving directory '/construction/biology/cufflinks/cufflinks-2.2.1-83-gb4fa050' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for cufflinks-2.2.1.83 file sizes/checksums [12]: . done packing files [12]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 24 JUL 2019 at 16:54:57 UTC Duration: 00:05:32