printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild libstaden-read1-shlibs 2>&1 The package 'libstaden-read1-shlibs' will be built without being installed. Reading build dependency for libstaden-read1-shlibs-1.13.3-1... Reading dependency for libstaden-read1-shlibs-1.13.3-1... Reading dependency for libstaden-read1-dev-1.13.3-1... Reading dependency for staden-io-lib-utils-1.13.3-1... Reading build conflict for libstaden-read1-shlibs-1.13.3-1... The package 'bzip2-dev' will be installed. Reading dependency for bzip2-dev-1.0.6-1... Reading runtime dependency for bzip2-dev-1.0.6-1... The package 'fink-package-precedence' will be installed. Reading dependency for fink-package-precedence-0.18-1... Reading runtime dependency for fink-package-precedence-0.18-1... The package 'libcurl4' will be installed. Reading dependency for libcurl4-7.37.1-1+10.8... Reading runtime dependency for libcurl4-7.37.1-1+10.8... The package 'libcurl4-shlibs' will be installed. Reading dependency for libcurl4-shlibs-7.37.1-1+10.8... Reading runtime dependency for libcurl4-shlibs-7.37.1-1+10.8... The package 'librtmp-shlibs' will be installed. Reading dependency for librtmp-shlibs-2.3-4... Reading runtime dependency for librtmp-shlibs-2.3-4... The package 'libssh2.1-shlibs' will be installed. Reading dependency for libssh2.1-shlibs-1.4.3-1... Reading runtime dependency for libssh2.1-shlibs-1.4.3-1... The package 'openssl100-shlibs' will be installed. Reading dependency for openssl100-shlibs-1.0.1h-1... Reading runtime dependency for openssl100-shlibs-1.0.1h-1... The following package will be rebuilt: libstaden-read1-shlibs The following 7 additional packages will be installed: bzip2-dev fink-package-precedence libcurl4 libcurl4-shlibs librtmp-shlibs libssh2.1-shlibs openssl100-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/io_lib-1.13.3.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 2 1621k 2 43195 0 0 54631 0 0:00:30 --:--:-- 0:00:30 54608 37 1621k 37 606k 0 0 345k 0 0:00:04 0:00:01 0:00:03 345k 41 1621k 41 668k 0 0 231k 0 0:00:06 0:00:02 0:00:04 231k 83 1621k 83 1348k 0 0 356k 0 0:00:04 0:00:03 0:00:01 356k 100 1621k 100 1621k 0 0 371k 0 0:00:04 0:00:04 --:--:-- 371k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/bzip2-dev_1.0.6-1_darwin-x86_64.deb Selecting previously deselected package bzip2-dev. (Reading database ... 4296 files and directories currently installed.) Unpacking bzip2-dev (from .../bzip2-dev_1.0.6-1_darwin-x86_64.deb) ... Setting up bzip2-dev (1.0.6-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/fink-package-precedence_0.18-1_darwin-x86_64.deb Selecting previously deselected package fink-package-precedence. (Reading database ... 4303 files and directories currently installed.) Unpacking fink-package-precedence (from .../fink-package-precedence_0.18-1_darwin-x86_64.deb) ... Setting up fink-package-precedence (0.18-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/base/openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb Selecting previously deselected package openssl100-shlibs. (Reading database ... 4304 files and directories currently installed.) Unpacking openssl100-shlibs (from .../openssl100-shlibs_1.0.1h-1_darwin-x86_64.deb) ... Setting up openssl100-shlibs (1.0.1h-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/net/librtmp-shlibs_2.3-4_darwin-x86_64.deb Selecting previously deselected package librtmp-shlibs. (Reading database ... 4325 files and directories currently installed.) Unpacking librtmp-shlibs (from .../librtmp-shlibs_2.3-4_darwin-x86_64.deb) ... Setting up librtmp-shlibs (2.3-4) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/net/libssh2.1-shlibs_1.4.3-1_darwin-x86_64.deb Selecting previously deselected package libssh2.1-shlibs. (Reading database ... 4330 files and directories currently installed.) Unpacking libssh2.1-shlibs (from .../libssh2.1-shlibs_1.4.3-1_darwin-x86_64.deb) ... Setting up libssh2.1-shlibs (1.4.3-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/libcurl4_7.37.1-1+10.8_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/net/libcurl4-shlibs_7.37.1-1+10.8_darwin-x86_64.deb Selecting previously deselected package libcurl4. (Reading database ... 4338 files and directories currently installed.) Unpacking libcurl4 (from .../libcurl4_7.37.1-1+10.8_darwin-x86_64.deb) ... Selecting previously deselected package libcurl4-shlibs. Unpacking libcurl4-shlibs (from .../libcurl4-shlibs_7.37.1-1+10.8_darwin-x86_64.deb) ... Setting up libcurl4-shlibs (7.37.1-1+10.8) ... Setting up libcurl4 (7.37.1-1+10.8) ... Clearing dependency_libs of .la files being installed Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-libstaden-read1-shlibs-1.13.3-1 /sw/build.build dpkg-deb: building package `fink-buildlock-libstaden-read1-shlibs-1.13.3-1' in `/sw/build.build/fink-buildlock-libstaden-read1-shlibs-1.13.3-1_2014.08.02-12.15.56_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-libstaden-read1-shlibs-1.13.3-1_2014.08.02-12.15.56_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-libstaden-read1-shlibs-1.13.3-1. (Reading database ... 4691 files and directories currently installed.) Unpacking fink-buildlock-libstaden-read1-shlibs-1.13.3-1 (from .../fink-buildlock-libstaden-read1-shlibs-1.13.3-1_2014.08.02-12.15.56_darwin-x86_64.deb) ... Setting up fink-buildlock-libstaden-read1-shlibs-1.13.3-1 (2014.08.02-12.15.56) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.eeLem env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/io_lib-1.13.3.tar.gz io_lib-1.13.3/ io_lib-1.13.3/docs/ io_lib-1.13.3/docs/ZTR_format io_lib-1.13.3/docs/Hash_File_Format io_lib-1.13.3/io_lib/ io_lib-1.13.3/io_lib/Read.h io_lib-1.13.3/io_lib/scf_extras.h io_lib-1.13.3/io_lib/translate.h io_lib-1.13.3/io_lib/abi.h io_lib-1.13.3/io_lib/fpoint.h io_lib-1.13.3/io_lib/seqIOABI.h io_lib-1.13.3/io_lib/alf.h io_lib-1.13.3/io_lib/expFileIO.h io_lib-1.13.3/io_lib/plain.h io_lib-1.13.3/io_lib/scf.h io_lib-1.13.3/io_lib/sff.h io_lib-1.13.3/io_lib/array.h io_lib-1.13.3/io_lib/compress.h io_lib-1.13.3/io_lib/error.h io_lib-1.13.3/io_lib/mach-io.h io_lib-1.13.3/io_lib/misc.h io_lib-1.13.3/io_lib/open_trace_file.h io_lib-1.13.3/io_lib/tar_format.h io_lib-1.13.3/io_lib/traceType.h io_lib-1.13.3/io_lib/xalloc.h io_lib-1.13.3/io_lib/mFILE.h io_lib-1.13.3/io_lib/stdio_hack.h io_lib-1.13.3/io_lib/vlen.h io_lib-1.13.3/io_lib/hash_table.h io_lib-1.13.3/io_lib/jenkins_lookup3.h io_lib-1.13.3/io_lib/os.h io_lib-1.13.3/io_lib/compression.h io_lib-1.13.3/io_lib/ztr.h io_lib-1.13.3/io_lib/deflate_interlaced.h io_lib-1.13.3/io_lib/srf.h io_lib-1.13.3/io_lib/pooled_alloc.h io_lib-1.13.3/io_lib/cram.h io_lib-1.13.3/io_lib/cram_structs.h io_lib-1.13.3/io_lib/cram_io.h io_lib-1.13.3/io_lib/cram_encode.h io_lib-1.13.3/io_lib/cram_decode.h io_lib-1.13.3/io_lib/cram_codecs.h io_lib-1.13.3/io_lib/cram_index.h io_lib-1.13.3/io_lib/cram_stats.h