[package - head-amd64-default][biology/tophat] Failed for tophat-2.1.1_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Sep 8 16:13:36 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: jwb at FreeBSD.org
Last committer: antoine at FreeBSD.org
Ident: $FreeBSD: head/biology/tophat/Makefile 528058 2020-03-08 17:01:46Z antoine $
Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p547958_s365440/logs/tophat-2.1.1_1.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p547958_s365440
Log:
=>> Building biology/tophat
build started at Tue Sep 8 16:13:10 UTC 2020
port directory: /usr/ports/biology/tophat
package name: tophat-2.1.1_1
building for: FreeBSD head-amd64-default-job-12 13.0-CURRENT FreeBSD 13.0-CURRENT 1300113 amd64
maintained by: jwb at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/tophat/Makefile 528058 2020-03-08 17:01:46Z antoine $
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!!! Jail is newer than host. (Jail: 1300113, Host: 1300100) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
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=======================<phase: check-sanity >============================
===> NOTICE:
This port is deprecated; you may wish to reconsider installing it:
Uses deprecated version of python.
It is scheduled to be removed on or after 2020-09-15.
===> License BSL accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> tophat-2.1.1_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.15.1.txz
[head-amd64-default-job-12] Installing pkg-1.15.1...
[head-amd64-default-job-12] Extracting pkg-1.15.1: .......... done
===> tophat-2.1.1_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of tophat-2.1.1_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> NOTICE:
This port is deprecated; you may wish to reconsider installing it:
Uses deprecated version of python.
It is scheduled to be removed on or after 2020-09-15.
===> License BSL accepted by the user
===> Fetching all distfiles required by tophat-2.1.1_1 for building
===========================================================================
=======================<phase: checksum >============================
===> NOTICE:
This port is deprecated; you may wish to reconsider installing it:
Uses deprecated version of python.
It is scheduled to be removed on or after 2020-09-15.
===> License BSL accepted by the user
===> Fetching all distfiles required by tophat-2.1.1_1 for building
=> SHA256 Checksum OK for tophat-2.1.1.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
<snip>
checking for size_t... (cached) yes
checking for ptrdiff_t... (cached) yes
checking for an ANSI C-conforming const... 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 gzread in -lz... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... (cached) yes
checking for memset... (cached) yes
checking for strdup... (cached) yes
checking for strrchr... (cached) yes
checking for strtol... (cached) yes
checking for strsep... (cached) yes
checking build system type... amd64-portbld-freebsd13.0
checking host system type... amd64-portbld-freebsd13.0
checking how to create a pax tar archive... gnutar
checking dependency style of cc... (cached) gcc3
checking dependency style of c++... (cached) gcc3
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
-- tophat 2.1.1 Configuration Results --
C++ compiler: c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include
Linker flags: -L./samtools-0.1.18 -L/usr/local/lib -fstack-protector-strong
BOOST libraries: -lboost_thread
GCC version: FreeBSD clang version 11.0.0 (git at github.com:llvm/llvm-project.git llvmorg-11.0.0-rc2-0-g414f32a9e86)
Host System type: amd64-portbld-freebsd13.0
Install prefix: /usr/local
Install eprefix: ${prefix}
See config.h for further configuration information.
Email bug reports to <tophat.cufflinks at gmail.com>.
===========================================================================
=======================<phase: build >============================
===> Building for tophat-2.1.1_1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1'
gmake all-recursive
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1'
Making all in src
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src'
Makefile:1679: warning: overriding recipe for target 'libbam.a'
Makefile:1203: warning: ignoring old recipe for target 'libbam.a'
cd ./samtools-0.1.18 && gmake samtools_0.1.18
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18'
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o
bgzf.c:275:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 139 to -117 [-Wconstant-conversion]
buffer[1] = GZIP_ID2;
~ ^~~~~~~~
bgzf.c:283:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 255 to -1 [-Wconstant-conversion]
buffer[9] = OS_UNKNOWN;
~ ^~~~~~~~~~
2 warnings generated.
