=> Building biology/viennarna Started : Wednesday, 24 JUL 2019 at 17:39:23 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 -------------------------------------------------- ===> The following configuration options are available for viennarna-2.4.13: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/construction/biology/viennarna XDG_CONFIG_HOME=/construction/biology/viennarna HOME=/construction/biology/viennarna TMPDIR="/tmp" PATH=/construction/biology/viennarna/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/usr/local/bin/bash CONFIG_SHELL=/usr/local/bin/bash CCVER=gcc80 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --enable-shared --disable-static --with-gsl --with-cluster --with-kinwalker --enable-mpfr --without-python --without-python3 --without-perl --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/viennarna XDG_CONFIG_HOME=/construction/biology/viennarna HOME=/construction/biology/viennarna TMPDIR="/tmp" PATH=/construction/biology/viennarna/.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 -O2 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS=" -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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/viennarna/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.6 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 PERL_VER=5.28 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.28 PROFILE="@comment " DOCSDIR="share/doc/ViennaRNA" EXAMPLESDIR="share/examples/ViennaRNA" DATADIR="share/viennarna" WWWDIR="www/viennarna" ETCDIR="etc/viennarna" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/viennarna DOCSDIR=/usr/local/share/doc/ViennaRNA EXAMPLESDIR=/usr/local/share/examples/ViennaRNA WWWDIR=/usr/local/www/viennarna ETCDIR=/usr/local/etc/viennarna -------------------------------------------------- -- /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 ViennaRNALicense accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> viennarna-2.4.13 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 ===> viennarna-2.4.13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of viennarna-2.4.13 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License ViennaRNALicense accepted by the user => ViennaRNA-2.4.13.tar.gz doesn't seem to exist in /distfiles/. => Attempting to fetch https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.13.tar.gz ViennaRNA-2.4.13.tar.gz 32 MB 2903 kBps 12s ===> Fetching all distfiles required by viennarna-2.4.13 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License ViennaRNALicense accepted by the user ===> Fetching all distfiles required by viennarna-2.4.13 for building => SHA256 Checksum OK for ViennaRNA-2.4.13.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License ViennaRNALicense accepted by the user ===> Fetching all distfiles required by viennarna-2.4.13 for building ===> Extracting for viennarna-2.4.13 => SHA256 Checksum OK for ViennaRNA-2.4.13.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for viennarna-2.4.13 ===> Applying ports patches for viennarna-2.4.13 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> viennarna-2.4.13 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.0.7.txz Installing bash-5.0.7... `-- Installing gettext-runtime-0.20.1... | `-- Installing indexinfo-0.3.1... | `-- Extracting indexinfo-0.3.1: .... done `-- Extracting gettext-runtime-0.20.1: .......... done `-- Installing ncurses-6.1.20190525... `-- Extracting ncurses-6.1.20190525: .......... done Extracting bash-5.0.7: .......... done ===> viennarna-2.4.13 depends on executable: bash - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on package: libgd>0 - not found ===> Installing existing package /packages/All/libgd-2.2.5_1,1.txz Installing libgd-2.2.5_1,1... `-- Installing fontconfig-2.12.6,1... | `-- Installing expat-2.2.6_1... | `-- Extracting expat-2.2.6_1: .......... done | `-- Installing freetype2-2.10.0... | `-- Extracting freetype2-2.10.0: .......... done `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded `-- Installing jpeg-turbo-2.0.2... `-- Extracting jpeg-turbo-2.0.2: .......... done `-- Installing png-1.6.37... `-- Extracting png-1.6.37: .......... done `-- Installing tiff-4.0.10_1... | `-- Installing jbigkit-2.1_1... | `-- Extracting jbigkit-2.1_1: .......... done `-- Extracting tiff-4.0.10_1: .......... done `-- Installing webp-1.0.2... | `-- Installing giflib-5.1.9... | `-- Extracting giflib-5.1.9: .......... done `-- Extracting webp-1.0.2: .......... done Extracting libgd-2.2.5_1,1: .......... done Message from freetype2-2.10.0: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/site/index.html, if documentation was installed). ===> viennarna-2.4.13 depends on package: libgd>0 - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 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 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. ===> viennarna-2.4.13 depends on package: autoconf>=2.69 - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 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 ===> viennarna-2.4.13 depends on package: automake>=1.16.1 - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.6_1.txz Installing libtool-2.4.6_1... Extracting libtool-2.4.6_1: .......... done ===> viennarna-2.4.13 depends on executable: libtoolize - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_3.txz Installing gmake-4.2.1_3... Extracting gmake-4.2.1_3: .......... done ===> viennarna-2.4.13 depends on executable: gmake - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.6.1,1.txz Installing pkgconf-1.6.1,1... Extracting pkgconf-1.6.1,1: .......... done ===> viennarna-2.4.13 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found ===> Installing existing package /packages/All/libX11-1.6.8,1.txz Installing libX11-1.6.8,1... `-- Installing libXau-1.0.9... `-- Extracting libXau-1.0.9: .......... done `-- Installing libXdmcp-1.1.3... | `-- Installing xorgproto-2019.1... | `-- Extracting xorgproto-2019.1: .......... done `-- Extracting libXdmcp-1.1.3: ......... done `-- Installing libxcb-1.13.1... | `-- Installing libpthread-stubs-0.4... | `-- Extracting libpthread-stubs-0.4: .... done | `-- Installing libxml2-2.9.9... | `-- Extracting libxml2-2.9.9: .......... done `-- Extracting libxcb-1.13.1: .......... done Extracting libX11-1.6.8,1: .......... done ===> viennarna-2.4.13 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on file: /usr/local/libdata/pkgconfig/xext.pc - not found ===> Installing existing package /packages/All/libXext-1.3.4,1.txz Installing libXext-1.3.4,1... Extracting libXext-1.3.4,1: .......... done ===> viennarna-2.4.13 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> viennarna-2.4.13 depends on shared library: libgmp.so - not found ===> Installing existing package /packages/All/gmp-6.1.2_1.txz Installing gmp-6.1.2_1... Extracting gmp-6.1.2_1: .......... done ===> viennarna-2.4.13 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.5_1.txz Installing gsl-2.5_1... Extracting gsl-2.5_1: .......... done ===> viennarna-2.4.13 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of viennarna-2.4.13 ===> viennarna-2.4.13 depends on shared library: libmpfr.so - not found ===> Installing existing package /packages/All/mpfr-4.0.2.txz Installing mpfr-4.0.2... Extracting mpfr-4.0.2: .......... done ===> viennarna-2.4.13 depends on shared library: libmpfr.so - found (/usr/local/lib/libmpfr.so) ===> Returning to build of viennarna-2.4.13 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for viennarna-2.4.13 libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:15: installing 'config/compile' configure.ac:21: installing 'config/missing' interfaces/Perl/Makefile.am: installing 'config/depcomp' configure: loading site script /xports/Templates/config.site checking for gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... 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(cached) yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for a sed that does not truncate output... (cached) /usr/bin/sed checking whether ln -s works... yes checking for cc option to accept ISO C99... none needed checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking the maximum length of command line arguments... (cached) 262144 checking how to convert x86_64-portbld-dragonfly5.6 file names to x86_64-portbld-dragonfly5.6 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.6 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for archiver @FILE support... @ checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... no checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... dragonfly5.6 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... dragonfly5.6 ld.so checking how to hardcode library paths into programs... immediate checking for exp in -lm... yes checking for ANSI C header files... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for malloc.h... (cached) no checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for math.h... (cached) yes checking for stdarg.h... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... 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(cached) /usr/local/bin/perl checking whether C compiler accepts -fno-strict-aliasing... yes checking whether C++ compiler accepts -fno-strict-aliasing... yes checking whether the linker accepts -fno-strict-aliasing... yes checking whether the C compiler allows unnamed unions of unnamed structs... yes checking whether the C++ compiler allows unnamed unions of unnamed structs... yes checking whether C compiler accepts -flto... yes checking whether C++ compiler accepts -flto... yes checking whether C compiler accepts -ffat-lto-objects... yes checking whether C++ compiler accepts -ffat-lto-objects... yes configure: WARNING: Trying to re-set ar/ranlib/nm to compiler specific wrappers checking for gcc-ar... no checking for gcc-ranlib... no checking for gcc-nm... no configure: WARNING: Your compiler/linker combination does not support link-time optimization (LTO) checking for ./src/libsvm-3.23/svm.cpp... yes checking for ./src/libsvm-3.23/svm.h... yes checking for ./src/json/json.c... yes checking for ./src/json/json.h... yes checking for cblas_dgemm in -lgslcblas... yes checking for gsl_blas_dgemm in -lgsl... yes checking for OpenMP flag of C compiler... -fopenmp checking for OpenMP flag of C++ compiler... -fopenmp checking whether cc is Clang... no checking whether pthreads work with -pthread... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking compiler support for AVX 512 instructions... yes checking compiler support for SSE 4.1 instructions... yes checking whether C compiler accepts -ftree-vectorize... yes checking mpfr.h usability... yes checking mpfr.h presence... yes checking for mpfr.h... yes checking whether we can compile programs with mpfr support... yes checking for ./interfaces/Makefile.am... yes checking for swig... no checking for swig2.0... no checking for doxygen... no checking for pdflatex... no checking for latex... no checking for dvipdf... no checking for bibtex... no checking for makeindex... no checking for dot... no checking for egrep... /usr/bin/egrep checking for perl... /usr/local/bin/perl checking for doc/RNAlib-2.4.13.pdf... yes checking for doc/html/index.html... yes checking for pdflatex... (cached) no checking for latex... (cached) no checking for dvipdf... (cached) no checking for htlatex... no configure: WARNING: neither latex or pdflatex exists on your system! configure: WARNING: deactivating automatic (re)generation of tutorial! checking for RNA-Tutorial/RNA-tutorial-2.4.13.pdf... yes checking for CHECK... no configure: WARNING: check not found -- will not build C-library Unit tests checking for diff... /usr/bin/diff checking for xxd... no checking for gengetopt... no checking for help2man... no checking for ./src/ViennaRNA/static/postscript/structure_plot_macro_base.hex... yes checking for ./src/ViennaRNA/static/postscript/structure_plot_macro_extras.hex... yes checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_base.hex... yes checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_turn.hex... yes checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_sd.hex... yes checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_ud.hex... yes checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_sc_motifs.hex... yes checking for ./src/ViennaRNA/static/postscript/dot_plot_macro_linear_data.hex... yes checking for ./src/ViennaRNA/static/postscript/aln_macro_base.hex... yes checking for ./src/Kinfold/Makefile.am... yes checking for ./src/RNAforester/Makefile.am... yes checking for ./src/Cluster/Makefile.am... yes checking for ./src/Kinwalker/Makefile.am... yes checking for ./src/RNAlocmin/Makefile.am... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating packaging/macosx/Makefile config.status: creating packaging/macosx/Distribution.xml config.status: creating packaging/macosx/resources/welcome.txt config.status: creating tests/Makefile config.status: creating tests/RNApath.py config.status: creating tests/RNAHelpers.pm config.status: creating tests/test-env.sh config.status: creating src/ViennaRNA/static/templates_postscript.h config.status: creating src/Cluster/Makefile config.status: creating src/ViennaRNA/vrna_config.h config.status: creating misc/Makefile config.status: creating interfaces/Makefile config.status: creating Makefile config.status: creating RNAlib2.pc config.status: creating src/Utils/Makefile config.status: creating src/bin/Makefile config.status: creating src/Makefile config.status: creating src/ViennaRNA/Makefile config.status: creating src/ViennaRNA/static/Makefile config.status: creating man/Makefile config.status: creating doc/Makefile config.status: creating RNA-Tutorial/Makefile config.status: creating man/cmdlopt.sh config.status: creating examples/Makefile config.status: creating packaging/viennarna.spec config.status: creating packaging/PKGBUILD config.status: creating packaging/win_installer_archlinux_i686.nsi config.status: creating packaging/win_installer_archlinux_x86_64.nsi config.status: creating packaging/win_installer_fedora_i686.nsi config.status: creating packaging/win_installer_fedora_x86_64.nsi config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in src/Kinfold (/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--enable-shared' '--disable-static' '--with-gsl' '--with-cluster' '--with-kinwalker' '--enable-mpfr' '--without-python' '--without-python3' '--without-perl' '--x-libraries=/usr/local/lib' '--x-includes=/usr/local/include' '--localstatedir=/var' '--mandir=/usr/local/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=x86_64-portbld-dragonfly5.6' 'build_alias=x86_64-portbld-dragonfly5.6' 'CC=cc' 'CFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS= ' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CPP=cpp' 'CXX=c++' 'CXXFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include' 'PKG_CONFIG=pkgconf' 'AR=ar' 'RANLIB=ranlib' 'NM=/usr/bin/nm -B' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp' --cache-file=/dev/null --srcdir=. configure: loading site script /xports/Templates/config.site checking whether gmake supports nested variables... yes 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 if malloc debugging is wanted... no checking for gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking whether gmake supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking build system type... x86_64-portbld-dragonfly5.6 checking host system type... x86_64-portbld-dragonfly5.6 checking for strdup... (cached) yes checking for memset... (cached) yes checking for strchr... (cached) yes checking pkg-config is at least version 0.9.0... yes checking for VRNA... 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 for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for exp in -lm... yes checking for an ANSI C-conforming const... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Example/Makefile config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in src/RNAforester (/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--enable-shared' '--disable-static' '--with-gsl' '--with-cluster' '--with-kinwalker' '--enable-mpfr' '--without-python' '--without-python3' '--without-perl' '--x-libraries=/usr/local/lib' '--x-includes=/usr/local/include' '--localstatedir=/var' '--mandir=/usr/local/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=x86_64-portbld-dragonfly5.6' 'build_alias=x86_64-portbld-dragonfly5.6' 'CC=cc' 'CFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS= ' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CPP=cpp' 'CXX=c++' 'CXXFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include' 'PKG_CONFIG=pkgconf' 'AR=ar' 'RANLIB=ranlib' 'NM=/usr/bin/nm -B' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp' --cache-file=/dev/null --srcdir=. configure: loading site script /xports/Templates/config.site checking whether gmake supports nested variables... yes 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 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 for flex... flex checking lex output file root... lex.yy checking lex library... none needed checking whether yytext is a pointer... no checking for bison... no checking for byacc... byacc checking for c++ option to support OpenMP... -fopenmp checking pkg-config is at least version 0.9.0... yes checking for VRNA... yes checking how to run the C++ preprocessor... c++ -E 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 g2.h usability... yes checking g2.h presence... yes checking for g2.