io_lib-1.13.3/io_lib/zfio.h io_lib-1.13.3/io_lib/scram.h io_lib-1.13.3/io_lib/bam.h io_lib-1.13.3/io_lib/sam_header.h io_lib-1.13.3/io_lib/dstring.h io_lib-1.13.3/io_lib/string_alloc.h io_lib-1.13.3/io_lib/md5.h io_lib-1.13.3/io_lib/thread_pool.h io_lib-1.13.3/io_lib/os.h.in io_lib-1.13.3/io_lib/Makefile.am io_lib-1.13.3/io_lib/Makefile.in io_lib-1.13.3/io_lib/Read.c io_lib-1.13.3/io_lib/scf_extras.c io_lib-1.13.3/io_lib/translate.c io_lib-1.13.3/io_lib/compression.c io_lib-1.13.3/io_lib/ztr.c io_lib-1.13.3/io_lib/ztr_translate.c io_lib-1.13.3/io_lib/deflate_interlaced.c io_lib-1.13.3/io_lib/fpoint.c io_lib-1.13.3/io_lib/seqIOABI.c io_lib-1.13.3/io_lib/seqIOALF.c io_lib-1.13.3/io_lib/expFileIO.c io_lib-1.13.3/io_lib/seqIOPlain.c io_lib-1.13.3/io_lib/misc_scf.c io_lib-1.13.3/io_lib/read_scf.c io_lib-1.13.3/io_lib/write_scf.c io_lib-1.13.3/io_lib/sff.c io_lib-1.13.3/io_lib/srf.c io_lib-1.13.3/io_lib/array.c io_lib-1.13.3/io_lib/compress.c io_lib-1.13.3/io_lib/error.c io_lib-1.13.3/io_lib/files.c io_lib-1.13.3/io_lib/find.c io_lib-1.13.3/io_lib/mach-io.c io_lib-1.13.3/io_lib/open_trace_file.c io_lib-1.13.3/io_lib/read_alloc.c io_lib-1.13.3/io_lib/strings.c io_lib-1.13.3/io_lib/traceType.c io_lib-1.13.3/io_lib/xalloc.c io_lib-1.13.3/io_lib/vlen.c io_lib-1.13.3/io_lib/hash_table.c io_lib-1.13.3/io_lib/jenkins_lookup3.c io_lib-1.13.3/io_lib/mFILE.c io_lib-1.13.3/io_lib/pooled_alloc.c io_lib-1.13.3/io_lib/bam.c io_lib-1.13.3/io_lib/sam_header.c io_lib-1.13.3/io_lib/cram_codecs.c io_lib-1.13.3/io_lib/cram_encode.c io_lib-1.13.3/io_lib/cram_decode.c io_lib-1.13.3/io_lib/cram_stats.c io_lib-1.13.3/io_lib/cram_io.c io_lib-1.13.3/io_lib/cram_index.c io_lib-1.13.3/io_lib/zfio.c io_lib-1.13.3/io_lib/dstring.c io_lib-1.13.3/io_lib/string_alloc.c io_lib-1.13.3/io_lib/md5.c io_lib-1.13.3/io_lib/scram.c io_lib-1.13.3/io_lib/thread_pool.c io_lib-1.13.3/README io_lib-1.13.3/acinclude.m4 io_lib-1.13.3/configure.in io_lib-1.13.3/aclocal.m4 io_lib-1.13.3/io_lib_config.h io_lib-1.13.3/Makefile.am io_lib-1.13.3/Makefile.in io_lib-1.13.3/io_lib-config.in io_lib-1.13.3/io_lib_config.h.in io_lib-1.13.3/configure io_lib-1.13.3/ChangeLog io_lib-1.13.3/compile io_lib-1.13.3/config.guess io_lib-1.13.3/config.sub io_lib-1.13.3/depcomp io_lib-1.13.3/install-sh io_lib-1.13.3/ltmain.sh io_lib-1.13.3/missing io_lib-1.13.3/COPYRIGHT io_lib-1.13.3/CHANGES io_lib-1.13.3/man/ io_lib-1.13.3/man/man1/ io_lib-1.13.3/man/man1/srf2fasta.1 io_lib-1.13.3/man/man1/srf2fastq.1 io_lib-1.13.3/man/man1/srf_index_hash.1 io_lib-1.13.3/man/man1/srf_info.1 io_lib-1.13.3/man/man1/srf_list.1 io_lib-1.13.3/man/man1/scramble.1 io_lib-1.13.3/man/man3/ io_lib-1.13.3/man/man3/ExperimentFile.3 io_lib-1.13.3/man/man3/exp2read.3 io_lib-1.13.3/man/man3/fread_reading.3 io_lib-1.13.3/man/man3/fread_scf.3 io_lib-1.13.3/man/man3/fwrite_reading.3 io_lib-1.13.3/man/man3/fwrite_scf.3 io_lib-1.13.3/man/man3/read2exp.3 io_lib-1.13.3/man/man3/read2scf.3 io_lib-1.13.3/man/man3/read_allocate.3 io_lib-1.13.3/man/man3/read_deallocate.3 io_lib-1.13.3/man/man3/read_reading.3 io_lib-1.13.3/man/man3/read_scf.3 io_lib-1.13.3/man/man3/read_scf_header.3 io_lib-1.13.3/man/man3/scf2read.3 io_lib-1.13.3/man/man3/write_reading.3 io_lib-1.13.3/man/man3/write_scf.3 io_lib-1.13.3/man/man3/write_scf_header.3 io_lib-1.13.3/man/man4/ io_lib-1.13.3/man/man4/Read.4 io_lib-1.13.3/options.mk io_lib-1.13.3/bootstrap io_lib-1.13.3/progs/ io_lib-1.13.3/progs/Makefile.am io_lib-1.13.3/progs/Makefile.in io_lib-1.13.3/progs/append_sff.c io_lib-1.13.3/progs/convert_trace.c io_lib-1.13.3/progs/cram_dump.c io_lib-1.13.3/progs/cram_index.c io_lib-1.13.3/progs/extract_fastq.c io_lib-1.13.3/progs/extract_qual.c io_lib-1.13.3/progs/extract_seq.c io_lib-1.13.3/progs/get_comment.c io_lib-1.13.3/progs/hash_exp.c io_lib-1.13.3/progs/hash_extract.c io_lib-1.13.3/progs/hash_list.c io_lib-1.13.3/progs/hash_sff.c io_lib-1.13.3/progs/hash_tar.c io_lib-1.13.3/progs/index_tar.c io_lib-1.13.3/progs/makeSCF.c io_lib-1.13.3/progs/scf_dump.c io_lib-1.13.3/progs/scf_info.c io_lib-1.13.3/progs/scf_update.c io_lib-1.13.3/progs/scram_flagstat.c io_lib-1.13.3/progs/scram_merge.c io_lib-1.13.3/progs/scram_pileup.c io_lib-1.13.3/progs/scram_pileup.h io_lib-1.13.3/progs/scramble.c io_lib-1.13.3/progs/srf2fasta.c io_lib-1.13.3/progs/srf2fastq.c io_lib-1.13.3/progs/srf_dump_all.c io_lib-1.13.3/progs/srf_extract_hash.c io_lib-1.13.3/progs/srf_extract_linear.c io_lib-1.13.3/progs/srf_filter.c io_lib-1.13.3/progs/srf_index_hash.c io_lib-1.13.3/progs/srf_info.c io_lib-1.13.3/progs/srf_list.c io_lib-1.13.3/progs/trace_dump.c io_lib-1.13.3/progs/ztr_dump.c io_lib-1.13.3/tests/ io_lib-1.13.3/tests/Makefile.am io_lib-1.13.3/tests/Makefile.in io_lib-1.13.3/tests/srf2fasta.test io_lib-1.13.3/tests/srf2fastq.test io_lib-1.13.3/tests/srf_info.test io_lib-1.13.3/tests/srf_filter.test io_lib-1.13.3/tests/srf_index.test io_lib-1.13.3/tests/scram.test io_lib-1.13.3/tests/scram_mt.test io_lib-1.13.3/tests/data/ io_lib-1.13.3/tests/data/both.run/ io_lib-1.13.3/tests/data/both.run/4_ILLUMINA_GA_MATRIX_FWD.txt io_lib-1.13.3/tests/data/both.run/4_ILLUMINA_GA_BUSTARD_PARAMS.txt io_lib-1.13.3/tests/data/both.run/4_ILLUMINA_GA_CHASTITY.txt io_lib-1.13.3/tests/data/both.run/4_ILLUMINA_GA_FIRECREST_PARAMS.txt io_lib-1.13.3/tests/data/both.run/4_ILLUMINA_GA_PHASING_FWD.txt io_lib-1.13.3/tests/data/both.run/4_PROGRAM_ID.txt io_lib-1.13.3/tests/data/both.run/s_4_0133_int.txt io_lib-1.13.3/tests/data/both.run/s_4_0133_nse.txt io_lib-1.13.3/tests/data/both.run/s_4_0133_prb.txt io_lib-1.13.3/tests/data/both.run/s_4_0133_seq.txt io_lib-1.13.3/tests/data/both.run/s_4_0133_sig2.txt io_lib-1.13.3/tests/data/both.run/s_4_0134_int.txt io_lib-1.13.3/tests/data/both.run/s_4_0134_nse.txt io_lib-1.13.3/tests/data/both.run/s_4_0134_prb.txt io_lib-1.13.3/tests/data/both.run/s_4_0134_seq.txt io_lib-1.13.3/tests/data/both.run/s_4_0134_sig2.txt io_lib-1.13.3/tests/data/test_run_4_134_369_182.srf io_lib-1.13.3/tests/data/both.info io_lib-1.13.3/tests/data/both.srf io_lib-1.13.3/tests/data/proc.info io_lib-1.13.3/tests/data/proc.srf io_lib-1.13.3/tests/data/proc.srf.indexed io_lib-1.13.3/tests/data/raw.info io_lib-1.13.3/tests/data/raw.srf io_lib-1.13.3/tests/data/slx-C.fasta io_lib-1.13.3/tests/data/slx-C.fastq io_lib-1.13.3/tests/data/slx.fasta io_lib-1.13.3/tests/data/slx.fastq io_lib-1.13.3/tests/data/traces.srf io_lib-1.13.3/tests/data/xx#blank.sam io_lib-1.13.3/tests/data/xx#minimal.sam io_lib-1.13.3/tests/data/xx#large_aux2.sam io_lib-1.13.3/tests/data/c1#pad1.sam io_lib-1.13.3/tests/data/c1#pad2.sam io_lib-1.13.3/tests/data/c1#clip.sam io_lib-1.13.3/tests/data/c1#pad3.sam io_lib-1.13.3/tests/data/ce#5b.sam io_lib-1.13.3/tests/data/ce#tag_padded.sam io_lib-1.13.3/tests/data/ce#tag_depadded.sam io_lib-1.13.3/tests/data/xx#triplet.sam io_lib-1.13.3/tests/data/ce#1.sam io_lib-1.13.3/tests/data/ce#2.sam