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam.c -o bam.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam.c -o sam.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. razf.c -o razf.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. knetfile.c -o knetfile.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o
ar cr 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
/usr/bin/ranlib libbam.a
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18/bcftools'
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf.c -o bcf.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. vcf.c -o vcf.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcfutils.c -o bcfutils.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. prob1.c -o prob1.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. em.c -o em.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kfunc.c -o kfunc.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kmin.c -o kmin.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. index.c -o index.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. fet.c -o fet.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. mut.c -o mut.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf2qcall.c -o bcf2qcall.o
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
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18/bcftools'
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview.c -o bam_tview.o
bam_tview.c:434:2: warning: "No curses library is available; tview is disabled." [-W#warnings]
#warning "No curses library is available; tview is disabled."
^
1 warning generated.
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_plcmd.c -o bam_plcmd.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_view.c -o sam_view.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdup.c -o bam_rmdup.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdupse.c -o bam_rmdupse.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_mate.c -o bam_mate.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_stat.c -o bam_stat.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_color.c -o bam_color.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bamtk.c -o bamtk.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kaln.c -o kaln.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf.c -o bam2bcf.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf_indel.c -o bam2bcf_indel.o
bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body]
for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p;
^
bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence this warning
bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body]
for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q;
^
bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence this warning
2 warnings generated.
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. errmod.c -o errmod.o
errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare]
if (m > m) return -1;
^
1 warning generated.
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sample.c -o sample.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. cut_target.c -o cut_target.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. phase.c -o phase.o
cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2depth.c -o bam2depth.o
cc -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -o samtools_0.1.18 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 -lm -lz #-lcurses
ld: error: undefined symbol: __ks_insertsort_uint32_t
>>> referenced by bam2bcf_indel.c:12
>>> bam2bcf_indel.o:(ks_combsort_uint32_t)
>>> referenced by bam2bcf_indel.c:12
>>> bam2bcf_indel.o:(ks_introsort_uint32_t)
ld: error: undefined symbol: __ks_insertsort_uint16_t
>>> referenced by errmod.c:4
>>> errmod.o:(ks_combsort_uint16_t)
>>> referenced by errmod.c:4
>>> errmod.o:(ks_introsort_uint16_t)
ld: error: undefined symbol: __ks_insertsort_rseq
>>> referenced by phase.c:51
>>> phase.o:(ks_combsort_rseq)
>>> referenced by phase.c:51
>>> phase.o:(ks_introsort_rseq)
ld: error: undefined symbol: unpackInt16
>>> referenced by bgzf.c:497
>>> bgzf.o:(bgzf_read_block) in archive libbam.a
>>> referenced by bgzf.c:407
>>> bgzf.o:(check_header) in archive libbam.a
>>> referenced by bgzf.c:410
>>> bgzf.o:(check_header) in archive libbam.a
ld: error: undefined symbol: packInt16
>>> referenced by bgzf.c:344
>>> bgzf.o:(deflate_block) in archive libbam.a
ld: error: undefined symbol: packInt32
>>> referenced by bgzf.c:347
>>> bgzf.o:(deflate_block) in archive libbam.a
>>> referenced by bgzf.c:348
>>> bgzf.o:(deflate_block) in archive libbam.a
ld: error: undefined symbol: __ks_insertsort_off
>>> referenced by bam_index.c:52
>>> bam_index.o:(ks_combsort_off) in archive libbam.a
>>> referenced by bam_index.c:52
>>> bam_index.o:(ks_introsort_off) in archive libbam.a
ld: error: undefined symbol: __ks_insertsort_uint64_t
>>> referenced by bedidx.c:12
>>> bedidx.o:(ks_combsort_uint64_t) in archive libbam.a
>>> referenced by bedidx.c:12
>>> bedidx.o:(ks_introsort_uint64_t) in archive libbam.a
ld: error: undefined symbol: __ks_insertsort_heap
>>> referenced by bam_sort.c:53
>>> bam_sort.o:(ks_combsort_heap) in archive libbam.a
>>> referenced by bam_sort.c:53
>>> bam_sort.o:(ks_introsort_heap) in archive libbam.a
ld: error: undefined symbol: __ks_insertsort_sort
>>> referenced by bam_sort.c:309
>>> bam_sort.o:(ks_combsort_sort) in archive libbam.a
>>> referenced by bam_sort.c:309
>>> bam_sort.o:(ks_introsort_sort) in archive libbam.a
cc: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[4]: *** [Makefile:50: samtools_0.1.18] Error 1
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18'
gmake[3]: *** [Makefile:1679: libbam.a] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src'
gmake[2]: *** [Makefile:313: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1'
gmake[1]: *** [Makefile:253: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/tophat
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