[package - main-armv7-default][biology/vcflib] Failed for vcflib-1.0.7 in build
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Date: Thu, 15 Jun 2023 17:18:02 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/ampere2/data/main-armv7-default/p18ee3527a17a_s1232c7884d/logs/vcflib-1.0.7.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p18ee3527a17a_s1232c7884d
Log:
=>> Building biology/vcflib
build started at Thu Jun 15 17:17:46 UTC 2023
port directory: /usr/ports/biology/vcflib
package name: vcflib-1.0.7
building for: FreeBSD main-armv7-default-job-12 14.0-CURRENT FreeBSD 14.0-CURRENT 1400090 arm
maintained by: jwb@FreeBSD.org
Makefile ident:
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Jail OSVERSION: 1400090
Job Id: 12
!!! Jail is newer than host. (Jail: 1400090, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
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===> The following configuration options are available for vcflib-1.0.7:
ZIG=off: Include Zig language support
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
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--End CONFIGURE_ENV--
--MAKE_ENV--
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=======================<phase: check-sanity >============================
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> vcflib-1.0.7 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-armv7-default-job-12] Installing pkg-1.19.1_1...
[main-armv7-default-job-12] Extracting pkg-1.19.1_1: .......... done
===> vcflib-1.0.7 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of vcflib-1.0.7
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.7 for building
===========================================================================
=======================<phase: checksum >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.7 for building
=> SHA256 Checksum OK for ekg-vcflib-v1.0.7_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-filevercmp-df20dcc_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fsom-56695e1_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-e1f94ae_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.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License MIT accepted by the user
===> Fetching all distfiles required by vcflib-1.0.7 for building
===> Extracting for vcflib-1.0.7
=> SHA256 Checksum OK for ekg-vcflib-v1.0.7_GH0.tar.gz.
=> SHA256 Checksum OK for ekg-fastahack-bb33265_GH0.tar.gz.
<snip>
[main-armv7-default-job-12] `-- Extracting libuv-1.45.0: .......... done
[main-armv7-default-job-12] `-- Installing rhash-1.4.3...
[main-armv7-default-job-12] | `-- Installing gettext-runtime-0.21.1...
[main-armv7-default-job-12] | | `-- Installing indexinfo-0.3.1...
[main-armv7-default-job-12] | | `-- Extracting indexinfo-0.3.1: .... done
[main-armv7-default-job-12] | `-- Extracting gettext-runtime-0.21.1: .......... done
[main-armv7-default-job-12] `-- Extracting rhash-1.4.3: .......... done
[main-armv7-default-job-12] Extracting cmake-core-3.26.1_1: .......... done
===> vcflib-1.0.7 depends on file: /usr/local/bin/cmake - found
===> Returning to build of vcflib-1.0.7
===> vcflib-1.0.7 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.pkg
[main-armv7-default-job-12] Installing gmake-4.3_2...
[main-armv7-default-job-12] Extracting gmake-4.3_2: .......... done
===> vcflib-1.0.7 depends on package: gmake>=4.3 - found
===> Returning to build of vcflib-1.0.7
===> vcflib-1.0.7 depends on package: pkgconf>=1.3.0_1 - not found
===> Installing existing package /packages/All/pkgconf-1.8.1,1.pkg
[main-armv7-default-job-12] Installing pkgconf-1.8.1,1...
[main-armv7-default-job-12] Extracting pkgconf-1.8.1,1: .......... done
===> vcflib-1.0.7 depends on package: pkgconf>=1.3.0_1 - found
===> Returning to build of vcflib-1.0.7
===> vcflib-1.0.7 depends on file: /usr/local/bin/python3.9 - not found
===> Installing existing package /packages/All/python39-3.9.16_2.pkg
[main-armv7-default-job-12] Installing python39-3.9.16_2...
[main-armv7-default-job-12] `-- Installing libffi-3.4.4...
[main-armv7-default-job-12] `-- Extracting libffi-3.4.4: .......... done
[main-armv7-default-job-12] `-- Installing mpdecimal-2.5.1...
[main-armv7-default-job-12] `-- Extracting mpdecimal-2.5.1: .......... done
[main-armv7-default-job-12] `-- Installing readline-8.2.1...
[main-armv7-default-job-12] `-- Extracting readline-8.2.1: .......... done
[main-armv7-default-job-12] Extracting python39-3.9.16_2: .......... done
=====
Message from python39-3.9.16_2:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
py39-gdbm databases/py-gdbm@py39
py39-sqlite3 databases/py-sqlite3@py39
py39-tkinter x11-toolkits/py-tkinter@py39
===> vcflib-1.0.7 depends on file: /usr/local/bin/python3.9 - found
===> Returning to build of vcflib-1.0.7
===========================================================================
=======================<phase: lib-depends >============================
===> vcflib-1.0.7 depends on shared library: libhts.so - not found
===> Installing existing package /packages/All/htslib-1.17.pkg
[main-armv7-default-job-12] Installing htslib-1.17...