io_lib-1.13.3/tests/data/ce#unmap1.sam io_lib-1.13.3/tests/data/ce#unmap2.sam io_lib-1.13.3/tests/data/ce#large_seq.sam io_lib-1.13.3/tests/data/xx#pair.sam io_lib-1.13.3/tests/data/aux.fa io_lib-1.13.3/tests/data/c1.fa io_lib-1.13.3/tests/data/ce.fa io_lib-1.13.3/tests/data/xx.fa io_lib-1.13.3/tests/data/aux.fa.fai io_lib-1.13.3/tests/data/c1.fa.fai io_lib-1.13.3/tests/data/ce.fa.fai io_lib-1.13.3/tests/data/xx.fa.fai io_lib-1.13.3/tests/data/aux#aux.sam io_lib-1.13.3/tests/data/ce#5.sam io_lib-1.13.3/tests/data/xx#unsorted.sam io_lib-1.13.3/tests/data/a io_lib-1.13.3/tests/data/c1#pad3.0.g5d io_lib-1.13.3/tests/data/xx#large_aux.sam io_lib-1.13.3/tests/data/ce#unmap.sam io_lib-1.13.3/tests/data/c1#pad3.0.g5x io_lib-1.13.3/tests/data/c1#pad3.0.log io_lib-1.13.3/tests/data/aux#aux.bam io_lib-1.13.3/tests/data/xx#rg.sam io_lib-1.13.3/tests/data/c1#pad2.0.g5d io_lib-1.13.3/tests/data/c1#pad2.0.g5x io_lib-1.13.3/tests/data/c1#pad2.0.log io_lib-1.13.3/tests/data/c1#pad1.0.g5d io_lib-1.13.3/tests/data/c1#pad1.0.g5x io_lib-1.13.3/tests/data/c1#pad1.0.log io_lib-1.13.3/tests/data/c1#bounds.sam io_lib-1.13.3/tests/data/xx#minimal.bam io_lib-1.13.3/tests/data/xx#minimal.bam.bai io_lib-1.13.3/tests/data/a.cram io_lib-1.13.3/tests/data/a.bam io_lib-1.13.3/tests/data/a.bam.bai io_lib-1.13.3/tests/data/core io_lib-1.13.3/tests/compare_sam.pl io_lib-1.13.3/tests/generate_data.pl sudo -u fink-bld [ENV] sh -c /tmp/fink.gYzHm /tmp/fink.oqB2c #!/bin/sh -ev ./configure --prefix=/sw --disable-static --enable-dependency-tracking checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking whether to enable maintainer-specific portions of Makefiles... no checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of gcc... gcc3 checking build system type... x86_64-apple-darwin13.3.0 checking host system type... x86_64-apple-darwin13.3.0 checking how to print strings... printf checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking how to convert x86_64-apple-darwin13.3.0 file names to x86_64-apple-darwin13.3.0 format... func_convert_file_noop checking how to convert x86_64-apple-darwin13.3.0 file names to toolchain format... func_convert_file_noop checking for /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld option to reload object files... -r checking for objdump... no 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... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc object... ok checking for sysroot... no checking for mt... no checking if : is a manifest tool... no checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for -force_load linker flag... yes checking how to run the C preprocessor... gcc -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc supports -fno-rtti -fno-exceptions... yes checking for gcc option to produce PIC... -fno-common -DPIC checking if gcc PIC flag -fno-common -DPIC works... yes checking if gcc static flag -static works... no checking if gcc supports -c -o file.o... yes checking if gcc supports -c -o file.o... (cached) yes checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.3.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gawk... (cached) awk checking for curl-config... /sw/bin/curl-config checking for the version of libcurl... 7.37.1 checking whether libcurl just needs -lcurl... yes checking whether libcurl is usable... yes checking for curl_free... yes checking for inflateEnd in -lz... yes checking zlib.h usability... yes checking zlib.h presence... yes checking for zlib.h... yes checking for library containing gethostbyname... none required checking for library containing socket... none required checking for BZ2_bzBuffToBuffCompress in -lbz2... 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... yes checking fcntl.h usability... yes checking fcntl.h presence... yes checking for fcntl.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking for unistd.h... (cached) yes checking for zlib.h... (cached) yes 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... yes 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 library containing pthread_join... none required checking for library containing cos... none required checking for strdup... yes 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 make -w make: Entering directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3' /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive make[1]: Entering directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3' Making all in io_lib make[2]: Entering directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3/io_lib' /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-scf_extras.lo -MD -MP -MF .deps/libstaden_read_la-scf_extras.Tpo -c scf_extras.c -fno-common -DPIC -o .libs/libstaden_read_la-scf_extras.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-Read.lo -MD -MP -MF .deps/libstaden_read_la-Read.Tpo -c Read.c -fno-common -DPIC -o .libs/libstaden_read_la-Read.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-compression.lo -MD -MP -MF .deps/libstaden_read_la-compression.Tpo -c compression.c -fno-common -DPIC -o .libs/libstaden_read_la-compression.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-translate.lo -MD -MP -MF .deps/libstaden_read_la-translate.Tpo -c translate.c -fno-common -DPIC -o .libs/libstaden_read_la-translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-fpoint.lo -MD -MP -MF .deps/libstaden_read_la-fpoint.Tpo -c fpoint.c -fno-common -DPIC -o .libs/libstaden_read_la-fpoint.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-deflate_interlaced.lo -MD -MP -MF .deps/libstaden_read_la-deflate_interlaced.Tpo -c deflate_interlaced.c -fno-common -DPIC -o .libs/libstaden_read_la-deflate_interlaced.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-ztr_translate.lo -MD -MP -MF .deps/libstaden_read_la-ztr_translate.Tpo -c ztr_translate.c -fno-common -DPIC -o .libs/libstaden_read_la-ztr_translate.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-ztr.lo -MD -MP -MF .deps/libstaden_read_la-ztr.Tpo -c ztr.c -fno-common -DPIC -o .libs/libstaden_read_la-ztr.o mv -f .deps/libstaden_read_la-fpoint.Tpo .deps/libstaden_read_la-fpoint.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 mv -f .deps/libstaden_read_la-Read.Tpo .deps/libstaden_read_la-Read.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-seqIOABI.lo -MD -MP -MF .deps/libstaden_read_la-seqIOABI.Tpo -c seqIOABI.c -fno-common -DPIC -o .libs/libstaden_read_la-seqIOABI.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-seqIOALF.lo -MD -MP -MF .deps/libstaden_read_la-seqIOALF.Tpo -c seqIOALF.c -fno-common -DPIC -o .libs/libstaden_read_la-seqIOALF.o mv -f .deps/libstaden_read_la-scf_extras.Tpo .deps/libstaden_read_la-scf_extras.