------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/indexinfo-0.3.1.txz Installing /packages/All/gettext-runtime-0.20.1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/gmake-4.2.1_3.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor Installing /packages/All/perl5-5.30.1.txz pkg: Cannot runscript POST-INSTALL:Bad file descriptor ===== Message from perl5-5.30.1: -- 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. SUCCEEDED 00:00:03 ------------------------------------------------------------------------------- -- Phase: check-sanity ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch ------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bwa-0.7.17 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: checksum ------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bwa-0.7.17 for building => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract ------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by bwa-0.7.17 for building ===> Extracting for bwa-0.7.17 => SHA256 Checksum OK for lh3-bwa-v0.7.17_GH0.tar.gz. Extracted Memory Use: 0.98M SUCCEEDED 00:00:01 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for bwa-0.7.17 ===> Applying ports patches for bwa-0.7.17 ===> Applying dragonfly patches for bwa-0.7.17 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on executable: gmake - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on executable: gmake - found ===> Configuring for bwa-0.7.17 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for bwa-0.7.17 gmake[1]: Entering directory '/construction/biology/bwa/bwa-0.7.17' cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS utils.c -o utils.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kthread.c -o kthread.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kstring.c -o kstring.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS ksw.c -o ksw.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt.c -o bwt.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bntseq.c -o bntseq.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwa.c -o bwa.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem.c -o bwamem.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_pair.c -o bwamem_pair.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwamem_extra.c -o bwamem_extra.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS malloc_wrap.c -o malloc_wrap.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.c -o QSufSort.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_gen.c -o bwt_gen.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rope.c -o rope.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS rle.c -o rle.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS is.c -o is.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtindex.c -o bwtindex.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.c -o bwashm.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwase.c -o bwase.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwaseqio.c -o bwaseqio.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtgap.c -o bwtgap.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtaln.c -o bwtaln.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bamlite.c -o bamlite.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwape.c -o bwape.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS kopen.c -o kopen.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS pemerge.c -o pemerge.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS maxk.c -o maxk.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_core.c -o bwtsw2_core.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_main.c -o bwtsw2_main.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_aux.c -o bwtsw2_aux.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwt_lite.c -o bwt_lite.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_chain.c -o bwtsw2_chain.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS fastmap.c -o fastmap.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwtsw2_pair.c -o bwtsw2_pair.o cc -c -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS main.c -o main.o ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o /usr/libexec/binutils227/elf/ar: `u' modifier ignored since `D' is the default (see `U') cc -pipe -msse2 -O2 -fno-strict-aliasing -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread gmake[1]: Leaving directory '/construction/biology/bwa/bwa-0.7.17' SUCCEEDED 00:00:07 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> bwa-0.7.17 depends on package: perl5>=5.30.r1<5.31 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for bwa-0.7.17 ===> bwa-0.7.17 depends on package: perl5>=5.30.r1<5.31 - found ===> Generating temporary packing list install -s -m 555 /construction/biology/bwa/bwa-0.7.17/bwa /construction/biology/bwa/stage/usr/local/bin install -m 555 /construction/biology/bwa/bwa-0.7.17/*.pl /construction/biology/bwa/stage/usr/local/bin install -m 444 /construction/biology/bwa/bwa-0.7.17/*.1 /construction/biology/bwa/stage/usr/local/man/man1 ====> 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 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for bwa-0.7.17 file sizes/checksums [4]: 0% file sizes/checksums [4]: 100% packing files [4]: 0% packing files [4]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:12