[MacPorts] #36104: port samtools failed

11 Sep 2012


      #36104: port samtools failed
-------------------------+--------------------------------
 Reporter:  pengyu.ut@…  |      Owner:  macports-tickets@…
     Type:  defect       |     Status:  new
 Priority:  Normal       |  Milestone:
Component:  ports        |    Version:  2.1.2
 Keywords:               |       Port:
-------------------------+--------------------------------
 I get the following error when I try to install samtools


 {{{
 version:1
 :debug:main epoch: in tree: 0 installed: 0
 :debug:main zlib 1.2.7_0 exists in the ports tree
 :debug:main zlib 1.2.7_0 +universal is the latest installed
 :debug:main zlib 1.2.7_0 +universal is active
 :debug:main Merging existing variants '+universal' into variants
 :debug:main new fully merged portvariants: universal +
 :debug:main Changing to port directory:
 /opt/local/var/macports/sources/rsync.macports.org/release/ports/archivers/zlib
 :debug:main OS darwin/12.1.0 (Mac OS X 10.8) arch i386
 :debug:main org.macports.load registered provides 'load', a pre-existing
 procedure. Target override will not be provided
 :debug:main org.macports.unload registered provides 'unload', a pre-
 existing procedure. Target override will not be provided
 :debug:main org.macports.distfiles registered provides 'distfiles', a pre-
 existing procedure. Target override will not be provided
 :debug:main Using group file
 /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/group/xcodeversion-1.0.tcl
 :debug:main adding the default universal variant
 :debug:main Reading variant descriptions from
 /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
 :debug:main Executing variant universal provides universal
 :debug:main No need to upgrade! zlib 1.2.7_0 >= zlib 1.2.7_0
 :debug:main epoch: in tree: 0 installed: 0
 :debug:main ncurses 5.9_1 exists in the ports tree
 :debug:main ncurses 5.9_1 +universal is the latest installed
 :debug:main ncurses 5.9_1 +universal is active
 :debug:main Merging existing variants '+universal' into variants
 :debug:main new fully merged portvariants: universal +
 :debug:main Changing to port directory:
 /opt/local/var/macports/sources/rsync.macports.org/release/ports/devel/ncurses
 :debug:main OS darwin/12.1.0 (Mac OS X 10.8) arch i386
 :debug:main org.macports.load registered provides 'load', a pre-existing
 procedure. Target override will not be provided
 :debug:main org.macports.unload registered provides 'unload', a pre-
 existing procedure. Target override will not be provided
 :debug:main org.macports.distfiles registered provides 'distfiles', a pre-
 existing procedure. Target override will not be provided
 :debug:main adding the default universal variant
 :debug:main Reading variant descriptions from
 /opt/local/var/macports/sources/rsync.macports.org/release/ports/_resources/port1.0/variant_descriptions.conf
 :debug:main Executing variant universal provides universal
 :debug:main No need to upgrade! ncurses 5.9_1 >= ncurses 5.9_1
 :msg:main --->  Computing dependencies for samtools:info:main .:debug:main
 samtools has no conflicts
 :debug:main Searching for dependency: zlib
 :debug:main Found Dependency: receipt exists for zlib
 :debug:main Searching for dependency: ncurses
 :debug:main Found Dependency: receipt exists for ncurses
 :msg:main
 :debug:main Executing org.macports.main (samtools)
 :debug:main changing euid/egid - current euid: 0 - current egid: 0
 :debug:main egid changed to: 502
 :debug:main euid changed to: 504
 :debug:archivefetch archivefetch phase started at Tue Sep 11 15:21:59 CDT
 2012
 :msg:archivefetch --->  Fetching archive for samtools
 :debug:archivefetch Executing org.macports.archivefetch (samtools)
 :debug:archivefetch euid/egid changed to: 0/0
 :debug:archivefetch chowned /opt/local/var/macports/incoming to macports
 :debug:archivefetch euid/egid changed to: 504/502
 :info:archivefetch --->  samtools-0.1.17_0.darwin_12.x86_64.tbz2 doesn't
 seem to exist in /opt/local/var/macports/incoming/verified
 :msg:archivefetch --->  Attempting to fetch
 samtools-0.1.17_0.darwin_12.x86_64.tbz2 from
 http://packages.macports.org/samtools
 :debug:archivefetch Fetching archive failed:: The requested URL returned
 error: 404
 :msg:archivefetch --->  Attempting to fetch
 samtools-0.1.17_0.darwin_12.x86_64.tbz2 from
 http://lil.fr.packages.macports.org/samtools
 :debug:archivefetch Fetching archive failed:: The requested URL returned
 error: 404
 :msg:archivefetch --->  Attempting to fetch
 samtools-0.1.17_0.darwin_12.x86_64.tbz2 from