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-expFileIO.lo -MD -MP -MF .deps/libstaden_read_la-expFileIO.Tpo -c -o 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'./'`write_scf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-misc_scf.lo -MD -MP -MF .deps/libstaden_read_la-misc_scf.Tpo -c misc_scf.c -fno-common -DPIC -o .libs/libstaden_read_la-misc_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-read_scf.lo -MD -MP -MF .deps/libstaden_read_la-read_scf.Tpo -c read_scf.c -fno-common -DPIC -o .libs/libstaden_read_la-read_scf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-write_scf.lo -MD -MP -MF .deps/libstaden_read_la-write_scf.Tpo -c write_scf.c -fno-common -DPIC -o .libs/libstaden_read_la-write_scf.o mv -f .deps/libstaden_read_la-seqIOPlain.Tpo .deps/libstaden_read_la-seqIOPlain.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-sff.lo -MD -MP -MF .deps/libstaden_read_la-sff.Tpo -c -o libstaden_read_la-sff.lo `test -f 'sff.c' || echo './'`sff.c mv -f .deps/libstaden_read_la-misc_scf.Tpo .deps/libstaden_read_la-misc_scf.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-srf.lo -MD -MP -MF .deps/libstaden_read_la-srf.Tpo -c -o libstaden_read_la-srf.lo `test -f 'srf.c' || echo './'`srf.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-sff.lo -MD -MP -MF .deps/libstaden_read_la-sff.Tpo -c sff.c -fno-common -DPIC -o .libs/libstaden_read_la-sff.o mv -f .deps/libstaden_read_la-seqIOABI.Tpo .deps/libstaden_read_la-seqIOABI.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-array.lo -MD -MP -MF .deps/libstaden_read_la-array.Tpo -c -o libstaden_read_la-array.lo `test -f 'array.c' || echo './'`array.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-srf.lo -MD -MP -MF .deps/libstaden_read_la-srf.Tpo -c srf.c -fno-common -DPIC -o .libs/libstaden_read_la-srf.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-array.lo -MD -MP -MF .deps/libstaden_read_la-array.Tpo -c array.c -fno-common -DPIC -o .libs/libstaden_read_la-array.o mv -f .deps/libstaden_read_la-compression.Tpo .deps/libstaden_read_la-compression.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-compress.lo -MD -MP -MF .deps/libstaden_read_la-compress.Tpo -c -o libstaden_read_la-compress.lo `test -f 'compress.c' || echo './'`compress.c mv -f .deps/libstaden_read_la-read_scf.Tpo .deps/libstaden_read_la-read_scf.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g 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--mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -fno-common -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -fno-common -DPIC -o .libs/libstaden_read_la-cram_index.o cram_io.c:683:12: warning: comparison of constant -1 with expression of type 'enum cram_block_method' is always false [-Wtautological-constant-out-of-range-compare] if (-1 == (b->method = getc(fd->fp))) { free(b); return NULL; } ~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cram_io.c:684:12: warning: comparison of constant -1 with expression of type 'enum cram_content_type' is always false [-Wtautological-constant-out-of-range-compare] if (-1 == (b->content_type = getc(fd->fp))) { free(b); return NULL; } ~~ ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ cram_io.c:961:12: warning: enumeration value 'ARITH1' not handled in switch [-Wswitch] switch(m) { ^ mv -f .deps/libstaden_read_la-sam_header.Tpo .deps/libstaden_read_la-sam_header.Plo /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c mv 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-DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c -o libstaden_read_la-md5.lo `test -f 'md5.c' || echo './'`md5.c libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-md5.lo -MD -MP -MF .deps/libstaden_read_la-md5.Tpo -c md5.c -fno-common -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -fno-common -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 gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -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 mv -f .deps/libstaden_read_la-md5.Tpo .deps/libstaden_read_la-md5.Plo libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -I/sw/include -g -O2 -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -fno-common -DPIC -o .libs/libstaden_read_la-thread_pool.o mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo mv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.Plo mv -f .deps/libstaden_read_la-thread_pool.Tpo .deps/libstaden_read_la-thread_pool.Plo mv -f .deps/libstaden_read_la-bam.Tpo .deps/libstaden_read_la-bam.Plo mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo 3 warnings generated. mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -version-info 5:0:4 -L/sw/lib -o libstaden-read.la -rpath /sw/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-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-scram.lo libstaden_read_la-thread_pool.lo -lz -lcurl -lbz2 libtool: link: gcc -dynamiclib -Wl,-undefined -Wl,dynamic_lookup -o .libs/libstaden-read.1.dylib .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-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-scram.o .libs/libstaden_read_la-thread_pool.o -L/sw/lib -lz /sw/lib/libcurl.dylib -lbz2 -O2 -install_name /sw/lib/libstaden-read.1.dylib -compatibility_version 6 -current_version 6.0 -Wl,-single_module libtool: link: (cd ".libs" && rm -f "libstaden-read.dylib" && ln -s "libstaden-read.1.dylib" "libstaden-read.dylib") libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) make[2]: Leaving directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3/io_lib' Making all in progs make[2]: Entering directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3/progs' gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT makeSCF.o -MD -MP -MF .deps/makeSCF.Tpo -c -o makeSCF.o makeSCF.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT extract_seq.o -MD -MP -MF .deps/extract_seq.Tpo -c -o extract_seq.o extract_seq.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT extract_qual.o -MD -MP -MF .deps/extract_qual.Tpo -c -o extract_qual.o extract_qual.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT extract_fastq.o -MD -MP -MF .deps/extract_fastq.Tpo -c -o extract_fastq.o extract_fastq.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT index_tar.o -MD -MP -MF .deps/index_tar.Tpo -c -o index_tar.o index_tar.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT scf_dump.o -MD -MP -MF .deps/scf_dump.Tpo -c -o scf_dump.o scf_dump.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT scf_info.o -MD -MP -MF .deps/scf_info.Tpo -c -o scf_info.o scf_info.c mv -f .deps/scf_info.Tpo .deps/scf_info.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT scf_update.o -MD -MP -MF .deps/scf_update.Tpo -c -o scf_update.o scf_update.c mv -f .deps/index_tar.Tpo .deps/index_tar.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT get_comment.o -MD -MP -MF .deps/get_comment.Tpo -c -o get_comment.o get_comment.c mv -f .deps/scf_dump.Tpo .deps/scf_dump.