=> Building biology/iolib Started : Thursday, 30 AUG 2018 at 09:33:25 UTC Platform: 5.3-DEVELOPMENT DragonFly 5.3-DEVELOPMENT #140: Wed Aug 29 22:06:30 PDT 2018 root@test.backplane.com:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.3-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.3-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- MAKE=gmake XDG_DATA_HOME=/construction/biology/iolib XDG_CONFIG_HOME=/construction/biology/iolib HOME=/construction/biology/iolib TMPDIR="/tmp" PATH=/construction/biology/iolib/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- XDG_DATA_HOME=/construction/biology/iolib XDG_CONFIG_HOME=/construction/biology/iolib HOME=/construction/biology/iolib TMPDIR="/tmp" PATH=/construction/biology/iolib/.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=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -lpthread" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" 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/iolib/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- PORTDOCS="" PORTEXAMPLES="" OSREL=5.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PROFILE="@comment " DOCSDIR="share/doc/io_lib" EXAMPLESDIR="share/examples/io_lib" DATADIR="share/io_lib" WWWDIR="www/io_lib" ETCDIR="etc/io_lib" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/io_lib DOCSDIR=/usr/local/share/doc/io_lib EXAMPLESDIR=/usr/local/share/examples/io_lib WWWDIR=/usr/local/www/io_lib ETCDIR=/usr/local/etc/io_lib -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=LiveSystem 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=12 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=32 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500316 OSVERSION=9999999 OSREL=5.3 _OSRELEASE=5.3-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> io_lib-1.14.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz Installing pkg-1.10.5_1... Extracting pkg-1.10.5_1: .......... done ===> io_lib-1.14.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of io_lib-1.14.9 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by io_lib-1.14.9 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by io_lib-1.14.9 for building => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by io_lib-1.14.9 for building ===> Extracting for io_lib-1.14.9 ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by io_lib-1.14.9 for building => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-9_GH0.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for io_lib-1.14.9 ===> Applying ports patches for io_lib-1.14.9 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> io_lib-1.14.9 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_1.txz Installing autoconf-2.69_1... `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: .......... done `-- Installing indexinfo-0.3.1... `-- Extracting indexinfo-0.3.1: .... done `-- Installing m4-1.4.18,1... `-- Extracting m4-1.4.18,1: .......... done `-- Installing perl5-5.26.2... `-- Extracting perl5-5.26.2: .......... done Extracting autoconf-2.69_1: .......... done Message from perl5-5.26.2: 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. ===> io_lib-1.14.9 depends on package: autoconf>=2.69 - found ===> Returning to build of io_lib-1.14.9 ===> io_lib-1.14.9 depends on package: automake>=1.16.1 - not found ===> Installing existing package /packages/All/automake-1.16.1.txz Installing automake-1.16.1... Extracting automake-1.16.1: .......... done ===> io_lib-1.14.9 depends on package: automake>=1.16.1 - found ===> Returning to build of io_lib-1.14.9 ===> io_lib-1.14.9 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.4.6.txz Installing libtool-2.4.6... Extracting libtool-2.4.6: .......... done ===> io_lib-1.14.9 depends on executable: libtoolize - found ===> Returning to build of io_lib-1.14.9 ===> io_lib-1.14.9 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz Installing gmake-4.2.1_2... `-- Installing gettext-runtime-0.19.8.1_1... `-- Extracting gettext-runtime-0.19.8.1_1: .......... done Extracting gmake-4.2.1_2: .......... done ===> io_lib-1.14.9 depends on executable: gmake - found ===> Returning to build of io_lib-1.14.9 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- ===> io_lib-1.14.9 depends on shared library: libcurl.so - not found ===> Installing existing package /packages/All/curl-7.60.0.txz Installing curl-7.60.0... `-- Installing ca_root_nss-3.38... `-- Extracting ca_root_nss-3.38: ........ done `-- Installing krb5-1.16.1_5... | `-- Installing libressl-2.7.4... | `-- Extracting libressl-2.7.4: .......... done | `-- Installing pkgconf-1.4.2,1... | `-- Extracting pkgconf-1.4.2,1: .......... done | `-- Installing readline-7.0.3_1... | | `-- Installing ncurses-6.0.0s20171223_1... | | `-- Extracting ncurses-6.0.0s20171223_1: .......... done | `-- Extracting readline-7.0.3_1: .......... done `-- Extracting krb5-1.16.1_5: .......... done `-- Installing libnghttp2-1.32.0... `-- Extracting libnghttp2-1.32.0: .......... done Extracting curl-7.60.0: .......... done Message from ca_root_nss-3.38: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> io_lib-1.14.9 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Returning to build of io_lib-1.14.9 -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for io_lib-1.14.9 aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' libtoolize: putting auxiliary files in '.'