Opened 7 years ago

Closed 7 years ago

#36104 closed defect (fixed)

port samtools failed

Reported by: pengyu.ut@… Owned by: macports-tickets@…
Priority: Normal Milestone:
Component: ports Version: 2.1.2
Keywords: Cc: haroldpimentel@…
Port: samtools

Description

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

Change History (1)

comment:1 Changed 7 years ago by ci42

Cc: haroldpimentel@… added
Port: samtools added
Resolution: fixed
Status: newclosed

Samtools won't compile with clang. Fixed in r97678.

In the future please remember to cc the maintainer and fill in the port field.

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