------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.2.txz Installing /packages/All/gmake-4.3_2.txz Installing /packages/All/m4-1.4.18_1,1.txz Installing /packages/All/autoconf-wrapper-20131203.txz Installing /packages/All/perl5-5.30.3.txz ===== Message from perl5-5.30.3: -- 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. Installing /packages/All/autoconf-2.69_3.txz Installing /packages/All/automake-1.16.2.txz Installing /packages/All/libtool-2.4.6_1.txz Installing /packages/All/libnghttp2-1.41.0.txz Installing /packages/All/ca_root_nss-3.53.txz ===== Message from ca_root_nss-3.53: -- 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. 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 Installing /packages/All/openssl-1.1.1g,1.txz Installing /packages/All/curl-7.70.0_1.txz SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by io_lib-1.14.10 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by io_lib-1.14.10 for building => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by io_lib-1.14.10 for building ===> Extracting for io_lib-1.14.10 ===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by io_lib-1.14.10 for building => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz. Extracted Memory Use: 12.92M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for io_lib-1.14.10 ===> Applying ports patches for io_lib-1.14.10 from /xports/biology/iolib/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> io_lib-1.14.10 depends on package: gmake>=4.3 - found ===> io_lib-1.14.10 depends on package: autoconf>=2.69 - found ===> io_lib-1.14.10 depends on package: automake>=1.16.1 - found ===> io_lib-1.14.10 depends on executable: libtoolize - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- ===> io_lib-1.14.10 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> io_lib-1.14.10 depends on package: gmake>=4.3 - found ===> io_lib-1.14.10 depends on package: autoconf>=2.69 - found ===> io_lib-1.14.10 depends on package: automake>=1.16.1 - found ===> io_lib-1.14.10 depends on executable: libtoolize - found ===> io_lib-1.14.10 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so) ===> Configuring for io_lib-1.14.10 aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in' libtoolize: putting auxiliary files in '.'. libtoolize: copying file './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' 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:65: installing './compile' configure.in:67: installing './config.guess' configure.in:67: installing './config.sub' configure.in:5: installing './install-sh' configure.in:5: installing './missing' io_lib/Makefile.am:152: 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:59: 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-dragonfly5.9 checking host system type... x86_64-portbld-dragonfly5.9 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-dragonfly5.9 file names to x86_64-portbld-dragonfly5.9 format... func_convert_file_noop checking how to convert x86_64-portbld-dragonfly5.9 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... dragonfly5.9 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... 7.70.0 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 for bsc_compress in -lbsc... no 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 malloc.h usability... no checking malloc.h presence... no checking for malloc.h... 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 SUCCEEDED 00:00:19 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for io_lib-1.14.10 gmake[2]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' gmake all-recursive gmake[3]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' Making all in io_lib gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/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 libtool: 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 translate.c -fPIC -DPIC -o .libs/libstaden_read_la-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-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-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c Read.c -fPIC -DPIC -o .libs/libstaden_read_la-Read.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-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-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c seqIOABI.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOABI.o libtool: 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 seqIOALF.c -fPIC -DPIC -o .libs/libstaden_read_la-seqIOALF.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-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c fpoint.c -fPIC -DPIC -o .libs/libstaden_read_la-fpoint.o libtool: 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 Read.c -o libstaden_read_la-Read.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-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c fpoint.c -o libstaden_read_la-fpoint.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-fpoint.Tpo .deps/libstaden_read_la-fpoint.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-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 mv -f .deps/libstaden_read_la-Read.Tpo .deps/libstaden_read_la-Read.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-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-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -fPIC -DPIC -o .libs/libstaden_read_la-ztr.o libtool: 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 translate.c -o libstaden_read_la-translate.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-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c scf_extras.c -o libstaden_read_la-scf_extras.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-expFileIO.lo -MD -MP -MF .deps/libstaden_read_la-expFileIO.Tpo -c expFileIO.c -fPIC -DPIC -o .libs/libstaden_read_la-expFileIO.o libtool: 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 seqIOALF.c -o libstaden_read_la-seqIOALF.o >/dev/null 2>&1 libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. 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-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-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c -o libstaden_read_la-crc32.lo `test -f 'crc32.c' || echo './'`crc32.c mv -f .deps/libstaden_read_la-cram_index.Tpo .deps/libstaden_read_la-cram_index.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-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 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-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 mv -f .deps/libstaden_read_la-crc32.Tpo .deps/libstaden_read_la-crc32.