 http://mse.uk.packages.macports.org/sites/packages.macports.org/samtools
 :debug:archivefetch Fetching archive failed:: The requested URL returned
 error: 404
 :debug:archivefetch Privilege de-escalation not attempted as not running
 as root.
 :debug:fetch fetch phase started at Tue Sep 11 15:22:00 CDT 2012
 :notice:fetch --->  Fetching distfiles for samtools
 :debug:fetch Executing org.macports.fetch (samtools)
 :debug:fetch Privilege de-escalation not attempted as not running as root.
 :debug:checksum checksum phase started at Tue Sep 11 15:22:00 CDT 2012
 :notice:checksum --->  Verifying checksum(s) for samtools
 :debug:checksum Executing org.macports.checksum (samtools)
 :info:checksum --->  Checksumming samtools-0.1.17.tar.bz2
 :debug:checksum Correct (sha1) checksum for samtools-0.1.17.tar.bz2
 :debug:checksum Correct (rmd160) checksum for samtools-0.1.17.tar.bz2
 :debug:checksum Privilege de-escalation not attempted as not running as
 root.
 :debug:extract extract phase started at Tue Sep 11 15:22:00 CDT 2012
 :notice:extract --->  Extracting samtools
 :debug:extract setting option extract.cmd to /usr/bin/bzip2
 :debug:extract Executing org.macports.extract (samtools)
 :info:extract --->  Extracting samtools-0.1.17.tar.bz2
 :debug:extract setting option extract.args to
 '/opt/local/var/macports/distfiles/samtools/samtools-0.1.17.tar.bz2'
 :debug:extract Environment: CPATH='/opt/local/include'
 CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/.CC_PRINT_OPTIONS'
 LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES'
 MACOSX_DEPLOYMENT_TARGET='10.8'
 :debug:extract Assembled command: 'cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work"
 && /usr/bin/bzip2 -dc
 '/opt/local/var/macports/distfiles/samtools/samtools-0.1.17.tar.bz2' |
 /usr/bin/gnutar --no-same-owner -xf -'
 :debug:extract Executing command line:  cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work"
 && /usr/bin/bzip2 -dc
 '/opt/local/var/macports/distfiles/samtools/samtools-0.1.17.tar.bz2' |
 /usr/bin/gnutar --no-same-owner -xf -
 :debug:extract euid/egid changed to: 0/0
 :debug:extract chowned
 /opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work
 to macports
 :debug:extract euid/egid changed to: 504/502
 :debug:extract Privilege de-escalation not attempted as not running as
 root.
 :debug:patch patch phase started at Tue Sep 11 15:22:00 CDT 2012
 :debug:patch Executing org.macports.patch (samtools)
 :debug:patch Privilege de-escalation not attempted as not running as root.
 :debug:configure configure phase started at Tue Sep 11 15:22:01 CDT 2012
 :notice:configure --->  Configuring samtools
 :debug:configure Using compiler 'Mac OS X clang'
 :debug:configure Executing org.macports.configure (samtools)
 :debug:configure Privilege de-escalation not attempted as not running as
 root.
 :debug:build build phase started at Tue Sep 11 15:22:01 CDT 2012
 :notice:build --->  Building samtools
 :debug:build Executing org.macports.build (samtools)
 :debug:build Environment: CPATH='/opt/local/include'
 CC_PRINT_OPTIONS_FILE='/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/.CC_PRINT_OPTIONS'
 LIBRARY_PATH='/opt/local/lib' CC_PRINT_OPTIONS='YES'
 MACOSX_DEPLOYMENT_TARGET='10.8'
 :debug:build Assembled command: 'cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17"
 && /usr/bin/make -j8 -w all CC=/usr/bin/clang CFLAGS="-g -Wall -O2 -arch
 x86_64"'
 :debug:build Executing command line:  cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17"
 && /usr/bin/make -j8 -w all CC=/usr/bin/clang CFLAGS="-g -Wall -O2 -arch
 x86_64"
 :info:build make: Entering directory
 `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17'
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o
 :info:build make[1]: Entering directory
 `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17'
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bgzf.c -o bgzf.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. kstring.c -o kstring.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_plcmd.c -o bam_plcmd.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. sam_view.c -o sam_view.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_rmdup.c -o bam_rmdup.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_rmdupse.c -o bam_rmdupse.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam.c -o bam.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_mate.c -o bam_mate.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_stat.c -o bam_stat.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_color.c -o bam_color.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bamtk.c -o bamtk.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. sam.c -o sam.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. kaln.c -o kaln.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam2bcf.c -o bam2bcf.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam2bcf_indel.c -o bam2bcf_indel.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. errmod.c -o errmod.o
