Hi,
I got the following error when I install samtools, which I don't quite
understand what the problem is and how to fix it. Could anybody let me
know? Thanks!
~$ cat /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/main.log
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:main Skipping completed org.macports.archivefetch (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.fetch (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.checksum (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.extract (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.patch (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.configure (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:build build phase started at Tue Sep 11 10:44:58 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 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 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'
: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 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/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 67675 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 $targetname"
:info:build Warning: targets not executed for samtools:
org.macports.activate org.macports.build org.macports.destroot
org.macports.install
:notice:build Please see the log file for port samtools for details:
/opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/main.log
~$ cat /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_science_samtools/samtools/main.log
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:main Skipping completed org.macports.archivefetch (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.fetch (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.checksum (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.extract (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.patch (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:main Skipping completed org.macports.configure (samtools)
:debug:main Privilege de-escalation not attempted as not running as root.
:debug:build build phase started at Tue Sep 11 10:44:58 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 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 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'
: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 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/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 67675 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
--
Regards,
Peng