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 /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 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 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 mv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.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-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.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_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 mv -f .deps/libstaden_read_la-binning.Tpo .deps/libstaden_read_la-binning.Plo 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 /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 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 mv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.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-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c -o libstaden_read_la-tokenise_name3.lo `test -f 'tokenise_name3.c' || echo './'`tokenise_name3.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c tokenise_name3.c -fPIC -DPIC -o .libs/libstaden_read_la-tokenise_name3.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 /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-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c -o libstaden_read_la-fqzcomp_qual.lo `test -f 'fqzcomp_qual.c' || echo './'`fqzcomp_qual.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c fqzcomp_qual.c -fPIC -DPIC -o .libs/libstaden_read_la-fqzcomp_qual.o 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 .deps/libstaden_read_la-cram_bambam.Tpo .deps/libstaden_read_la-cram_bambam.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_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 mv -f .deps/libstaden_read_la-bgzip.Tpo .deps/libstaden_read_la-bgzip.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -o libstaden_read_la-rANS_static4x16pr.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-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c fqzcomp_qual.c -o libstaden_read_la-fqzcomp_qual.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_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -o libstaden_read_la-cram_encode.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-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c tokenise_name3.c -o libstaden_read_la-tokenise_name3.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_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-bam.Tpo .deps/libstaden_read_la-bam.Plo mv -f .deps/libstaden_read_la-rANS_static4x16pr.Tpo .deps/libstaden_read_la-rANS_static4x16pr.Plo mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo mv -f .deps/libstaden_read_la-fqzcomp_qual.Tpo .deps/libstaden_read_la-fqzcomp_qual.Plo In function 'full_path', inlined from 'cram_write_SAM_hdr' at cram_io.c:4506:3: cram_io.c:4448:6: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ cram_io.c:4440:2: warning: 'strncpy' specified bound 1024 equals destination size [-Wstringop-truncation] strncpy(out, in, PATH_MAX); ^~~~~~~~~~~~~~~~~~~~~~~~~~ mv -f .deps/libstaden_read_la-tokenise_name3.Tpo .deps/libstaden_read_la-tokenise_name3.Plo cram_io.c: In function 'cram_open': cram_io.c:5016:2: warning: 'strncpy' specified bound 20 equals destination size [-Wstringop-truncation] strncpy(def.file_id, filename, 20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cram_io.c: In function 'cram_openw_by_callbacks': cram_io.c:5246:6: warning: 'strncpy' specified bound 20 equals destination size [-Wstringop-truncation] strncpy(def.file_id, filename, 20); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -pipe -O2 -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.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_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -version-info 13:0:0 -lpthread -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-rANS_static4x16pr.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 libstaden_read_la-tokenise_name3.lo libstaden_read_la-fqzcomp_qual.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-rANS_static4x16pr.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 .libs/libstaden_read_la-tokenise_name3.o .libs/libstaden_read_la-fqzcomp_qual.o -lpthread -lz -L/usr/local/lib -lcurl -lm -llzma -lbz2 -O2 -Wl,-soname -Wl,libstaden-read.so.13 -o .libs/libstaden-read.so.13.0.0 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.13" && ln -s "libstaden-read.so.13.0.0" "libstaden-read.so.13") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.13.0.0" "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-rANS_static4x16pr.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 libstaden_read_la-tokenise_name3.o libstaden_read_la-fqzcomp_qual.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-1-14-10/io_lib' Making all in progs gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/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 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/bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 mv -f .deps/scram_test.Tpo .deps/scram_test.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 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 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/makeSCF makeSCF.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib mv -f .deps/srf_info.Tpo .deps/srf_info.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o index_tar index_tar.o -lm -llzma -lbz2 mv -f .deps/cram_size.Tpo .deps/cram_size.Po mv -f .deps/srf2fastq.Tpo .deps/srf2fastq.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o scf_info scf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/extract_seq extract_seq.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 -lpthread -o scf_update scf_update.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/extract_qual extract_qual.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lpthread -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib mv -f .deps/scram_pileup.Tpo .deps/scram_pileup.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o get_comment get_comment.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o index_tar index_tar.o -lpthread -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/scf_dump scf_dump.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 -lpthread -o hash_list hash_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/scf_info scf_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/get_comment get_comment.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 -lpthread -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o append_sff append_sff.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/scf_update scf_update.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 -lpthread -o ztr_dump ztr_dump.