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... (cached) yes 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 man/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in g2-0.72 (/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/g2-0.72) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--enable-shared' '--disable-static' '--with-gsl' '--with-cluster' '--with-kinwalker' '--enable-mpfr' '--without-python' '--without-python3' '--without-perl' '--x-libraries=/usr/local/lib' '--x-includes=/usr/local/include' '--localstatedir=/var' '--mandir=/usr/local/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=x86_64-portbld-dragonfly5.6' 'build_alias=x86_64-portbld-dragonfly5.6' 'CC=cc' 'CFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS= ' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CPP=cpp' 'CXX=c++' 'CXXFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include' 'PKG_CONFIG=pkgconf' 'AR=ar' 'RANLIB=ranlib' 'NM=/usr/bin/nm -B' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp' --cache-file=/dev/null --srcdir=. configure: loading site script /xports/Templates/config.site checking build system type... x86_64-portbld-dragonfly5.6 checking host system type... x86_64-portbld-dragonfly5.6 checking for gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking how to run the C preprocessor... cpp checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking for a BSD-compatible install... /usr/bin/install -c checking for find... find checking for makedepend... : checking for dlopen in -ldl... yes checking for X... libraries /usr/local/lib, headers /usr/local/include checking whether -R must be followed by a space... no checking for gethostbyname... (cached) yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... no checking for main in -lm... yes checking for main in -lX11... yes checking for main in -lXext... yes checking for main in -lgd... yes checking for gdImagePng... yes checking for gdImageGif... yes 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 for limits.h... (cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating demo/Makefile config.status: creating g2_perl/Makefile.PL config.status: creating g2_python/Makefile Supported devices: PostScript FIG X11 Xdbe GD GD (GIF) Unsupported devices: Win32 Run 'make depend' to create dependencies. === configuring in src/Kinwalker (/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--enable-shared' '--disable-static' '--with-gsl' '--with-cluster' '--with-kinwalker' '--enable-mpfr' '--without-python' '--without-python3' '--without-perl' '--x-libraries=/usr/local/lib' '--x-includes=/usr/local/include' '--localstatedir=/var' '--mandir=/usr/local/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=x86_64-portbld-dragonfly5.6' 'build_alias=x86_64-portbld-dragonfly5.6' 'CC=cc' 'CFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS= ' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CPP=cpp' 'CXX=c++' 'CXXFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include' 'PKG_CONFIG=pkgconf' 'AR=ar' 'RANLIB=ranlib' 'NM=/usr/bin/nm -B' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp' --cache-file=/dev/null --srcdir=. configure: loading site script /xports/Templates/config.site checking whether gmake supports nested variables... yes 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 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 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 for malloc.h... (cached) no checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for inline... inline checking pkg-config is at least version 0.9.0... yes checking for VRNA... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in src/RNAlocmin (/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--enable-shared' '--disable-static' '--with-gsl' '--with-cluster' '--with-kinwalker' '--enable-mpfr' '--without-python' '--without-python3' '--without-perl' '--x-libraries=/usr/local/lib' '--x-includes=/usr/local/include' '--localstatedir=/var' '--mandir=/usr/local/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=x86_64-portbld-dragonfly5.6' 'build_alias=x86_64-portbld-dragonfly5.6' 'CC=cc' 'CFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS= ' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CPP=cpp' 'CXX=c++' 'CXXFLAGS=-pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include' 'PKG_CONFIG=pkgconf' 'AR=ar' 'RANLIB=ranlib' 'NM=/usr/bin/nm -B' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp' --cache-file=/dev/null --srcdir=. configure: loading site script /xports/Templates/config.site checking for gcc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... 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 for minix/config.h... (cached) no checking whether it is safe to define __EXTENSIONS__... yes checking whether gmake supports nested variables... yes 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 the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking build system type... x86_64-portbld-dragonfly5.6 checking host system type... x86_64-portbld-dragonfly5.6 checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E checking for gcc... (cached) cc checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... (cached) none needed checking whether cc understands -c and -o together... (cached) yes checking how to run the C preprocessor... cpp checking whether c++ supports C++11 features by default... yes checking for strchr... (cached) yes checking for strdup... (cached) yes checking for strtol... (cached) yes checking for limits.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for inline... inline checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... (cached) yes checking for size_t... (cached) yes checking pkg-config is at least version 0.9.0... yes checking for VRNA... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: ====================================== ViennaRNA Package 2.4.13 ====================================== Sub Packages ------------ * Kinfold : yes * RNAforester : yes * Analyse{Dists,Seqs} : yes * RNAlocmin : yes * Kinwalker : yes Extra Libraries --------------- * Support Vector Machine : yes * GNU Scientific Library : yes * GNU MPFR : yes * JSON : yes Features -------- * Boustrophedon : yes * Use hash for NR Sampling : no * C11 features : yes * TTY colors : yes * Float Precision(PF} : no * Deprecation Warnings : no Optimizations ------------- * Auto Vectorization : yes * Explicit SIMD Extension : yes * Link Time Optimization : no * POSIX Threads : yes * OpenMP : yes Scripting Language Interfaces ----------------------------- * Perl 5 : no * Python 2 : no * Python 3 : no Documentation ------------- * Reference Manual (PDF) : yes * Reference Manual (HTML) : yes * Tutorial (PDF) : yes * Tutorial (HTML) : no Unit Tests ---------- * Executable Programs : yes * C-Library : no * Perl 5 Interface : no * Python 2 Interface : no * Python 3 Interface : no MacOS X ------- * Universal Binary : no * Installer : no * SDK : custom Install Directories ------------------- * Executables : /usr/local/bin * Libraries : /usr/local/lib * Header files : /usr/local/include * Extra Data : /usr/local/share * Man pages : /usr/local/man * Documentation : /usr/local/share/doc/ViennaRNA (HTML) : /usr/local/share/doc/ViennaRNA/html (PDF) : /usr/local/share/doc/ViennaRNA * Perl5 Interface : Not to be installed (binaries) : (scripts) : * Python2 Interface : Not to be installed (binaries) : (scripts) : * Python3 Interface : Not to be installed (binaries) : (scripts) : You can run 'make', 'make check' and 'make install' now! -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for viennarna-2.4.13 gmake[1]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13' gmake all-recursive gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13' Making all in src gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' Making all in ViennaRNA gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA' Making all in static gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake all-am gmake[6]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake[6]: Nothing to be done for 'all-am'. gmake[6]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA' depbase=`echo fold_compound.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT fold_compound.lo -MD -MP -MF $depbase.Tpo -c -o fold_compound.lo fold_compound.c &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo dist_vars.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT dist_vars.lo -MD -MP -MF $depbase.Tpo -c -o dist_vars.lo dist_vars.c &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo part_func.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT part_func.lo -MD -MP -MF $depbase.Tpo -c -o part_func.lo part_func.c &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo part_func_wrappers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem 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concentrations.lo -MD -MP -MF $depbase.Tpo -c -o concentrations.lo concentrations.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT concentrations.lo -MD -MP -MF .deps/concentrations.Tpo -c concentrations.c -fPIC -DPIC -o .libs/concentrations.o depbase=`echo ProfileAln.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT ProfileAln.lo -MD -MP -MF $depbase.Tpo -c -o ProfileAln.lo ProfileAln.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. 