. libtoolize: copying file './ltmain.sh' libtoolize: Consider adding 'AC_CONFIG_MACRO_DIRS([m4])' to configure.in, libtoolize: and rerunning libtoolize and aclocal. libtoolize: Consider adding '-I m4' to ACLOCAL_AMFLAGS in Makefile.am. aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' configure.in:64: installing './compile' configure.in:66: installing './config.guess' configure.in:66: installing './config.sub' configure.in:4: installing './install-sh' configure.in:4: installing './missing' io_lib/Makefile.am:143: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') automake: warning: autoconf input should be named 'configure.ac', not 'configure.in' io_lib/Makefile.am: installing './depcomp' progs/Makefile.am:150: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') tests/Makefile.am:60: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS') parallel-tests: installing './test-driver' configure: loading site script /xports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking whether gmake supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... 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-dragonfly5.3 checking host system type... x86_64-portbld-dragonfly5.3 checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep 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 whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking how to convert x86_64-portbld-dragonfly5.3 file names to x86_64-portbld-dragonfly5.3 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.3 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 ar... ar 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 how to run the C preprocessor... cpp 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 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... dragonfly5.3 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... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for gawk... (cached) /usr/bin/awk checking for curl-config... /usr/local/bin/curl-config checking for the version of libcurl... 7.60.0 checking whether libcurl just needs -lcurl... no checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking for zlib.h... (cached) yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether byte ordering is bigendian... no checking for ANSI C header files... (cached) yes checking for sys/wait.h that is POSIX.1 compatible... (cached) yes checking for fcntl.h... (cached) yes checking for limits.h... (cached) yes checking for unistd.h... (cached) yes checking for malloc.h... (cached) no checking for zlib.h... (cached) yes checking stdio_ext.h usability... no checking stdio_ext.h presence... no checking for stdio_ext.h... no checking whether byte ordering is bigendian... (cached) no checking size of short... 2 checking size of int... 4 checking size of long... 8 checking for inline... inline checking for mode_t... (cached) yes checking for fileno... (cached) yes checking for fstat... (cached) yes checking for mallopt... no checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for _LARGEFILE_SOURCE value needed for large files... no checking for stdlib.h... (cached) yes checking for unistd.h... (cached) yes checking for sys/param.h... (cached) yes checking for getpagesize... (cached) yes checking for working mmap... yes checking for library containing pthread_join... none required checking for library containing cos... -lm checking for strdup... (cached) yes checking for fsync... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating io_lib/Makefile config.status: creating progs/Makefile config.status: creating tests/Makefile config.status: creating io_lib-config config.status: creating io_lib/os.h config.status: creating io_lib_config.h config.status: executing depfiles commands config.status: executing libtool commands -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for io_lib-1.14.9 gmake[2]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' gmake all-recursive gmake[3]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' Making all in io_lib gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/io_lib' /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c -o libstaden_read_la-Read.lo `test -f 'Read.c' || echo './'`Read.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c -o libstaden_read_la-scf_extras.lo `test -f 'scf_extras.c' || echo './'`scf_extras.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c -o libstaden_read_la-translate.lo `test -f 'translate.c' || echo './'`translate.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c -o libstaden_read_la-compression.lo `test -f 'compression.c' || echo './'`compression.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c -o libstaden_read_la-ztr.lo `test -f 'ztr.c' || echo './'`ztr.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c -o libstaden_read_la-ztr_translate.lo `test -f 'ztr_translate.c' || echo './'`ztr_translate.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c -o libstaden_read_la-deflate_interlaced.lo `test -f 'deflate_interlaced.c' || echo './'`deflate_interlaced.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c -o libstaden_read_la-fpoint.lo `test -f 'fpoint.c' || echo './'`fpoint.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c -o libstaden_read_la-seqIOABI.lo `test -f 'seqIOABI.c' || echo './'`seqIOABI.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c -o libstaden_read_la-seqIOALF.lo `test -f 'seqIOALF.c' || echo './'`seqIOALF.