[main-armv7-default-job-12] `-- Installing curl-8.1.2...
[main-armv7-default-job-12] | `-- Installing ca_root_nss-3.89.1...
[main-armv7-default-job-12] | `-- Extracting ca_root_nss-3.89.1: .......... done
[main-armv7-default-job-12] | `-- Installing libnghttp2-1.53.0...
[main-armv7-default-job-12] | `-- Extracting libnghttp2-1.53.0: .......... done
[main-armv7-default-job-12] | `-- Installing libpsl-0.21.2_3...
[main-armv7-default-job-12] | | `-- Installing libidn2-2.3.4...
[main-armv7-default-job-12] | | `-- Installing libunistring-1.1...
[main-armv7-default-job-12] | | `-- Extracting libunistring-1.1: .......... done
[main-armv7-default-job-12] | | `-- Extracting libidn2-2.3.4: .......... done
[main-armv7-default-job-12] | `-- Extracting libpsl-0.21.2_3: .......... done
[main-armv7-default-job-12] | `-- Installing libssh2-1.11.0,3...
[main-armv7-default-job-12] | `-- Extracting libssh2-1.11.0,3: .......... done
[main-armv7-default-job-12] `-- Extracting curl-8.1.2: .......... done
[main-armv7-default-job-12] `-- Installing libdeflate-1.18...
[main-armv7-default-job-12] `-- Extracting libdeflate-1.18: .......... done
[main-armv7-default-job-12] Extracting htslib-1.17: .......... done
=====
Message from ca_root_nss-3.89.1:
--
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-1.0.7 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of vcflib-1.0.7
===> vcflib-1.0.7 depends on shared library: libcurl.so - found (/usr/local/lib/libcurl.so)
===> vcflib-1.0.7 depends on shared library: libwfa2.so - not found
===> Installing existing package /packages/All/wfa2-lib-2.3.2_1.pkg
[main-armv7-default-job-12] Installing wfa2-lib-2.3.2_1...
[main-armv7-default-job-12] Extracting wfa2-lib-2.3.2_1: .......... done
===> vcflib-1.0.7 depends on shared library: libwfa2.so - found (/usr/local/lib/libwfa2.so)
===> Returning to build of vcflib-1.0.7
===========================================================================
=======================<phase: configure >============================
===> Configuring for vcflib-1.0.7
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/vcflib/work/.build
-- The C compiler identification is Clang 15.0.7
-- The CXX compiler identification is Clang 15.0.7
-- 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 "2.10.4")
-- 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 "5.4.3")
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.13")
-- Found CURL: /usr/local/lib/libcurl.so (found version "8.1.2")
--
-- Could NOT find OpenMP_C (missing: OpenMP_C_FLAGS OpenMP_C_LIB_NAMES)
-- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES)
-- Could NOT find OpenMP (missing: OpenMP_C_FOUND OpenMP_CXX_FOUND)
-- 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 - not found
-- Found Threads: TRUE
-- Checking for module 'htslib'
-- Found htslib, version 1.17
-- Checking for module 'tabixpp'
-- Package 'tabixpp', required by 'virtual:world', not found
-- WFA using include /usr/local/include/wfa2lib
Pandoc needs to be installed to generate the man pages
-- Configuring done (5.8s)
-- Generating done (0.6s)
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-1.0.7
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
/usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 -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/vcflib.dir/build.make CMakeFiles/vcflib.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-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7 /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build /wrkdirs/usr/ports/biology/vcflib/work/.build/CMakeFiles/vcflib.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/vcflib/work/.build'
gmake -f CMakeFiles/vcflib.dir/build.make CMakeFiles/vcflib.dir/build
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/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib NOTFOUND -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o -MF CMakeFiles/vcflib.dir/src/vcf-c-api.cpp.o.d -o CMakeFiles/vcflib.dir/sr
c/vcf-c-api.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/vcf-c-api.cpp
/usr/bin/c++ -DNO_ZIG=1 -DVCFLIB_VERSION=\"1.0.7\" -DVERSION=\"1.0.7\" -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/include -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/fastahack -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/intervaltree -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/smithwaterman -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/multichoose -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/filevercmp -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/c-progress-bar -I/wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/contrib/tabixpp -I/usr/local/include/wfa2lib NOTFOUND -D_FILE_OFFSET_BITS=64 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=gnu++14 -flto=thin -fPIC -MD -MT CMakeFiles/vcflib.dir/src/legacy.cpp.o -MF CMakeFiles/vcflib.dir/src/legacy.cpp.o.d -o CMakeFiles/vcflib.dir/src/lega
cy.cpp.o -c /wrkdirs/usr/ports/biology/vcflib/work/vcflib-1.0.7/src/legacy.cpp
c++: error: no such file or directory: 'NOTFOUND'
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===> 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/vcflib