[package - 123amd64-default][biology/vcflib] Failed for vcflib-1.0.5_1 in build
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Date: Thu, 26 Jan 2023 10:29:15 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/beefy6/data/123amd64-default/d1d6df7c230b/logs/vcflib-1.0.5_1.log
Build URL: https://pkg-status.freebsd.org/beefy6/build.html?mastername=123amd64-default&build=d1d6df7c230b
Log:
=>> Building biology/vcflib
build started at Thu Jan 26 10:28:02 UTC 2023
port directory: /usr/ports/biology/vcflib
package name: vcflib-1.0.5_1
building for: FreeBSD 123amd64-default-job-08 12.3-RELEASE-p10 FreeBSD 12.3-RELEASE-p10 amd64
maintained by: jwb@FreeBSD.org
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> vcflib-1.0.5_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.0.pkg
[123amd64-default-job-08] Installing pkg-1.19.0...
[123amd64-default-job-08] Extracting pkg-1.19.0: .......... done
===> vcflib-1.0.5_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of vcflib-1.0.5_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
=> ekg-vcflib-v1.0.5_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.5?dummy=/ekg-vcflib-v1.0.5_GH0.tar.gz
fetch: https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.5?dummy=/ekg-vcflib-v1.0.5_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/ekg/vcflib/tar.gz/v1.0.5?dummy=/ekg-vcflib-v1.0.5_GH0.tar.gz: size of remote file is not known
ekg-vcflib-v1.0.5_GH0.tar.gz 22 MB 5321 kBps 04s
=> vcflib-tabixpp-v1.1.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/vcflib/tabixpp/tar.gz/v1.1.2?dummy=/vcflib-tabixpp-v1.1.2_GH0.tar.gz
fetch: https://codeload.github.com/vcflib/tabixpp/tar.gz/v1.1.2?dummy=/vcflib-tabixpp-v1.1.2_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/vcflib/tabixpp/tar.gz/v1.1.2?dummy=/vcflib-tabixpp-v1.1.2_GH0.tar.gz: size of remote file is not known
vcflib-tabixpp-v1.1.2_GH0.tar.gz 6962 B 4145 kBps 00s
=> smarco-WFA2-lib-v2.3_GH0.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://codeload.github.com/smarco/WFA2-lib/tar.gz/v2.3?dummy=/smarco-WFA2-lib-v2.3_GH0.tar.gz
fetch: https://codeload.github.com/smarco/WFA2-lib/tar.gz/v2.3?dummy=/smarco-WFA2-lib-v2.3_GH0.tar.gz: size unknown
fetch: https://codeload.github.com/smarco/WFA2-lib/tar.gz/v2.3?dummy=/smarco-WFA2-lib-v2.3_GH0.tar.gz: size of remote file is not known
smarco-WFA2-lib-v2.3_GH0.tar.gz 4051 kB 5829 kBps 00s
===> Fetching all distfiles required by vcflib-1.0.5_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.5_1 for building
=> SHA256 Checksum OK for ekg-vcflib-v1.0.5_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-filevercmp-1a9b779_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fsom-a6ef318_GH0.tar.gz.
=> SHA256 Checksum OK for google-googletest-d225acc_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-intervaltree-aa59377_GH0.tar.gz.
=> SHA256 Checksum OK for edawson-libVCFH-44b6580_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-multichoose-68733cd_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-smithwaterman-2610e25_GH0.tar.gz.
=> SHA256 Checksum OK for simd-everywhere-simde-no-tests-9af03cd_GH0.tar.gz.
=> SHA256 Checksum OK for vcflib-tabixpp-v1.1.2_GH0.tar.gz.
=> SHA256 Checksum OK for smarco-WFA2-lib-v2.3_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
<snip>
[123amd64-default-job-08] | | `-- Extracting icu-72.1,1: .......... done
[123amd64-default-job-08] | `-- Extracting libpsl-0.21.2: .......... done
[123amd64-default-job-08] | `-- Installing libssh2-1.10.0_1,3...
[123amd64-default-job-08] | `-- Extracting libssh2-1.10.0_1,3: .......... done
[123amd64-default-job-08] `-- Extracting curl-7.87.0_1: .......... done
[123amd64-default-job-08] `-- Installing libdeflate-1.17...
[123amd64-default-job-08] `-- Extracting libdeflate-1.17: .......... done
[123amd64-default-job-08] Extracting htslib-1.16: .......... done
=====
Message from ca_root_nss-3.87:
--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.
Assessment and verification of trust is the complete responsibility of the
system administrator.
This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.
This enables SSL Certificate Verification by client software without manual
intervention.
If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.