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT hash_tar.o -MD -MP -MF .deps/hash_tar.Tpo -c -o hash_tar.o hash_tar.c mv -f .deps/extract_fastq.Tpo .deps/extract_fastq.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT hash_extract.o -MD -MP -MF .deps/hash_extract.Tpo -c -o hash_extract.o hash_extract.c mv -f .deps/scf_update.Tpo .deps/scf_update.Po mv -f .deps/extract_seq.Tpo .deps/extract_seq.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT hash_list.o -MD -MP -MF .deps/hash_list.Tpo -c -o hash_list.o hash_list.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT trace_dump.o -MD -MP -MF .deps/trace_dump.Tpo -c -o trace_dump.o trace_dump.c mv -f .deps/extract_qual.Tpo .deps/extract_qual.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT hash_sff.o -MD -MP -MF .deps/hash_sff.Tpo -c -o hash_sff.o hash_sff.c mv -f .deps/get_comment.Tpo .deps/get_comment.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT append_sff.o -MD -MP -MF .deps/append_sff.Tpo -c -o append_sff.o append_sff.c mv -f .deps/hash_extract.Tpo .deps/hash_extract.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT ztr_dump.o -MD -MP -MF .deps/ztr_dump.Tpo -c -o ztr_dump.o ztr_dump.c mv -f .deps/hash_list.Tpo .deps/hash_list.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf_dump_all.o -MD -MP -MF .deps/srf_dump_all.Tpo -c -o srf_dump_all.o srf_dump_all.c mv -f .deps/trace_dump.Tpo .deps/trace_dump.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf_index_hash.o -MD -MP -MF .deps/srf_index_hash.Tpo -c -o srf_index_hash.o srf_index_hash.c mv -f .deps/makeSCF.Tpo .deps/makeSCF.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf_extract_linear.o -MD -MP -MF .deps/srf_extract_linear.Tpo -c -o srf_extract_linear.o srf_extract_linear.c mv -f .deps/hash_tar.Tpo .deps/hash_tar.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf_extract_hash.o -MD -MP -MF .deps/srf_extract_hash.Tpo -c -o srf_extract_hash.o srf_extract_hash.c srf_dump_all.c:121:15: warning: comparison of unsigned expression >= 0 is always true [-Wtautological-compare] while (*i >= 0 && isdigit(name[*i])) { ~~ ^ ~ srf_dump_all.c:126:11: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] if(*i < 0 || last == *i) { ~~ ^ ~ mv -f .deps/append_sff.Tpo .deps/append_sff.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf2fastq.o -MD -MP -MF .deps/srf2fastq.Tpo -c -o srf2fastq.o srf2fastq.c mv -f .deps/srf_index_hash.Tpo .deps/srf_index_hash.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf2fasta.o -MD -MP -MF .deps/srf2fasta.Tpo -c -o srf2fasta.o srf2fasta.c mv -f .deps/hash_sff.Tpo .deps/hash_sff.Po mv -f .deps/ztr_dump.Tpo .deps/ztr_dump.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf_filter.o -MD -MP -MF .deps/srf_filter.Tpo -c -o srf_filter.o srf_filter.c mv -f .deps/srf_extract_linear.Tpo .deps/srf_extract_linear.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf_info.o -MD -MP -MF .deps/srf_info.Tpo -c -o srf_info.o srf_info.c gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT srf_list.o -MD -MP -MF .deps/srf_list.Tpo -c -o srf_list.o srf_list.c mv -f .deps/convert_trace.Tpo .deps/convert_trace.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT hash_exp.o -MD -MP -MF .deps/hash_exp.Tpo -c -o hash_exp.o hash_exp.c mv -f .deps/srf_extract_hash.Tpo .deps/srf_extract_hash.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT cram_dump.o -MD -MP -MF .deps/cram_dump.Tpo -c -o cram_dump.o cram_dump.c mv -f .deps/srf2fasta.Tpo .deps/srf2fasta.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT cram_index.o -MD -MP -MF .deps/cram_index.Tpo -c -o cram_index.o cram_index.c mv -f .deps/srf_list.Tpo .deps/srf_list.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT scramble.o -MD -MP -MF .deps/scramble.Tpo -c -o scramble.o scramble.c mv -f .deps/hash_exp.Tpo .deps/hash_exp.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT scram_merge.o -MD -MP -MF .deps/scram_merge.Tpo -c -o scram_merge.o scram_merge.c mv -f .deps/srf2fastq.Tpo .deps/srf2fastq.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT scram_pileup.o -MD -MP -MF .deps/scram_pileup.Tpo -c -o scram_pileup.o scram_pileup.c mv -f .deps/cram_index.Tpo .deps/cram_index.Po gcc -DHAVE_CONFIG_H -I. -I.. -I.. -I/sw/include -g -O2 -MT scram_flagstat.o -MD -MP -MF .deps/scram_flagstat.Tpo -c -o scram_flagstat.o scram_flagstat.c 2 warnings generated. mv -f .deps/srf_dump_all.Tpo .deps/srf_dump_all.Po /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lbz2 mv -f .deps/scramble.Tpo .deps/scramble.Po mv -f .deps/srf_info.Tpo .deps/srf_info.Po /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o makeSCF makeSCF.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o extract_seq extract_seq.o ../io_lib/libstaden-read.la -lbz2 mv -f .deps/scram_merge.Tpo .deps/scram_merge.Po /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o extract_qual extract_qual.o ../io_lib/libstaden-read.la -lbz2 mv -f .deps/srf_filter.Tpo .deps/srf_filter.Po /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o extract_fastq extract_fastq.o ../io_lib/libstaden-read.la -lbz2 mv -f .deps/scram_flagstat.Tpo .deps/scram_flagstat.Po /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o index_tar index_tar.o -lbz2 mv -f .deps/cram_dump.Tpo .deps/cram_dump.Po /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o scf_dump scf_dump.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/convert_trace convert_trace.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/makeSCF makeSCF.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/extract_seq extract_seq.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 mv -f .deps/scram_pileup.Tpo .deps/scram_pileup.Po libtool: link: gcc -g -O2 -o index_tar index_tar.o -L/sw/lib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o scf_info scf_info.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/extract_qual extract_qual.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o scf_update scf_update.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o get_comment get_comment.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o hash_tar hash_tar.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o hash_extract hash_extract.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/extract_fastq extract_fastq.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o hash_list hash_list.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o trace_dump trace_dump.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/scf_dump scf_dump.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o hash_sff hash_sff.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/scf_info scf_info.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/scf_update scf_update.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/hash_extract hash_extract.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/hash_tar hash_tar.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/get_comment get_comment.