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-expFileIO.lo -MD -MP -MF .deps/libstaden_read_la-expFileIO.Tpo -c -o libstaden_read_la-expFileIO.lo `test -f 'expFileIO.c' || echo './'`expFileIO.c /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-seqIOPlain.lo -MD -MP -MF .deps/libstaden_read_la-seqIOPlain.Tpo -c -o libstaden_read_la-seqIOPlain.lo `test -f 'seqIOPlain.c' || echo './'`seqIOPlain.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -fPIC -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c scf_extras.c -fPIC -DPIC -o .libs/libstaden_read_la-scf_extras.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c ztr_translate.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr_translate.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c deflate_interlaced.c -fPIC -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c fpoint.c -fPIC -DPIC -o 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../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -fPIC -DPIC -o .libs/libstaden_read_la-md5.o mv -f .deps/libstaden_read_la-string_alloc.Tpo .deps/libstaden_read_la-string_alloc.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -o libstaden_read_la-md5.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o mv -f .deps/libstaden_read_la-dstring.Tpo .deps/libstaden_read_la-dstring.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c -o libstaden_read_la-binning.lo `test -f 'binning.c' || echo './'`binning.c mv -f .deps/libstaden_read_la-crc32.Tpo .deps/libstaden_read_la-crc32.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -o libstaden_read_la-thread_pool.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -fPIC -DPIC -o .libs/libstaden_read_la-binning.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-binning.Tpo .deps/libstaden_read_la-binning.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c mv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-thread_pool.Tpo .deps/libstaden_read_la-thread_pool.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 mv -f 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.deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -version-info 12:0:1 -lpthread -o libstaden-read.la -rpath /usr/local/lib libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo libstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-rANS_static.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo -lz -L/usr/local/lib -lcurl -lm -llzma -lbz2 libtool: link: cc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstaden_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-rANS_static.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o -lpthread -lz -L/usr/local/lib -lcurl -lm -llzma -lbz2 -O2 -Wl,-soname -Wl,libstaden-read.so.11 -o .libs/libstaden-read.so.11.1.0 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.11" && ln -s "libstaden-read.so.11.1.0" "libstaden-read.so.11") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.11.1.0" "libstaden-read.so") libtool: link: ar cru .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-rANS_static.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/io_lib' Making all in progs gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/progs' cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT makeSCF.o -MD -MP -MF .deps/makeSCF.Tpo -c -o makeSCF.o makeSCF.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT extract_seq.o -MD -MP -MF .deps/extract_seq.Tpo -c -o extract_seq.o extract_seq.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT extract_qual.o -MD -MP -MF .deps/extract_qual.Tpo -c -o extract_qual.o extract_qual.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT extract_fastq.o -MD -MP -MF .deps/extract_fastq.Tpo -c -o extract_fastq.o extract_fastq.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT index_tar.o -MD -MP -MF .deps/index_tar.Tpo -c -o index_tar.o index_tar.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT scf_dump.o -MD -MP -MF .deps/scf_dump.Tpo -c -o scf_dump.o scf_dump.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT scf_info.o -MD -MP -MF .deps/scf_info.Tpo -c -o scf_info.o scf_info.c cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT scf_update.o -MD -MP -MF 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srf_extract_linear.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/srf_info srf_info.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/srf_list srf_list.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/srf2fasta srf2fasta.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -o cram_filter cram_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/cram_dump cram_dump.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/cram_index cram_index.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/scramble scramble.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/scram_merge scram_merge.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/srf_filter srf_filter.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/hash_exp hash_exp.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/scram_pileup scram_pileup.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/scram_flagstat scram_flagstat.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/scram_test scram_test.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/cram_size cram_size.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/cram_filter cram_filter.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/progs' Making all in tests gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/tests' cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -pipe -O2 -fno-strict-aliasing -MT cram_io_test.o -MD -MP -MF .deps/cram_io_test.Tpo -c -o cram_io_test.o cram_io_test.c mv -f .deps/cram_io_test.Tpo .deps/cram_io_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -o cram_io_test cram_io_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/cram_io_test cram_io_test.