[package - main-i386-default][biology/vcftools] Failed for vcftools-0.1.16 in build
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Date: Sat, 01 Jul 2023 15:35:39 UTC
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@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/pf46bd2c58425_s0631830a7a/logs/vcftools-0.1.16.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=pf46bd2c58425_s0631830a7a
Log:
=>> Building biology/vcftools
build started at Sat Jul 1 15:34:54 UTC 2023
port directory: /usr/ports/biology/vcftools
package name: vcftools-0.1.16
building for: FreeBSD main-i386-default-job-09 14.0-CURRENT FreeBSD 14.0-CURRENT 1400092 i386
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400092
Job Id: 09
!!! Jail is newer than host. (Jail: 1400092, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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jwb@FreeBSD.org
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--SUB_LIST--
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--End resource limits--
=======================<phase: check-sanity >============================
===> License LGPL3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> vcftools-0.1.16 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.2.pkg
[main-i386-default-job-09] Installing pkg-1.19.2...
[main-i386-default-job-09] Extracting pkg-1.19.2: .......... done
===> vcftools-0.1.16 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of vcftools-0.1.16
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by vcftools-0.1.16 for building
===========================================================================
=======================<phase: checksum >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by vcftools-0.1.16 for building
=> SHA256 Checksum OK for vcftools-vcftools-v0.1.16_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License LGPL3 accepted by the user
===> Fetching all distfiles required by vcftools-0.1.16 for building
===> Extracting for vcftools-0.1.16
=> SHA256 Checksum OK for vcftools-vcftools-v0.1.16_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for vcftools-0.1.16
===========================================================================
=======================<phase: build-depends >============================
===> vcftools-0.1.16 depends on package: gmake>=4.3 - not found
<snip>
[main-i386-default-job-09] | `-- Extracting indexinfo-0.3.1: .... done
[main-i386-default-job-09] `-- Extracting gettext-runtime-0.21.1: .......... done
[main-i386-default-job-09] Extracting gmake-4.3_2: .......... done
===> vcftools-0.1.16 depends on package: gmake>=4.3 - found
===> Returning to build of vcftools-0.1.16
===> vcftools-0.1.16 depends on package: pkgconf>=1.3.0_1 - not found
===> Installing existing package /packages/All/pkgconf-1.8.1,1.pkg
[main-i386-default-job-09] Installing pkgconf-1.8.1,1...
[main-i386-default-job-09] Extracting pkgconf-1.8.1,1: .......... done
===> vcftools-0.1.16 depends on package: pkgconf>=1.3.0_1 - found
===> Returning to build of vcftools-0.1.16
===> vcftools-0.1.16 depends on package: autoconf>=2.71 - not found
===> Installing existing package /packages/All/autoconf-2.71.pkg
[main-i386-default-job-09] Installing autoconf-2.71...
[main-i386-default-job-09] `-- Installing autoconf-switch-20220527...
[main-i386-default-job-09] `-- Extracting autoconf-switch-20220527: .......... done
[main-i386-default-job-09] `-- Installing m4-1.4.19,1...
[main-i386-default-job-09] `-- Extracting m4-1.4.19,1: .......... done
[main-i386-default-job-09] `-- Installing perl5-5.32.1_3...
[main-i386-default-job-09] `-- Extracting perl5-5.32.1_3: .......... done
[main-i386-default-job-09] Extracting autoconf-2.71: .......... done
===> vcftools-0.1.16 depends on package: autoconf>=2.71 - found
===> Returning to build of vcftools-0.1.16
===> vcftools-0.1.16 depends on package: automake>=1.16.5 - not found
===> Installing existing package /packages/All/automake-1.16.5.pkg
[main-i386-default-job-09] Installing automake-1.16.5...
[main-i386-default-job-09] Extracting automake-1.16.5: .......... done
===> vcftools-0.1.16 depends on package: automake>=1.16.5 - found
===> Returning to build of vcftools-0.1.16
===> vcftools-0.1.16 depends on package: perl5>=5.32.r0<5.33 - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for vcftools-0.1.16
configure.ac:16: installing './compile'
configure.ac:66: installing './config.guess'
configure.ac:66: installing './config.sub'
configure.ac:12: installing './install-sh'
configure.ac:12: installing './missing'
src/cpp/Makefile.am: installing './depcomp'
configure: loading site script /usr/ports/Templates/config.site
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a race-free mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
checking whether gmake supports nested variables... yes
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 the compiler supports GNU C++... yes
checking whether c++ accepts -g... yes
checking for c++ option to enable C++11 features... none needed
checking whether gmake supports the include directive... yes (GNU style)
checking dependency style of c++... gcc3
checking for gcc... cc
checking whether the compiler supports GNU C... yes
checking whether cc accepts -g... yes
checking for cc option to enable C11 features... none needed
checking whether cc understands -c and -o together... yes
checking dependency style of cc... gcc3
checking how to run the C preprocessor... cpp
checking for perl... (cached) /usr/local/bin/perl
checking pkg-config is at least version 0.9.0... yes
checking for ZLIB... yes
checking for stdio.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for strings.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for sys/types.h... (cached) yes
checking for unistd.h... (cached) yes
checking for arpa/inet.h... (cached) yes
checking for fcntl.h... (cached) yes
checking for limits.h... (cached) yes
checking for netdb.h... (cached) yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for sys/socket.h... (cached) yes
checking for unistd.h... (cached) yes
checking for _Bool... (cached) yes
checking for stdbool.h that conforms to C99... (cached) yes
checking for inline... inline
checking for int16_t... (cached) yes
checking for int32_t... (cached) yes
checking for int64_t... (cached) yes
checking for int8_t... (cached) yes
checking for off_t... (cached) yes
checking for size_t... (cached) yes
checking for ssize_t... (cached) yes
checking for uint16_t... (cached) yes
checking for uint32_t... (cached) yes