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/hash_list hash_list.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o append_sff append_sff.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o ztr_dump ztr_dump.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf_dump_all srf_dump_all.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf_index_hash srf_index_hash.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf_extract_linear srf_extract_linear.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/trace_dump trace_dump.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf_extract_hash srf_extract_hash.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf2fastq srf2fastq.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/hash_sff hash_sff.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf2fasta srf2fasta.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/ztr_dump ztr_dump.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/append_sff append_sff.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/srf_dump_all srf_dump_all.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/srf_index_hash srf_index_hash.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/srf_extract_linear srf_extract_linear.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf_filter srf_filter.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf_info srf_info.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o srf_list srf_list.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o hash_exp hash_exp.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o cram_dump cram_dump.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/srf_extract_hash srf_extract_hash.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/srf2fastq srf2fastq.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o cram_index cram_index.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o scramble scramble.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/srf2fasta srf2fasta.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o scram_merge scram_merge.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/srf_filter srf_filter.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/srf_info srf_info.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/srf_list srf_list.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/hash_exp hash_exp.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/cram_dump cram_dump.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o scram_pileup scram_pileup.o ../io_lib/libstaden-read.la -lbz2 /bin/sh ../libtool --tag=CC --mode=link gcc -g -O2 -L/sw/lib -o scram_flagstat scram_flagstat.o ../io_lib/libstaden-read.la -lbz2 libtool: link: gcc -g -O2 -o .libs/cram_index cram_index.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/scramble scramble.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/scram_merge scram_merge.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/scram_pileup scram_pileup.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 libtool: link: gcc -g -O2 -o .libs/scram_flagstat scram_flagstat.o -L/sw/lib ../io_lib/.libs/libstaden-read.dylib -lz /sw/lib/libcurl.dylib -lbz2 make[2]: Leaving directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3/progs' Making all in tests make[2]: Entering directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3/tests' make[2]: Nothing to be done for `all'. make[2]: Leaving directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3/tests' make[2]: Entering directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3' make[2]: Nothing to be done for `all-am'. make[2]: Leaving directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3' make[1]: Leaving directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3' make: Leaving directory `/sw/build.build/libstaden-read1-shlibs-1.13.3-1/io_lib-1.13.3' fink-package-precedence --prohibit-bdep=libstaden-read1-dev . Scanning /\.Plo,\.Po$/ dependency files... ./io_lib/.deps/libstaden_read_la-array.Plo ./io_lib/.deps/libstaden_read_la-bam.Plo ./io_lib/.deps/libstaden_read_la-compress.Plo ./io_lib/.deps/libstaden_read_la-compression.Plo ./io_lib/.deps/libstaden_read_la-cram_codecs.Plo ./io_lib/.deps/libstaden_read_la-cram_decode.Plo ./io_lib/.deps/libstaden_read_la-cram_encode.Plo ./io_lib/.deps/libstaden_read_la-cram_index.Plo ./io_lib/.deps/libstaden_read_la-cram_io.Plo ./io_lib/.deps/libstaden_read_la-cram_stats.Plo ./io_lib/.deps/libstaden_read_la-deflate_interlaced.Plo ./io_lib/.deps/libstaden_read_la-dstring.Plo ./io_lib/.deps/libstaden_read_la-error.Plo ./io_lib/.deps/libstaden_read_la-expFileIO.Plo ./io_lib/.deps/libstaden_read_la-files.Plo ./io_lib/.deps/libstaden_read_la-find.Plo ./io_lib/.deps/libstaden_read_la-fpoint.Plo ./io_lib/.deps/libstaden_read_la-hash_table.Plo ./io_lib/.deps/libstaden_read_la-jenkins_lookup3.Plo ./io_lib/.deps/libstaden_read_la-mach-io.Plo ./io_lib/.deps/libstaden_read_la-md5.Plo ./io_lib/.deps/libstaden_read_la-mFILE.Plo ./io_lib/.deps/libstaden_read_la-misc_scf.Plo ./io_lib/.deps/libstaden_read_la-open_trace_file.Plo ./io_lib/.deps/libstaden_read_la-pooled_alloc.Plo ./io_lib/.deps/libstaden_read_la-Read.Plo ./io_lib/.deps/libstaden_read_la-read_alloc.Plo ./io_lib/.deps/libstaden_read_la-read_scf.Plo ./io_lib/.deps/libstaden_read_la-sam_header.Plo ./io_lib/.deps/libstaden_read_la-scf_extras.Plo ./io_lib/.deps/libstaden_read_la-scram.Plo ./io_lib/.deps/libstaden_read_la-seqIOABI.Plo ./io_lib/.deps/libstaden_read_la-seqIOALF.Plo ./io_lib/.deps/libstaden_read_la-seqIOPlain.Plo ./io_lib/.deps/libstaden_read_la-sff.Plo ./io_lib/.deps/libstaden_read_la-srf.Plo ./io_lib/.deps/libstaden_read_la-string_alloc.Plo ./io_lib/.deps/libstaden_read_la-strings.Plo ./io_lib/.deps/libstaden_read_la-thread_pool.Plo ./io_lib/.deps/libstaden_read_la-traceType.Plo ./io_lib/.deps/libstaden_read_la-translate.Plo ./io_lib/.deps/libstaden_read_la-vlen.Plo ./io_lib/.deps/libstaden_read_la-write_scf.Plo ./io_lib/.deps/libstaden_read_la-xalloc.Plo ./io_lib/.deps/libstaden_read_la-zfio.Plo ./io_lib/.deps/libstaden_read_la-ztr.Plo ./io_lib/.deps/libstaden_read_la-ztr_translate.Plo ./progs/.deps/append_sff.Po ./progs/.deps/convert_trace.Po ./progs/.deps/cram_dump.Po ./progs/.deps/cram_index.Po ./progs/.deps/extract_fastq.Po ./progs/.deps/extract_qual.Po ./progs/.deps/extract_seq.Po ./progs/.deps/get_comment.Po ./progs/.deps/hash_exp.Po ./progs/.deps/hash_extract.Po ./progs/.deps/hash_list.Po ./progs/.deps/hash_sff.Po ./progs/.deps/hash_tar.Po ./progs/.deps/index_tar.Po ./progs/.deps/makeSCF.Po ./progs/.deps/scf_dump.Po ./progs/.deps/scf_info.Po ./progs/.deps/scf_update.Po ./progs/.deps/scram_flagstat.Po ./progs/.deps/scram_merge.Po ./progs/.deps/scram_pileup.Po ./progs/.deps/scramble.Po ./progs/.deps/srf2fasta.Po ./progs/.deps/srf2fastq.Po ./progs/.deps/srf_dump_all.Po ./progs/.deps/srf_extract_hash.Po ./progs/.deps/srf_extract_linear.Po ./progs/.deps/srf_filter.Po ./progs/.deps/srf_index_hash.Po ./progs/.deps/srf_info.Po ./progs/.deps/srf_list.Po ./progs/.deps/trace_dump.Po ./progs/.deps/ztr_dump.Po Looking for incorrect headers in 80 dependency files... Determining fink providers of 7 headers... 