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/hash_sff hash_sff.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/append_sff append_sff.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_extract hash_extract.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/trace_dump trace_dump.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 -lpthread -o srf_dump_all srf_dump_all.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o srf_index_hash srf_index_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o srf_extract_linear srf_extract_linear.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o srf_extract_hash srf_extract_hash.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/extract_fastq extract_fastq.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_tar hash_tar.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_list hash_list.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 -lpthread -o srf2fastq srf2fastq.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/srf_extract_linear 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_index_hash srf_index_hash.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/ztr_dump ztr_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/srf_extract_hash srf_extract_hash.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 -lpthread -o srf_info srf_info.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/srf_dump_all srf_dump_all.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 -lpthread -o srf_list srf_list.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 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 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o cram_index cram_index.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -pipe -O2 -fno-strict-aliasing -o .libs/srf2fastq srf2fastq.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 -lpthread -o scramble scramble.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 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 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -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 -lpthread -o scram_test scram_test.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 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/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 /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o cram_size cram_size.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 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/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/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 mv -f .deps/cram_filter.Tpo .deps/cram_filter.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -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/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/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/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_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 mv -f .deps/cram_dump.Tpo .deps/cram_dump.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -pipe -O2 -fno-strict-aliasing -lpthread -lpthread -o cram_dump cram_dump.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 gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/progs' Making all in tests gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/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 -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-1-14-10/tests' gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' gmake[4]: Nothing to be done for 'all-am'. gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' gmake[3]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' gmake[2]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' SUCCEEDED 00:00:28 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for io_lib-1.14.10 ===> Generating temporary packing list gmake[2]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' if test -z 'strip'; then \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-10/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-10/install-sh -c -s" INSTALL_STRIP_FLAG=-s \ install; \ else \ gmake INSTALL_PROGRAM="/bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-10/install-sh -c -s" \ install_sh_PROGRAM="/bin/sh /construction/biology/iolib/io_lib-io_lib-1-14-10/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-1-14-10' Making install in io_lib gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/io_lib' gmake[5]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/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.13.0.0 /construction/biology/iolib/stage/usr/local/lib/libstaden-read.so.13.0.0 libtool: install: strip --strip-unneeded /construction/biology/iolib/stage/usr/local/lib/libstaden-read.so.13.0.0 libtool: install: (cd /construction/biology/iolib/stage/usr/local/lib && { ln -s -f libstaden-read.so.13.0.0 libstaden-read.so.13 || { rm -f libstaden-read.so.13 && ln -s libstaden-read.so.13.0.0 libstaden-read.so.13; }; }) libtool: install: (cd /construction/biology/iolib/stage/usr/local/lib && { ln -s -f libstaden-read.so.13.0.0 libstaden-read.so || { rm -f libstaden-read.so && ln -s libstaden-read.so.13.0.0 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-1-14-10/io_lib' gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/io_lib' Making install in progs gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/progs' gmake[5]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/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-1-14-10/progs' gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/progs' Making install in tests gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/tests' gmake[5]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/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-1-14-10/tests' gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10/tests' gmake[4]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' gmake[5]: Entering directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' /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-1-14-10' gmake[4]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' gmake[3]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' gmake[2]: Leaving directory '/construction/biology/iolib/io_lib-io_lib-1-14-10' ====> Compressing man pages (compress-man) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks SUCCEEDED 00:00:05 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for io_lib-1.14.10 file sizes/checksums [115]: 0% file sizes/checksums [115]: 86% file sizes/checksums [115]: 100% packing files [115]: 0% packing files [115]: 86% packing files [115]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:03 TOTAL TIME 00:01:04