checking for uint8_t... (cached) 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 error_at_line... no
checking build system type... i386-portbld-freebsd14.0
checking host system type... i386-portbld-freebsd14.0
checking for GNU libc compatible malloc... (cached) yes
checking for GNU libc compatible realloc... yes
checking for gethostbyaddr... yes
checking for gethostbyname... (cached) yes
checking for memset... (cached) yes
checking for pow... no
checking for select... (cached) yes
checking for socket... yes
checking for sqrt... no
checking for strchr... (cached) yes
checking for strdup... (cached) yes
checking for strerror... (cached) yes
checking for strstr... (cached) yes
checking for strtol... (cached) yes
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 src/cpp/Makefile
config.status: creating src/perl/Makefile
config.status: creating config.h
config.status: executing depfiles commands
===========================================================================
=======================<phase: build >============================
===> Building for vcftools-0.1.16
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16'
gmake all-recursive
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16'
Making all in src
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src'
Making all in cpp
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/cpp'
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bcf_entry.o -MD -MP -MF .deps/vcftools-bcf_entry.Tpo -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bcf_entry_setters.o -MD -MP -MF .deps/vcftools-bcf_entry_setters.Tpo -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp
bcf_entry_setters.cpp:309:13: warning: implicit conversion from 'int' to 'float' changes value from 2139095041 to 2139095040 [-Wimplicit-const-int-float-conversion]
if (tmp == 0x7F800001)
~~ ^~~~~~~~~~
bcf_entry_setters.cpp:326:28: warning: implicit conversion from 'int' to 'float' changes value from 2139095041 to 2139095040 [-Wimplicit-const-int-float-conversion]
if ( (in == -1) or (in == 0x7F800001) )
~~ ^~~~~~~~~~
2 warnings generated.
mv -f .deps/vcftools-bcf_entry_setters.Tpo .deps/vcftools-bcf_entry_setters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bcf_file.o -MD -MP -MF .deps/vcftools-bcf_file.Tpo -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp
mv -f .deps/vcftools-bcf_entry.Tpo .deps/vcftools-bcf_entry.Po
cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-bgzf.o -MD -MP -MF .deps/vcftools-bgzf.Tpo -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c
mv -f .deps/vcftools-bgzf.Tpo .deps/vcftools-bgzf.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-dgeev.o -MD -MP -MF .deps/vcftools-dgeev.Tpo -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp
mv -f .deps/vcftools-dgeev.Tpo .deps/vcftools-dgeev.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-entry.o -MD -MP -MF .deps/vcftools-entry.Tpo -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp
entry.cpp:601:12: warning: implicit conversion from 'int' to 'float' changes value from 2139095042 to 2139095040 [-Wimplicit-const-int-float-conversion]
value = 0x7F800002;
~ ^~~~~~~~~~
1 warning generated.
mv -f .deps/vcftools-entry.Tpo .deps/vcftools-entry.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-entry_filters.o -MD -MP -MF .deps/vcftools-entry_filters.Tpo -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp
mv -f .deps/vcftools-bcf_file.Tpo .deps/vcftools-bcf_file.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-entry_getters.o -MD -MP -MF .deps/vcftools-entry_getters.Tpo -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp
mv -f .deps/vcftools-entry_getters.Tpo .deps/vcftools-entry_getters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-entry_setters.o -MD -MP -MF .deps/vcftools-entry_setters.Tpo -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp
mv -f .deps/vcftools-entry_filters.Tpo .deps/vcftools-entry_filters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-gamma.o -MD -MP -MF .deps/vcftools-gamma.Tpo -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp
mv -f .deps/vcftools-entry_setters.Tpo .deps/vcftools-entry_setters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-header.o -MD -MP -MF .deps/vcftools-header.Tpo -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp
mv -f .deps/vcftools-gamma.Tpo .deps/vcftools-gamma.Po
cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-knetfile.o -MD -MP -MF .deps/vcftools-knetfile.Tpo -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c
mv -f .deps/vcftools-knetfile.Tpo .deps/vcftools-knetfile.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-output_log.o -MD -MP -MF .deps/vcftools-output_log.Tpo -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp
mv -f .deps/vcftools-output_log.Tpo .deps/vcftools-output_log.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-parameters.o -MD -MP -MF .deps/vcftools-parameters.Tpo -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp
mv -f .deps/vcftools-header.Tpo .deps/vcftools-header.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-variant_file.o -MD -MP -MF .deps/vcftools-variant_file.Tpo -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp
mv -f .deps/vcftools-variant_file.Tpo .deps/vcftools-variant_file.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-variant_file_diff.o -MD -MP -MF .deps/vcftools-variant_file_diff.Tpo -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp
mv -f .deps/vcftools-parameters.Tpo .deps/vcftools-parameters.Po
c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT vcftools-variant_file_filters.o -MD -MP -MF .deps/vcftools-variant_file_filters.Tpo -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp
variant_file_filters.cpp:129:2: error: use of undeclared identifier 'random_shuffle'
random_shuffle(keep_index.begin(), keep_index.end()); // Get a random order
^
1 error generated.
gmake[4]: *** [Makefile:766: vcftools-variant_file_filters.o] Error 1
gmake[4]: *** Waiting for unfinished jobs....
mv -f .deps/vcftools-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.Po
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src/cpp'
gmake[3]: *** [Makefile:329: all-recursive] Error 1
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16/src'
gmake[2]: *** [Makefile:374: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16'
gmake[1]: *** [Makefile:315: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcftools/work/vcftools-0.1.16'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/vcftools