1 - 7 Found use of headers from 2 fink packages: bzip2-dev libcurl4 Scanning binaries for incorrect dyld linking... /bin/rm -rf /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1 /bin/mkdir -p /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw /bin/mkdir -p /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.w4Nsh make install DESTDIR=/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1 Making install in io_lib test -z "/sw/lib" || .././install-sh -c -d "/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/lib" /bin/sh ../libtool --mode=install /usr/bin/install -c libstaden-read.la '/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/lib' libtool: install: /usr/bin/install -c .libs/libstaden-read.1.dylib /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/lib/libstaden-read.1.dylib libtool: install: (cd /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/lib && { ln -s -f libstaden-read.1.dylib libstaden-read.dylib || { rm -f libstaden-read.dylib && ln -s libstaden-read.1.dylib libstaden-read.dylib; }; }) libtool: install: /usr/bin/install -c .libs/libstaden-read.lai /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/lib/libstaden-read.la libtool: install: warning: remember to run `libtool --finish /sw/lib' make[2]: Nothing to be done for `install-data-am'. Making install in progs test -z "/sw/bin" || .././install-sh -c -d "/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c 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 '/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin' libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/convert_trace /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/convert_trace libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/makeSCF /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/makeSCF libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/extract_seq /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/extract_seq libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/extract_qual /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/extract_qual libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/extract_fastq /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/extract_fastq libtool: install: /usr/bin/install -c index_tar /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/index_tar libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/scf_dump /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/scf_dump libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/scf_info /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/scf_info libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/scf_update /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/scf_update libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/get_comment /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/get_comment libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/hash_tar /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/hash_tar libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/hash_extract /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/hash_extract libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/hash_list /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/hash_list libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/trace_dump /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/trace_dump libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/hash_sff /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/hash_sff libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/append_sff /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/append_sff libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/ztr_dump /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/ztr_dump libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf_dump_all /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf_dump_all libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf_index_hash /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf_index_hash libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf_extract_linear /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf_extract_linear libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf_extract_hash /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf_extract_hash libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf2fastq /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf2fastq libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf2fasta /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf2fasta libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf_filter /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf_filter libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf_info /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf_info libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/srf_list /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/srf_list libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/hash_exp /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/hash_exp libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/cram_dump /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/cram_dump libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/cram_index /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/cram_index libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/scramble /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/scramble libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/scram_merge /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/scram_merge libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/scram_pileup /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/scram_pileup libtool: install: warning: `../io_lib/libstaden-read.la' has not been installed in `/sw/lib' libtool: install: /usr/bin/install -c .libs/scram_flagstat /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/scram_flagstat make[2]: Nothing to be done for `install-data-am'. Making install in tests make[2]: Nothing to be done for `install-exec-am'. make[2]: Nothing to be done for `install-data-am'. test -z "/sw/bin" || ./install-sh -c -d "/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin" /usr/bin/install -c io_lib-config '/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin' test -z "/sw/share/man/man1" || ./install-sh -c -d "/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man1" /usr/bin/install -c -m 644 