* /etc/ssl/cert.pem
* /usr/local/etc/ssl/cert.pem
* /usr/local/openssl/cert.pem
===> vcflib-1.0.5_1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of vcflib-1.0.5_1
===> vcflib-1.0.5_1 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
===========================================================================
=======================<phase: configure >============================
===> Configuring for vcflib-1.0.5_1
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/vcflib/work/.build
-- The C compiler identification is Clang 10.0.1
-- The CXX compiler identification is Clang 10.0.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found PkgConfig: /usr/local/bin/pkgconf (found version "1.8.1")
-- Found PythonInterp: /usr/local/bin/python3.9 (found suitable version "3.9.16", minimum required is "3.6")
-- Found PythonLibs: /usr/local/lib/libpython3.9.so
-- Performing Test HAS_FLTO
-- Performing Test HAS_FLTO - Success
-- Performing Test HAS_FLTO_THIN
-- Performing Test HAS_FLTO_THIN - Success
-- Found pybind11: /usr/local/include (found version "2.10.3")
-- Found BZip2: /usr/lib/libbz2.so (found version "1.0.8")
-- Looking for BZ2_bzCompressInit
-- Looking for BZ2_bzCompressInit - found
-- Looking for lzma_auto_decoder in /usr/lib/liblzma.so
-- Looking for lzma_auto_decoder in /usr/lib/liblzma.so - found
-- Looking for lzma_easy_encoder in /usr/lib/liblzma.so
-- Looking for lzma_easy_encoder in /usr/lib/liblzma.so - found
-- Looking for lzma_lzma_preset in /usr/lib/liblzma.so
-- Looking for lzma_lzma_preset in /usr/lib/liblzma.so - found
-- Found LibLZMA: /usr/lib/liblzma.so (found version "5.2.5")
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.11")
-- Found CURL: /usr/local/lib/libcurl.so (found version "7.87.0")
--
-- Found OpenMP_C: -fopenmp=libomp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp=libomp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Checking for module 'htslib'
-- Found htslib, version 1.16
-- Checking for module 'tabixpp'
-- Package 'tabixpp', required by 'virtual:world', not found
-- /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/lib/libwfa.a
Pandoc needs to be installed to generate the man pages
-- Configuring done
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
BOOST_PYTHON_SUFFIX
CMAKE_SHARED_LINKER_FLAGS
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /wrkdirs/usr/ports/biology/vcflib/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for vcflib-1.0.5_1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
/usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5 -B/wrkdirs/usr/ports/biology/vcflib/work/.build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/vcflib/work/.build//CMakeFiles/progress.marks
gmake -f CMakeFiles/Makefile2 all
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake -f CMakeFiles/ZIG-EXT.dir/build.make CMakeFiles/ZIG-EXT.dir/depend
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
cd /wrkdirs/usr/ports/biology/vcflib/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/ZIG-EXT.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake -f CMakeFiles/ZIG-EXT.dir/build.make CMakeFiles/ZIG-EXT.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
[ 0%] Creating directories for 'ZIG-EXT'
/usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/tmp/ZIG-EXT-mkdirs.cmake
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-mkdir
[ 0%] No download step for 'ZIG-EXT'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-download
[ 0%] No update step for 'ZIG-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E echo_append
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-update
[ 1%] No patch step for 'ZIG-EXT'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-patch
[ 2%] No configure step for 'ZIG-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E echo_append
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-configure
[ 2%] Performing build step for 'ZIG-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig/compile.sh -Drelease-fast=true -freference-trace
[ 3%] No install step for 'ZIG-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/src/zig && /usr/local/bin/cmake -E echo_append
[ 3%] Completed 'ZIG-EXT'
/usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/ZIG-EXT-complete
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/ZIG-EXT-prefix/src/ZIG-EXT-stamp/ZIG-EXT-done
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
[ 3%] Built target ZIG-EXT
gmake -f CMakeFiles/wfa-EXT.dir/build.make CMakeFiles/wfa-EXT.dir/depend
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
cd /wrkdirs/usr/ports/biology/vcflib/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/wfa-EXT.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake -f CMakeFiles/wfa-EXT.dir/build.make CMakeFiles/wfa-EXT.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
[ 4%] Creating directories for 'wfa-EXT'
/usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/tmp/wfa-EXT-mkdirs.cmake
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-mkdir
[ 5%] No download step for 'wfa-EXT'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-download
[ 6%] No update step for 'wfa-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && /usr/local/bin/cmake -E echo_append
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-update
[ 6%] No patch step for 'wfa-EXT'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-patch
[ 6%] No configure step for 'wfa-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && /usr/local/bin/cmake -E echo_append
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/vcflib/work/.build/wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-configure
[ 7%] Performing build step for 'wfa-EXT'
cd /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib && gmake BUILD_WFA_PARALLEL=1 BUILD_TOOLS=0 BUILD_EXAMPLES=0 CC_FLAGS=-fPIC setup lib_wfa
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib'
gmake --directory=alignment all
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/alignment'
cc -fPIC -I.. -c affine_penalties.c -o ../build/affine_penalties.o
cc -fPIC -I.. -c affine2p_penalties.c -o ../build/affine2p_penalties.o
cc -fPIC -I.. -c cigar.c -o ../build/cigar.o
cc -fPIC -I.. -c score_matrix.c -o ../build/score_matrix.o
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/alignment'
gmake --directory=bindings/cpp all
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/bindings/cpp'
c++ -fPIC -I../.. -c WFAligner.cpp -o ../../build/cpp/WFAligner.o
In file included from WFAligner.cpp:32:
In file included from ./WFAligner.hpp:37:
In file included from ./../../wavefront/wfa.hpp:35:
In file included from ./../../wavefront/wfa.h:36:
In file included from ./../../wavefront/wavefront_attributes.h:39:
./../system/profiler_timer.h:60:19: error: field has incomplete type 'struct timespec'
struct timespec begin_timer; // Timer begin
^
./../system/profiler_timer.h:53:35: note: forward declaration of 'timespec'
void timer_get_system_time(struct timespec *ts);
^
1 error generated.
gmake[5]: *** [Makefile:23: ../../build/cpp/WFAligner.o] Error 1
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib/bindings/cpp'
gmake[4]: *** [Makefile:87: bindings/cpp] Error 2
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.5/contrib/WFA2-lib'
gmake[3]: *** [CMakeFiles/wfa-EXT.dir/build.make:89: wfa-EXT-prefix/src/wfa-EXT-stamp/wfa-EXT-build] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake[2]: *** [CMakeFiles/Makefile2:290: CMakeFiles/wfa-EXT.dir/all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake[1]: *** [Makefile:149: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/vcflib