 :info:build errmod.c:79:8: warning: self-comparison always evaluates to
 false [-Wtautological-compare]
 :info:build         if (m > m) return -1;
 :info:build               ^
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. sample.c -o sample.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o
 :info:build 1 warning generated.
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. razf.c -o razf.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. faidx.c -o faidx.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. phase.c -o phase.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o
 :info:build ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o
 bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o
 faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o
 kprobaln.o bam_cat.o
 :info:build make[1]: Leaving directory
 `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17'
 :info:build make[1]: Entering directory
 `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17/bcftools'
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. em.c -o em.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. index.c -o index.o
 :info:build vcf.c:238:15: warning: explicitly assigning a variable of type
 'int' to itself [-Wself-assign]
 :info:build                 endblock: i = i;
 :info:build                           ~ ^ ~
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o
 :info:build /usr/bin/clang -c -g -Wall -O2 -arch x86_64
 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE
 -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o
 :info:build 1 warning generated.
 :info:build ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o
 kmin.o index.o fet.o mut.o bcf2qcall.o
 :info:build make[1]: Leaving directory
 `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17/bcftools'
 :info:build make[1]: Entering directory
 `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17/misc'
 :info:build make[1]: Nothing to be done for `lib'.
 :info:build make[1]: Leaving directory
 `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17/misc'
 :info:build /usr/bin/clang -g -Wall -O2 -arch x86_64 -o samtools
 bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o
 bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o
 sample.o cut_target.o phase.o bam2depth.o -Lbcftools  libbam.a -lbcf
 -lcurses  -lm -lz
 :info:build Undefined symbols for architecture x86_64:
 :info:build   "___ks_insertsort_heap", referenced from:
 :info:build       _ks_combsort_heap in libbam.a(bam_sort.o)
 :info:build       _ks_introsort_heap in libbam.a(bam_sort.o)
 :info:build   "___ks_insertsort_sort", referenced from:
 :info:build       _ks_combsort_sort in libbam.a(bam_sort.o)
 :info:build       _ks_introsort_sort in libbam.a(bam_sort.o)
 :info:build ld: symbol(s) not found for architecture x86_64
 :info:build clang: error: linker command failed with exit code 1 (use -v
 to see invocation)
 :info:build make: *** [samtools] Error 1
 :info:build make: Leaving directory
 `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17'
 :info:build Command failed:  cd
 "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/work/samtools-0.1.17"
 && /usr/bin/make -j8 -w all CC=/usr/bin/clang CFLAGS="-g -Wall -O2 -arch
 x86_64"
 :info:build Exit code: 2
 :error:build org.macports.build for port samtools returned: command
 execution failed
 :debug:build Error code: CHILDSTATUS 86479 2
 :debug:build Backtrace: command execution failed
     while executing
 "system -nice 0 $fullcmdstring"
     ("eval" body line 1)
     invoked from within
 "eval system $notty $nice \$fullcmdstring"
     invoked from within
 "command_exec build"
     (procedure "portbuild::build_main" line 8)
     invoked from within
 "$procedure $targetname"
 :info:build Warning: targets not executed for samtools:
 org.macports.activate org.macports.build org.macports.destroot
 org.macports.install
 :notice:build Please see the log file for port samtools for details:
 /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/main.log

 }}}

-- 
Ticket URL: <https://trac.macports.org/ticket/36104>
MacPorts <http://www.macports.org/>
Ports system for Mac OS