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/tests' gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' gmake[3]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' gmake[2]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for io_lib-1.14.9 ===> Generating temporary packing list gmake[2]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' if test -z 'strip'; then \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ "INSTALL_PROGRAM_ENV=STRIPPROG='strip'" install; \ fi gmake[3]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' Making install in io_lib gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/io_lib' gmake[5]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/io_lib' /bin/mkdir -p '/construction/biology/iolib/stage/usr/local/lib' /bin/sh ../libtool --mode=install /usr/bin/install -c -s libstaden-read.la '/construction/biology/iolib/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libstaden-read.so.11.1.0 /construction/biology/iolib/stage/usr/local/lib/libstaden-read.so.11.1.0 libtool: install: strip --strip-unneeded /construction/biology/iolib/stage/usr/local/lib/libstaden-read.so.11.1.0 libtool: install: (cd /construction/biology/iolib/stage/usr/local/lib && { ln -s -f libstaden-read.so.11.1.0 libstaden-read.so.11 || { rm -f libstaden-read.so.11 && ln -s libstaden-read.so.11.1.0 libstaden-read.so.11; }; }) libtool: install: (cd /construction/biology/iolib/stage/usr/local/lib && { ln -s -f libstaden-read.so.11.1.0 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.11.1.0 libstaden-read.so; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /construction/biology/iolib/stage/usr/local/lib/libstaden-read.la libtool: install: /usr/bin/install -c .libs/libstaden-read.a /construction/biology/iolib/stage/usr/local/lib/libstaden-read.a libtool: install: strip --strip-debug /construction/biology/iolib/stage/usr/local/lib/libstaden-read.a libtool: install: chmod 644 /construction/biology/iolib/stage/usr/local/lib/libstaden-read.a libtool: install: ranlib /construction/biology/iolib/stage/usr/local/lib/libstaden-read.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/io_lib' gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/io_lib' Making install in progs gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/progs' gmake[5]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/progs' /bin/mkdir -p '/construction/biology/iolib/stage/usr/local/bin' STRIPPROG='strip' /bin/sh ../libtool --mode=install /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s convert_trace makeSCF extract_seq extract_qual extract_fastq index_tar scf_dump scf_info scf_update get_comment hash_tar hash_extract hash_list trace_dump hash_sff append_sff ztr_dump srf_dump_all srf_index_hash srf_extract_linear srf_extract_hash srf2fastq srf2fasta srf_filter srf_info srf_list hash_exp cram_dump cram_index scramble scram_merge scram_pileup scram_flagstat scram_test cram_size cram_filter '/construction/biology/iolib/stage/usr/local/bin' libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/convert_trace /construction/biology/iolib/stage/usr/local/bin/convert_trace libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/makeSCF /construction/biology/iolib/stage/usr/local/bin/makeSCF libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/extract_seq /construction/biology/iolib/stage/usr/local/bin/extract_seq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/extract_qual /construction/biology/iolib/stage/usr/local/bin/extract_qual libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/extract_fastq /construction/biology/iolib/stage/usr/local/bin/extract_fastq libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s index_tar /construction/biology/iolib/stage/usr/local/bin/index_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/scf_dump /construction/biology/iolib/stage/usr/local/bin/scf_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/scf_info /construction/biology/iolib/stage/usr/local/bin/scf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/scf_update /construction/biology/iolib/stage/usr/local/bin/scf_update libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/get_comment /construction/biology/iolib/stage/usr/local/bin/get_comment libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/hash_tar /construction/biology/iolib/stage/usr/local/bin/hash_tar libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/hash_extract /construction/biology/iolib/stage/usr/local/bin/hash_extract libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/hash_list /construction/biology/iolib/stage/usr/local/bin/hash_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/trace_dump /construction/biology/iolib/stage/usr/local/bin/trace_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/hash_sff /construction/biology/iolib/stage/usr/local/bin/hash_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/append_sff /construction/biology/iolib/stage/usr/local/bin/append_sff libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/ztr_dump /construction/biology/iolib/stage/usr/local/bin/ztr_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf_dump_all /construction/biology/iolib/stage/usr/local/bin/srf_dump_all libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf_index_hash /construction/biology/iolib/stage/usr/local/bin/srf_index_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf_extract_linear /construction/biology/iolib/stage/usr/local/bin/srf_extract_linear libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf_extract_hash /construction/biology/iolib/stage/usr/local/bin/srf_extract_hash libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf2fastq /construction/biology/iolib/stage/usr/local/bin/srf2fastq libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf2fasta /construction/biology/iolib/stage/usr/local/bin/srf2fasta libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf_filter /construction/biology/iolib/stage/usr/local/bin/srf_filter libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf_info /construction/biology/iolib/stage/usr/local/bin/srf_info libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/srf_list /construction/biology/iolib/stage/usr/local/bin/srf_list libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/hash_exp /construction/biology/iolib/stage/usr/local/bin/hash_exp libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/cram_dump /construction/biology/iolib/stage/usr/local/bin/cram_dump libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/cram_index /construction/biology/iolib/stage/usr/local/bin/cram_index libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/scramble /construction/biology/iolib/stage/usr/local/bin/scramble libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/scram_merge /construction/biology/iolib/stage/usr/local/bin/scram_merge libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/scram_pileup /construction/biology/iolib/stage/usr/local/bin/scram_pileup libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/scram_flagstat /construction/biology/iolib/stage/usr/local/bin/scram_flagstat libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/scram_test /construction/biology/iolib/stage/usr/local/bin/scram_test libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/cram_size /construction/biology/iolib/stage/usr/local/bin/cram_size libtool: warning: '../io_lib/libstaden-read.la' has not been installed in '/usr/local/lib' libtool: install: /bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-9/install-sh -c -s .libs/cram_filter /construction/biology/iolib/stage/usr/local/bin/cram_filter gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/progs' gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/progs' Making install in tests gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/tests' gmake[5]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/tests' gmake[5]: Nothing to be done for 'install-exec-am'. gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/tests' gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9/tests' gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' gmake[5]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' /bin/mkdir -p '/construction/biology/iolib/stage/usr/local/bin' install -m 555 io_lib-config '/construction/biology/iolib/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/iolib/stage/usr/local/man/man1' install -m 0644 man/man1/srf_index_hash.1 man/man1/srf_info.1 man/man1/srf_list.1 man/man1/srf2fasta.1 man/man1/srf2fastq.1 man/man1/scramble.1 '/construction/biology/iolib/stage/usr/local/man/man1' /bin/mkdir -p '/construction/biology/iolib/stage/usr/local/man/man3' install -m 0644 man/man3/read_scf_header.3 man/man3/read_allocate.3 man/man3/ExperimentFile.3 man/man3/write_reading.3 man/man3/write_scf.3 man/man3/read_deallocate.3 man/man3/fwrite_reading.3 man/man3/read2scf.3 man/man3/scf2read.3 man/man3/fwrite_scf.3 man/man3/write_scf_header.3 man/man3/read_reading.3 man/man3/read_scf.3 man/man3/exp2read.3 man/man3/fread_reading.3 man/man3/read2exp.3 man/man3/fread_scf.3 '/construction/biology/iolib/stage/usr/local/man/man3' /bin/mkdir -p '/construction/biology/iolib/stage/usr/local/man/man4' install -m 0644 man/man4/Read.4 '/construction/biology/iolib/stage/usr/local/man/man4' /bin/mkdir -p '/construction/biology/iolib/stage/usr/local/include/io_lib' install -m 0644 io_lib/Read.h io_lib/scf_extras.h io_lib/translate.h io_lib/abi.h io_lib/fpoint.h io_lib/seqIOABI.h io_lib/alf.h io_lib/expFileIO.h io_lib/plain.h io_lib/scf.h io_lib/sff.h io_lib/array.h io_lib/compress.h io_lib/error.h io_lib/mach-io.h io_lib/misc.h io_lib/open_trace_file.h io_lib/tar_format.h io_lib/traceType.h io_lib/xalloc.h io_lib/mFILE.h io_lib/stdio_hack.h io_lib/vlen.h io_lib/hash_table.h io_lib/jenkins_lookup3.h io_lib/os.h io_lib/compression.h io_lib/ztr.h io_lib/deflate_interlaced.h io_lib/srf.h io_lib/pooled_alloc.h io_lib/cram.h io_lib/cram_structs.h io_lib/cram_io.h io_lib/cram_encode.h io_lib/cram_decode.h io_lib/cram_codecs.h io_lib/cram_index.h io_lib/cram_stats.h io_lib/zfio.h '/construction/biology/iolib/stage/usr/local/include/io_lib' install -m 0644 io_lib/scram.h io_lib/bam.h io_lib/sam_header.h io_lib/dstring.h io_lib/string_alloc.h io_lib_config.h io_lib/md5.h io_lib/thread_pool.h io_lib/binning.h io_lib/bgzip.h '/construction/biology/iolib/stage/usr/local/include/io_lib' gmake[5]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' gmake[3]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' gmake[2]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-9' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for io_lib-1.14.9 file sizes/checksums [118]: .. done packing files [118]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 30 AUG 2018 at 09:34:23 UTC Duration: 00:00:57