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duplex.lo -MD -MP -MF .deps/duplex.Tpo -c duplex.c -fPIC -DPIC -o .libs/duplex.o depbase=`echo alifold.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT alifold.lo -MD -MP -MF $depbase.Tpo -c -o alifold.lo alifold.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT alifold.lo -MD -MP -MF .deps/alifold.Tpo -c alifold.c -fPIC -DPIC -o .libs/alifold.o depbase=`echo alipfold.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc 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cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT gquad.lo -MD -MP -MF $depbase.Tpo -c -o gquad.lo gquad.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT gquad.lo -MD -MP -MF .deps/gquad.Tpo -c gquad.c -fPIC -DPIC -o .libs/gquad.o depbase=`echo perturbation_fold.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libsvm-3.23 -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include 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.libs/libRNA_conv.lax/libRNA_landscape.a/findpath.o .libs/libRNA_conv.lax/libRNA_landscape.a/move.o .libs/libRNA_conv.lax/libRNA_landscape.a/move_set.o .libs/libRNA_conv.lax/libRNA_landscape.a/neighbor.o .libs/libRNA_conv.lax/libRNA_landscape.a/walk.o .libs/libRNA_conv.lax/libRNA_utils_sse41.a/libRNA_utils_sse41_la-higher_order_functions_sse41.o .libs/libRNA_conv.lax/libRNA_utils_avx512.a/libRNA_utils_avx512_la-higher_order_functions_avx512.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libRNA_conv.a libtool: link: rm -fr .libs/libRNA_conv.lax libtool: link: ( cd ".libs" && rm -f "libRNA_conv.la" && ln -s "../libRNA_conv.la" "libRNA_conv.la" ) /usr/local/bin/bash ../../libtool --tag=CXX --mode=link c++ -fno-strict-aliasing -fopenmp -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -avoid-version -static -flto -o libRNA.la -rpath /usr/local/lib libRNA_conv.la -lgsl 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$depbase.Tpo $depbase.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT ../cthreadpool/thpool.lo -MD -MP -MF ../cthreadpool/.deps/thpool.Tpo -c ../cthreadpool/thpool.c -fPIC -DPIC -o ../cthreadpool/.libs/thpool.o /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -avoid-version -static -flto -o libhelpers.la input_id_helpers.lo parallel_helpers.lo ../cthreadpool/thpool.lo -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: ar cru .libs/libhelpers.a .libs/input_id_helpers.o .libs/parallel_helpers.o ../cthreadpool/.libs/thpool.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libhelpers.a libtool: link: ( cd ".libs" && rm -f "libhelpers.la" && ln -s "../libhelpers.la" "libhelpers.la" ) /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAfold RNAfold_cmdl.o RNAfold.o ../../src/ViennaRNA/libRNA_special_const.la ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAeval RNAeval_cmdl.o RNAeval.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAheat RNAheat_cmdl.o RNAheat.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAfold RNAfold_cmdl.o RNAfold.o ../../src/ViennaRNA/.libs/libRNA_special_const.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAeval RNAeval_cmdl.o RNAeval.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAheat RNAheat_cmdl.o RNAheat.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNApdist RNApdist_cmdl.o RNApdist.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNApdist RNApdist_cmdl.o RNApdist.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAdistance RNAdistance_cmdl.o RNAdistance.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAplot RNAplot_cmdl.o RNAplot.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAinverse RNAinverse_cmdl.o RNAinverse.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNALfold RNALfold_cmdl.o RNALfold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAplot RNAplot_cmdl.o RNAplot.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNALfold RNALfold_cmdl.o RNALfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNApaln RNApaln_cmdl.o RNApaln.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAduplex RNAduplex_cmdl.o RNAduplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAalifold RNAalifold_cmdl.o RNAalifold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAcofold RNAcofold_cmdl.o RNAcofold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNApaln RNApaln_cmdl.o RNApaln.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAup RNAup_cmdl.o RNAup.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAalifold RNAalifold_cmdl.o RNAalifold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAduplex RNAduplex_cmdl.o RNAduplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAup RNAup_cmdl.o RNAup.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAplfold RNAplfold_cmdl.o RNAplfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAparconv RNAparconv_cmdl.o RNAparconv.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNALalifold RNALalifold_cmdl.o RNALalifold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNApvmin RNApvmin_cmdl.o RNApvmin.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAparconv RNAparconv_cmdl.o RNAparconv.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNApvmin RNApvmin_cmdl.o RNApvmin.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAplex RNAplex_cmdl.o RNAplex.o ../../src/ViennaRNA/libRNA_conv.la libhelpers.la -lmpfr -lgmp -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o RNAplex RNAplex_cmdl.o RNAplex.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib ./.libs/libhelpers.a -lmpfr -lgmp -lgsl -lgslcblas -lm -pthread -fopenmp gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/bin' Making all in Utils gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Utils' cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT b2ct.o -MD -MP -MF .deps/b2ct.Tpo -c -o b2ct.o b2ct.c cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread 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split.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo distance_matrix.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT distance_matrix.o -MD -MP -MF $depbase.Tpo -c -o distance_matrix.o distance_matrix.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo cluster.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT cluster.o -MD -MP -MF $depbase.Tpo -c -o cluster.o cluster.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo treeplot.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT treeplot.o -MD -MP -MF $depbase.Tpo -c -o treeplot.o treeplot.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo AD_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT AD_main.o -MD -MP -MF $depbase.Tpo -c -o AD_main.o AD_main.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo statgeom.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT statgeom.o -MD -MP -MF $depbase.Tpo -c -o statgeom.o statgeom.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo AS_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT AS_main.o -MD -MP -MF $depbase.Tpo -c -o AS_main.o AS_main.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo PS3D.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -I../../src -I../.. -I../.. -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT PS3D.o -MD -MP -MF $depbase.Tpo -c -o PS3D.o PS3D.c &&\ mv -f $depbase.Tpo $depbase.Po /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/libRNA_conv.la -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o AnalyseDists split.o distance_matrix.o cluster.o treeplot.o AD_main.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -o AnalyseSeqs statgeom.o distance_matrix.o cluster.o AS_main.o split.o treeplot.o PS3D.o ../../src/ViennaRNA/.libs/libRNA_conv.a -L/usr/local/lib -lgsl -lgslcblas -lm -pthread -fopenmp gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Cluster' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' Making all in man gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/man' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/man' Making all in misc gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/misc' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/misc' Making all in doc gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/doc' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/doc' Making all in RNA-Tutorial gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/RNA-Tutorial' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/RNA-Tutorial' Making all in interfaces gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' Making all in src/Kinfold gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' gmake all-recursive gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' Making all in Example gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold/Example' gmake[5]: Nothing to be done for 'all'. gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold/Example' gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c mv -f .deps/cache.Tpo .deps/cache.Po cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c mv -f .deps/globals.Tpo .deps/globals.Po mv -f .deps/nachbar.Tpo .deps/nachbar.Po mv -f .deps/main.Tpo .deps/main.Po mv -f .deps/baum.Tpo .deps/baum.Po mv -f .deps/cmdline.Tpo .deps/cmdline.Po cc -I./../../src/ViennaRNA -I./../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -fno-strict-aliasing -L./../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp -lm -L/usr/local/lib gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' Making all in src/RNAforester gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' gmake all-recursive gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' Making all in g2-0.72 gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/g2-0.72' Makefile:101: warning: overriding recipe for target 'libg2.so' Makefile:98: warning: ignoring old recipe for target 'libg2.so' cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o cc -I./src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/GD/g2_gd.c -o src/GD/g2_gd.o ar cr libg2.a ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o ./src/GD/g2_gd.o test ! -n "ranlib" || ranlib libg2.a test -d ./include || mkdir ./include cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./src/GD/g2_gd.h ./include/ gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/g2-0.72' Making all in src gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' gmake all-am gmake[6]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' depbase=`echo aligner.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT aligner.o -MD -MP -MF $depbase.Tpo -c -o aligner.o aligner.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT main.o -MD -MP -MF $depbase.Tpo -c -o main.o main.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo forestbase.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT forestbase.o -MD -MP -MF $depbase.Tpo -c -o forestbase.o forestbase.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo parser.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT parser.o -MD -MP -MF $depbase.Tpo -c -o parser.o parser.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo progressive_align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT progressive_align.o -MD -MP -MF $depbase.Tpo -c -o progressive_align.o progressive_align.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rna_profile_alignment.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rna_profile_alignment.o -MD -MP -MF $depbase.Tpo -c -o rna_profile_alignment.o rna_profile_alignment.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rna_alignment.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rna_alignment.o -MD -MP -MF $depbase.Tpo -c -o rna_alignment.o rna_alignment.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rna_algebra.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rna_algebra.o -MD -MP -MF $depbase.Tpo -c -o rna_algebra.o rna_algebra.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rna_alphabet.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rna_alphabet.o -MD -MP -MF $depbase.Tpo -c -o rna_alphabet.o rna_alphabet.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rnaforest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rnaforest.o -MD -MP -MF $depbase.Tpo -c -o rnaforest.o rnaforest.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rnafuncs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rnafuncs.o -MD -MP -MF $depbase.Tpo -c -o rnafuncs.o rnafuncs.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo anchors/bplex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT anchors/bplex.o -MD -MP -MF $depbase.Tpo -c -o anchors/bplex.o anchors/bplex.cpp &&\ mv -f $depbase.Tpo $depbase.Po anchors/bplex.cpp: In function 'yy_buffer_state* yy_scan_bytes(const char*, int)': anchors/bplex.cpp:1516:17: warning: comparison of integer expressions of different signedness: 'yy_size_t' {aka 'long unsigned int'} and 'int' [-Wsign-compare] for ( i = 0; i < _yybytes_len; ++i ) ~~^~~~~~~~~~~~~~ depbase=`echo anchors/shape.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT anchors/shape.o -MD -MP -MF $depbase.Tpo -c -o anchors/shape.o anchors/shape.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo anchors/anchors.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT anchors/anchors.o -MD -MP -MF $depbase.Tpo -c -o anchors/anchors.o anchors/anchors.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo frontend/Arguments.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT frontend/Arguments.o -MD -MP -MF $depbase.Tpo -c -o frontend/Arguments.o frontend/Arguments.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo frontend/rnaforester_options.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT frontend/rnaforester_options.o -MD -MP -MF $depbase.Tpo -c -o frontend/rnaforester_options.o frontend/rnaforester_options.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo TED/rnaforestsz.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT TED/rnaforestsz.o -MD -MP -MF $depbase.Tpo -c -o TED/rnaforestsz.o TED/rnaforestsz.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo wmatch/glib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -I../../../src/ViennaRNA -I../../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT wmatch/glib.o -MD -MP -MF $depbase.Tpo -c -o wmatch/glib.o wmatch/glib.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo wmatch/wmatch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -isystem /usr/local/include -I../g2-0.72/include/ -I../../../src/ViennaRNA -I../../../src -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT wmatch/wmatch.o -MD -MP -MF $depbase.Tpo -c -o wmatch/wmatch.o wmatch/wmatch.c &&\ mv -f $depbase.Tpo $depbase.Po c++ -Wall -std=c++98 -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L../g2-0.72 -o RNAforester anchors/bplex.o anchors/shape.o anchors/anchors.o aligner.o main.o forestbase.o parser.o progressive_align.o rna_profile_alignment.o rna_alignment.o rna_algebra.o rna_alphabet.o rnaforest.o rnafuncs.o frontend/Arguments.o frontend/rnaforester_options.o TED/rnaforestsz.o wmatch/glib.o wmatch/wmatch.o -lg2 -fno-strict-aliasing -L../../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp -L/usr/local/lib gmake[6]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' Making all in man gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/man' gmake[5]: Nothing to be done for 'all'. gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/man' gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' gmake[5]: Nothing to be done for 'all-am'. gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' Making all in src/Kinwalker gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' gmake all-recursive gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' Making all in man gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker/man' gmake[5]: Nothing to be done for 'all'. gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker/man' gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Energy.o -MD -MP -MF .deps/Energy.Tpo -c -o Energy.o Energy.cpp c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT MorganHiggs.o -MD -MP -MF .deps/MorganHiggs.Tpo -c -o MorganHiggs.o MorganHiggs.cpp c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Node.o -MD -MP -MF .deps/Node.Tpo -c -o Node.o Node.cpp cc -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT options.o -MD -MP -MF .deps/options.Tpo -c -o options.o options.c mv -f .deps/options.Tpo .deps/options.Po c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Util.o -MD -MP -MF .deps/Util.Tpo -c -o Util.o Util.cpp mv -f .deps/Energy.Tpo .deps/Energy.Po mv -f .deps/main.Tpo .deps/main.Po mv -f .deps/Util.Tpo .deps/Util.Po mv -f .deps/Node.Tpo .deps/Node.Po mv -f .deps/MorganHiggs.Tpo .deps/MorganHiggs.Po c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -o kinwalker main.o Energy.o MorganHiggs.o Node.o options.o Util.o -fno-strict-aliasing -L./../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp -L/usr/local/lib gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' Making all in src/RNAlocmin gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin' gmake all-am gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin' cc -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -fexceptions -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT RNAlocmin_cmdline.o -MD -MP -MF .deps/RNAlocmin_cmdline.Tpo -c -o RNAlocmin_cmdline.o RNAlocmin_cmdline.c c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT barrier_tree.o -MD -MP -MF .deps/barrier_tree.Tpo -c -o barrier_tree.o barrier_tree.cpp c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT findpath_pk.o -MD -MP -MF .deps/findpath_pk.Tpo -c -o findpath_pk.o findpath_pk.cpp c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT flood.o -MD -MP -MF .deps/flood.Tpo -c -o flood.o flood.cpp c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.cpp mv -f .deps/RNAlocmin_cmdline.Tpo .deps/RNAlocmin_cmdline.Po c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT hash_util.o -MD -MP -MF .deps/hash_util.Tpo -c -o hash_util.o hash_util.cpp mv -f .deps/barrier_tree.Tpo .deps/barrier_tree.Po c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp mv -f .deps/globals.Tpo .deps/globals.Po cc -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -fexceptions -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -MT move_set_inside.o -MD -MP -MF .deps/move_set_inside.Tpo -c -o move_set_inside.o move_set_inside.c mv -f .deps/hash_util.Tpo .deps/hash_util.Po c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT move_set_pk.o -MD -MP -MF .deps/move_set_pk.Tpo -c -o move_set_pk.o move_set_pk.cpp mv -f .deps/move_set_inside.Tpo .deps/move_set_inside.Po c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT neighbourhood.o -MD -MP -MF .deps/neighbourhood.Tpo -c -o neighbourhood.o neighbourhood.cpp mv -f .deps/findpath_pk.Tpo .deps/findpath_pk.Po c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT pknots.o -MD -MP -MF .deps/pknots.Tpo -c -o pknots.o pknots.cpp mv -f .deps/flood.Tpo .deps/flood.Po c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT RNAlocmin.o -MD -MP -MF .deps/RNAlocmin.Tpo -c -o RNAlocmin.o RNAlocmin.cpp mv -f .deps/move_set_pk.Tpo .deps/move_set_pk.Po c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -Wno-write-strings -isystem /usr/local/include -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT treeplot.o -MD -MP -MF .deps/treeplot.Tpo -c -o treeplot.o treeplot.cpp mv -f .deps/treeplot.Tpo .deps/treeplot.Po mv -f .deps/neighbourhood.Tpo .deps/neighbourhood.Po mv -f .deps/RNAlocmin.Tpo .deps/RNAlocmin.Po mv -f .deps/main.Tpo .deps/main.Po mv -f .deps/pknots.Tpo .deps/pknots.Po c++ -pipe -O2 -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -o RNAlocmin RNAlocmin_cmdline.o barrier_tree.o findpath_pk.o flood.o globals.o hash_util.o main.o move_set_inside.o move_set_pk.o neighbourhood.o pknots.o RNAlocmin.o treeplot.o -fno-strict-aliasing -L./../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lmpfr -lgmp -L/usr/local/lib gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin' Making all in tests gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' gmake all-am gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' Making all in examples gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/examples' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/examples' Making all in packaging/macosx gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/packaging/macosx' gmake[3]: Nothing to be done for 'all'. gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/packaging/macosx' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13' gmake[3]: Nothing to be done for 'all-am'. gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13' gmake[1]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> viennarna-2.4.13 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> viennarna-2.4.13 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> viennarna-2.4.13 depends on package: perl5>=5.28.r1<5.29 - found ===> viennarna-2.4.13 depends on executable: indexinfo - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for viennarna-2.4.13 ===> Generating temporary packing list gmake[1]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13' Making install in src gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' Making install in ViennaRNA gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA' Making install in static gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake install-am gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake[6]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake[6]: Nothing to be done for 'install-exec-am'. gmake[6]: Nothing to be done for 'install-data-am'. gmake[6]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA/static' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA' gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/lib' /usr/local/bin/bash ../../libtool --mode=install /usr/bin/install -c libRNA.la '/construction/biology/viennarna/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libRNA.lai /construction/biology/viennarna/stage/usr/local/lib/libRNA.la libtool: install: /usr/bin/install -c .libs/libRNA.a /construction/biology/viennarna/stage/usr/local/lib/libRNA.a libtool: install: chmod 644 /construction/biology/viennarna/stage/usr/local/lib/libRNA.a libtool: install: ranlib /construction/biology/viennarna/stage/usr/local/lib/libRNA.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA' install -m 0644 vrna_config.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA' install -m 0644 pair_mat.h RNAstruct.h dist_vars.h mfe.h mfe_window.h fold.h part_func.h part_func_window.h stringdist.h edit_cost.h fold_vars.h profiledist.h treedist.h inverse.h subopt.h cofold.h duplex.h alifold.h part_func_co.h concentrations.h ProfileAln.h LPfold.h Lfold.h part_func_up.h ribo.h findpath.h data_structures.h char_stream.h stream_output.h fold_compound.h MEA.h mm.h loop_energies.h exterior_loops.h hairpin_loops.h interior_loops.h multibranch_loops.h 2Dfold.h 2Dpfold.h PKplex.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA' install -m 0644 ali_plex.h plex.h snofold.h snoop.h move_set.h gquad.h constraints.h eval.h perturbation_fold.h centroid.h utils.h structure_utils.h string_utils.h aln_util.h model.h dp_matrices.h PS_dot.h plot_structure.h plot_aln.h plot_utils.h plot_layouts.h naview.h boltzmann_sampling.h equilibrium_probs.h constraints_ligand.h constraints_SHAPE.h constraints_hard.h constraints_soft.h alphabet.h sequence.h grammar.h structured_domains.h unstructured_domains.h file_utils.h file_formats.h file_formats_msa.h energy_par.h energy_const.h params.h read_epars.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA' install -m 0644 convert_epars.h commands.h units.h combinatorics.h neighbor.h walk.h svm_utils.h ../libsvm-3.23/svm.h ../json/json.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/constraints' install -m 0644 constraints/basic.h constraints/ligand.h constraints/SHAPE.h constraints/hard.h constraints/soft.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/constraints' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/datastructures' install -m 0644 datastructures/basic.h datastructures/lists.h datastructures/char_stream.h datastructures/stream_output.h datastructures/hash_tables.h datastructures/heap.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/datastructures' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/io' install -m 0644 io/utils.h io/file_formats.h io/file_formats_msa.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/io' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/landscape' install -m 0644 landscape/paths.h landscape/findpath.h landscape/neighbor.h landscape/walk.h landscape/move.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/landscape' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/loops' install -m 0644 loops/all.h loops/external.h loops/hairpin.h loops/internal.h loops/multibranch.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/loops' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/params' install -m 0644 params/default.h params/constants.h params/basic.h params/io.h params/convert.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/params' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/plotting' install -m 0644 plotting/alignments.h plotting/layouts.h plotting/probabilities.h plotting/structures.h plotting/utils.h plotting/naview.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/plotting' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/plotting/RNApuzzler' install -m 0644 plotting/RNApuzzler/RNApuzzler.h plotting/RNApuzzler/RNAturtle.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/plotting/RNApuzzler' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/search' install -m 0644 search/BoyerMoore.