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 '/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man1' test -z "/sw/share/man/man3" || ./install-sh -c -d "/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man3" /usr/bin/install -c -m 644 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 '/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man3' test -z "/sw/share/man/man4" || ./install-sh -c -d "/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man4" /usr/bin/install -c -m 644 man/man4/Read.4 '/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man4' test -z "/sw/include/io_lib" || ./install-sh -c -d "/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/include/io_lib" /usr/bin/install -c -m 644 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 '/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/include/io_lib' /usr/bin/install -c -m 644 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 '/sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/include/io_lib' sudo -u fink-bld [ENV] sh -c /tmp/fink.FnG5a /usr/bin/install -d -m 700 /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/doc/libstaden-read1-shlibs /bin/cp -r CHANGES /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/doc/libstaden-read1-shlibs/ /bin/cp -r COPYRIGHT /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/doc/libstaden-read1-shlibs/ /bin/cp -r ChangeLog /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/doc/libstaden-read1-shlibs/ /bin/cp -r README /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/doc/libstaden-read1-shlibs/ /bin/chmod -R go=u-w /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/doc/libstaden-read1-shlibs /bin/rm -f /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/info/dir /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/info/dir.old /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/info/dir /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/info/dir.old /bin/rm -rf /sw/build.build/root-libstaden-read1-dev-1.13.3-1 /bin/mkdir -p /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw /bin/mkdir -p /sw/build.build/root-libstaden-read1-dev-1.13.3-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-libstaden-read1-dev-1.13.3-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.r3GXt /usr/bin/install -d -m 755 /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/bin /bin/mv /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin/io_lib-config /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/bin/ /usr/bin/install -d -m 755 /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw /bin/mv /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/include /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/ /usr/bin/install -d -m 755 /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/lib /bin/mv /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/lib/libstaden-read.dylib /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/lib/ /usr/bin/install -d -m 755 /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/man /bin/mv /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man3 /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/man/ /bin/mv /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man4 /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/man/ /usr/bin/install -d -m 700 /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/doc/libstaden-read1-dev /bin/cp -r CHANGES /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/doc/libstaden-read1-dev/ /bin/cp -r COPYRIGHT /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/doc/libstaden-read1-dev/ /bin/cp -r ChangeLog /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/doc/libstaden-read1-dev/ /bin/cp -r README /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/doc/libstaden-read1-dev/ /bin/chmod -R go=u-w /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/doc/libstaden-read1-dev /bin/rm -f /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/info/dir /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/info/dir.old /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/info/dir /sw/build.build/root-libstaden-read1-dev-1.13.3-1/sw/share/info/dir.old /bin/rm -rf /sw/build.build/root-staden-io-lib-utils-1.13.3-1 /bin/mkdir -p /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw /bin/mkdir -p /sw/build.build/root-staden-io-lib-utils-1.13.3-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-staden-io-lib-utils-1.13.3-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.uxPSn /usr/bin/install -d -m 755 /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw /bin/mv /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/bin /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/ /usr/bin/install -d -m 755 /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/man /bin/mv /sw/build.build/root-libstaden-read1-shlibs-1.13.3-1/sw/share/man/man1 /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/man/ /usr/bin/install -d -m 700 /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/doc/staden-io-lib-utils /bin/cp -r CHANGES /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/doc/staden-io-lib-utils/ /bin/cp -r COPYRIGHT /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/doc/staden-io-lib-utils/ /bin/cp -r ChangeLog /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/doc/staden-io-lib-utils/ /bin/cp -r README /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/doc/staden-io-lib-utils/ /bin/chmod -R go=u-w /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/doc/staden-io-lib-utils /bin/rm -f /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/info/dir /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/info/dir.old /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/info/dir /sw/build.build/root-staden-io-lib-utils-1.13.3-1/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Creating shlibs files... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-libstaden-read1-shlibs-1.13.3-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `libstaden-read1-shlibs' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/libstaden-read1-shlibs_1.13.3-1_darwin-x86_64.deb'. Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-libstaden-read1-dev-1.13.3-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `libstaden-read1-dev' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/libstaden-read1-dev_1.13.3-1_darwin-x86_64.deb'. Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-staden-io-lib-utils-1.13.3-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `staden-io-lib-utils' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/staden-io-lib-utils_1.13.3-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-libstaden-read1-shlibs-1.13.3-1 (Reading database ... 4692 files and directories currently installed.) Removing fink-buildlock-libstaden-read1-shlibs-1.13.3-1 ...