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/search' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/utils' install -m 0644 utils/basic.h utils/strings.h utils/structures.h utils/alignments.h utils/higher_order_functions.h utils/cpu.h utils/svm.h '/construction/biology/viennarna/stage/usr/local/include/ViennaRNA/utils' gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/ViennaRNA' Making install in bin gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/bin' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/bin' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/bin' /usr/local/bin/bash ../../libtool --mode=install install -s -m 555 RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex RNALalifold RNA2Dfold RNAparconv RNAPKplex RNAplex RNAsnoop RNApvmin '/construction/biology/viennarna/stage/usr/local/bin' libtool: install: install -m 555 -s RNAfold /construction/biology/viennarna/stage/usr/local/bin/RNAfold libtool: install: install -m 555 -s RNAeval /construction/biology/viennarna/stage/usr/local/bin/RNAeval libtool: install: install -m 555 -s RNAheat /construction/biology/viennarna/stage/usr/local/bin/RNAheat libtool: install: install -m 555 -s RNApdist /construction/biology/viennarna/stage/usr/local/bin/RNApdist libtool: install: install -m 555 -s RNAdistance /construction/biology/viennarna/stage/usr/local/bin/RNAdistance libtool: install: install -m 555 -s RNAinverse /construction/biology/viennarna/stage/usr/local/bin/RNAinverse libtool: install: install -m 555 -s RNAplot /construction/biology/viennarna/stage/usr/local/bin/RNAplot libtool: install: install -m 555 -s RNAsubopt /construction/biology/viennarna/stage/usr/local/bin/RNAsubopt libtool: install: install -m 555 -s RNALfold /construction/biology/viennarna/stage/usr/local/bin/RNALfold libtool: install: install -m 555 -s RNAcofold /construction/biology/viennarna/stage/usr/local/bin/RNAcofold libtool: install: install -m 555 -s RNApaln /construction/biology/viennarna/stage/usr/local/bin/RNApaln libtool: install: install -m 555 -s RNAduplex /construction/biology/viennarna/stage/usr/local/bin/RNAduplex libtool: install: install -m 555 -s RNAalifold /construction/biology/viennarna/stage/usr/local/bin/RNAalifold libtool: install: install -m 555 -s RNAplfold /construction/biology/viennarna/stage/usr/local/bin/RNAplfold libtool: install: install -m 555 -s RNAup /construction/biology/viennarna/stage/usr/local/bin/RNAup libtool: install: install -m 555 -s RNAaliduplex /construction/biology/viennarna/stage/usr/local/bin/RNAaliduplex libtool: install: install -m 555 -s RNALalifold /construction/biology/viennarna/stage/usr/local/bin/RNALalifold libtool: install: install -m 555 -s RNA2Dfold /construction/biology/viennarna/stage/usr/local/bin/RNA2Dfold libtool: install: install -m 555 -s RNAparconv /construction/biology/viennarna/stage/usr/local/bin/RNAparconv libtool: install: install -m 555 -s RNAPKplex /construction/biology/viennarna/stage/usr/local/bin/RNAPKplex libtool: install: install -m 555 -s RNAplex /construction/biology/viennarna/stage/usr/local/bin/RNAplex libtool: install: install -m 555 -s RNAsnoop /construction/biology/viennarna/stage/usr/local/bin/RNAsnoop libtool: install: install -m 555 -s RNApvmin /construction/biology/viennarna/stage/usr/local/bin/RNApvmin gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/bin' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/bin' Making install in Utils gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Utils' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Utils' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/bin' /usr/local/bin/bash ../../libtool --mode=install install -s -m 555 b2ct popt ct2db '/construction/biology/viennarna/stage/usr/local/bin' libtool: install: install -m 555 -s b2ct /construction/biology/viennarna/stage/usr/local/bin/b2ct libtool: install: install -m 555 -s popt /construction/biology/viennarna/stage/usr/local/bin/popt libtool: install: install -m 555 -s ct2db /construction/biology/viennarna/stage/usr/local/bin/ct2db /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/ViennaRNA/bin' install -m 555 b2mt.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl coloraln.pl refold.pl switch.pl RNAdesign.pl '/construction/biology/viennarna/stage/usr/local/share/ViennaRNA/bin' gmake install-data-hook gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Utils' for i in b2mt.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl coloraln.pl refold.pl switch.pl RNAdesign.pl; \ do \ /usr/local/bin/perl -npi -e 's|^#!\S+|#!'/usr/local/bin/perl'|' /construction/biology/viennarna/stage/usr/local/share/ViennaRNA/bin/$i ; \ done gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Utils' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Utils' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Utils' Making install in Cluster gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Cluster' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Cluster' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/bin' /usr/local/bin/bash ../../libtool --mode=install install -s -m 555 AnalyseDists AnalyseSeqs '/construction/biology/viennarna/stage/usr/local/bin' libtool: install: install -m 555 -s AnalyseDists /construction/biology/viennarna/stage/usr/local/bin/AnalyseDists libtool: install: install -m 555 -s AnalyseSeqs /construction/biology/viennarna/stage/usr/local/bin/AnalyseSeqs /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/man/man1' install -m 0644 AnalyseDists.1 AnalyseSeqs.1 '/construction/biology/viennarna/stage/usr/local/man/man1' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Cluster' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Cluster' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src' Making install in man gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/man' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/man' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/info' install -m 0644 ./RNAlib.info '/construction/biology/viennarna/stage/usr/local/share/info' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/man/man1' install -m 0644 RNA2Dfold.1 RNAaliduplex.1 RNAalifold.1 RNAcofold.1 RNAduplex.1 RNAeval.1 RNAfold.1 RNAheat.1 RNAinverse.1 RNALalifold.1 RNALfold.1 RNApaln.1 RNAparconv.1 RNAplfold.1 RNAplot.1 RNApvmin.1 RNAsubopt.1 RNAup.1 RNAPKplex.1 RNAsnoop.1 RNAplex.1 RNAdistance.1 RNApdist.1 ct2db.1 '/construction/biology/viennarna/stage/usr/local/man/man1' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/man' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/man' Making install in misc gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/misc' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/misc' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/ViennaRNA' install -m 0644 rna_turner1999.par rna_turner2004.par rna_andronescu2007.par dna_mathews1999.par dna_mathews2004.par rna_langdon2018.par 2Dlandscape_mfe.gri 2Dlandscape_pf.gri '/construction/biology/viennarna/stage/usr/local/share/ViennaRNA' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/misc' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/misc' Making install in doc gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/doc' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/doc' gmake[3]: Nothing to be done for 'install-exec-am'. for dir in "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/html" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA" "/construction/biology/viennarna/stage/usr/local/share/ViennaRNA"; do \ test -z "$dir" || /bin/mkdir -p "$dir"; \ done test -d ./html || ln -s ./html ./html { for i in ./html/*; do cp -r "$i" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/html/"; done } { for i in "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/html"/*; do test -f "$i" && chmod 644 "$i"; done } chmod 755 "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/html" { for i in "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/html"/search/*; do test -f "$i" && chmod 644 "$i"; done } chmod 755 "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/html"/search { test ! -h ./html || rm -f ./html; } test -f ./RNAlib-2.4.13.pdf || ln -s ./RNAlib-2.4.13.pdf ./RNAlib-2.4.13.pdf install -m 0644 ./RNAlib-2.4.13.pdf /construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA { test ! -h ./RNAlib-2.4.13.pdf || rm -f ./RNAlib-2.4.13.pdf; } /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/ViennaRNA' install -m 0644 viennarna.bib DoxygenLayout.xml '/construction/biology/viennarna/stage/usr/local/share/ViennaRNA' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/doc' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/doc' Making install in RNA-Tutorial gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/RNA-Tutorial' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/RNA-Tutorial' gmake[3]: Nothing to be done for 'install-exec-am'. for dir in "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/html" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/alifoldz" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/programs" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/qrna" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/herpes" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/herpes/x" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/human" "/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/human/x"; do \ test -z "$dir" || /bin/mkdir -p "$dir"; \ done test -f ./RNA-tutorial-2.4.13.pdf || ln -s ./RNA-tutorial-2.4.13.pdf ./RNA-tutorial-2.4.13.pdf install -m 0644 ./RNA-tutorial-2.4.13.pdf /construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA { test ! -h ./RNA-tutorial-2.4.13.pdf || rm -f ./RNA-tutorial-2.4.13.pdf; } /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/alifoldz' install -m 0644 ./Data/alifoldz/miRNA.aln ./Data/alifoldz/unknown.aln '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/alifoldz' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial' install -m 0644 ./Data/5S.seq ./Data/duplex.seq ./Data/FOO.seq ./Data/four.seq ./Data/RNaseP.seq ./Data/RybB.seq ./Data/t.seq ./Data/dot.emacs ./Data/RNaseP.aln ./Data/RNaseP.dnd '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/programs' install -m 0644 ./Data/programs/alifoldz_adopted.tar.gz '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/programs' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/qrna' install -m 0644 ./Data/qrna/coding.fa ./Data/qrna/tRNA.fa '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/qrna' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz' install -m 0644 ./Data/rnaz/IRE.aln ./Data/rnaz/snoRNA.aln ./Data/rnaz/tRNA.aln ./Data/rnaz/unknown.aln ./Data/rnaz/miRNA.maf ./Data/rnaz/tRNA.maf '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/herpes' install -m 0644 ./Data/rnaz/herpes/annotation.bed ./Data/rnaz/herpes/NC_004367 ./Data/rnaz/herpes/NC_006146 ./Data/rnaz/herpes/NC_007605 '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/herpes' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/herpes/x' install -m 0644 ./Data/rnaz/herpes/x/annotation.bed ./Data/rnaz/herpes/x/NC_006146.NC_004367.orig.maf ./Data/rnaz/herpes/x/NC_006146.NC_004367.sing.maf ./Data/rnaz/herpes/x/NC_007605.NC_004367.orig.maf ./Data/rnaz/herpes/x/NC_007605.NC_004367.sing.maf ./Data/rnaz/herpes/x/NC_007605.NC_006146.orig.maf ./Data/rnaz/herpes/x/NC_007605.NC_006146.sing.maf ./Data/rnaz/herpes/x/final.maf ./Data/rnaz/herpes/x/random.maf ./Data/rnaz/herpes/x/raw-tba.maf ./Data/rnaz/herpes/x/windows.maf ./Data/rnaz/herpes/x/windows_random.maf ./Data/rnaz/herpes/x/results.dat ./Data/rnaz/herpes/x/results_annotated.dat ./Data/rnaz/herpes/x/results_random.dat ./Data/rnaz/herpes/x/rnaz.out ./Data/rnaz/herpes/x/rnaz_random.out '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/herpes/x' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/human' install -m 0644 ./Data/rnaz/human/annotation.bed '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/human' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/human/x' install -m 0644 ./Data/rnaz/human/x/annotation.bed ./Data/rnaz/human/x/prediction.bed ./Data/rnaz/human/x/region.maf ./Data/rnaz/human/x/windows.maf ./Data/rnaz/human/x/results.dat ./Data/rnaz/human/x/results_annotated.dat ./Data/rnaz/human/x/rnaz.out '/construction/biology/viennarna/stage/usr/local/share/doc/ViennaRNA/tutorial/rnaz/human/x' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/RNA-Tutorial' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/RNA-Tutorial' Making install in interfaces gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/interfaces' Making install in src/Kinfold gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' Making install in Example gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold/Example' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold/Example' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold/Example' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold/Example' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/bin' install -s -m 555 Kinfold '/construction/biology/viennarna/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/man/man1' install -m 0644 Kinfold.1 '/construction/biology/viennarna/stage/usr/local/man/man1' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinfold' Making install in src/RNAforester gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' Making install in g2-0.72 gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/g2-0.72' Makefile:101: warning: overriding recipe for target 'libg2.so' Makefile:98: warning: ignoring old recipe for target 'libg2.so' test -d /construction/biology/viennarna/stage//usr/local/lib || mkdir -p /construction/biology/viennarna/stage//usr/local/lib test -d /construction/biology/viennarna/stage//usr/local/include || mkdir -p /construction/biology/viennarna/stage//usr/local/include install -m 0644 libg2.a /construction/biology/viennarna/stage//usr/local/lib for IFILE in ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./src/GD/g2_gd.h; do \ install -m 0644 $IFILE /construction/biology/viennarna/stage//usr/local/include; \ done gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/g2-0.72' Making install in src gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' gmake install-am gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' gmake[5]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/bin' install -s -m 555 RNAforester '/construction/biology/viennarna/stage/usr/local/bin' gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/src' Making install in man gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/man' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/man' gmake[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/man/man1' install -m 0644 RNAforester.1 '/construction/biology/viennarna/stage/usr/local/man/man1' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/man' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester/man' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAforester' Making install in src/Kinwalker gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' Making install in man gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker/man' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker/man' gmake[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/man/man1' install -m 0644 kinwalker.1 '/construction/biology/viennarna/stage/usr/local/man/man1' gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker/man' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker/man' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/bin' install -s -m 555 kinwalker '/construction/biology/viennarna/stage/usr/local/bin' gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/Kinwalker' Making install in src/RNAlocmin gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/bin' install -s -m 555 RNAlocmin '/construction/biology/viennarna/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/man/man1' install -m 0644 RNAlocmin.1 '/construction/biology/viennarna/stage/usr/local/man/man1' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/src/RNAlocmin' Making install in tests gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' gmake install-am gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' gmake[4]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/tests' Making install in examples gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/examples' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/examples' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/examples/ViennaRNA' install -m 0644 callback_subopt.c example1.c example_old.c fold_compound_md.c fold_compound_mfe.c helloworld_mfe.c helloworld_mfe_comparative.c helloworld_probabilities.c soft_constraints_up.c '/construction/biology/viennarna/stage/usr/local/share/examples/ViennaRNA' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/examples/ViennaRNA/data' install -m 0644 files/alignment_clustal.aln files/alignment_fasta.fa files/alignment_stockholm.stk files/alignment_maf.maf '/construction/biology/viennarna/stage/usr/local/share/examples/ViennaRNA/data' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/examples/ViennaRNA/perl5' install -m 0644 Perl5/helloworld_mfe.pl Perl5/helloworld_mfe_comparative.pl Perl5/helloworld_nondefault.pl Perl5/maximum_matching.pl Perl5/oo_example1.pl '/construction/biology/viennarna/stage/usr/local/share/examples/ViennaRNA/perl5' /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/share/examples/ViennaRNA/python' install -m 0644 Python/boltzmann_sampling.py Python/helloworld_mfe_comparative.py Python/helloworld_mfe.py Python/helloworld_nondefault.py Python/maximum_matching.py Python/oo_example1.py Python/subopt.py '/construction/biology/viennarna/stage/usr/local/share/examples/ViennaRNA/python' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/examples' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/examples' Making install in packaging/macosx gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/packaging/macosx' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13/packaging/macosx' 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/viennarna/ViennaRNA-2.4.13/packaging/macosx' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13/packaging/macosx' gmake[2]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13' gmake[3]: Entering directory '/construction/biology/viennarna/ViennaRNA-2.4.13' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/construction/biology/viennarna/stage/usr/local/lib/pkgconfig' install -m 0644 RNAlib2.pc '/construction/biology/viennarna/stage/usr/local/lib/pkgconfig' gmake[3]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13' gmake[2]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13' gmake[1]: Leaving directory '/construction/biology/viennarna/ViennaRNA-2.4.13' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for viennarna-2.4.13 file sizes/checksums [2264]: .......... done packing files [2264]: .......... done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Wednesday, 24 JUL 2019 at 17:44:57 UTC Duration: 00:05:34