[package - main-armv7-default][biology/kallisto] Failed for kallisto-0.50.0,1 in build
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Date: Wed, 19 Jul 2023 20:15:54 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/p8fb94260154e_s7cd7a32041/logs/kallisto-0.50.0,1.log
Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p8fb94260154e_s7cd7a32041
Log:
=>> Building biology/kallisto
build started at Wed Jul 19 20:15:40 UTC 2023
port directory: /usr/ports/biology/kallisto
package name: kallisto-0.50.0,1
building for: FreeBSD main-armv7-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm
maintained by: jwb@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400093
Job Id: 06
!!! Jail is newer than host. (Jail: 1400093, 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 kallisto-0.50.0,1:
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===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
jwb@FreeBSD.org
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--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
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--PLIST_SUB--
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--End PLIST_SUB--
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PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/kallisto DOCSDIR=/usr/local/share/doc/kallisto EXAMPLESDIR=/usr/local/share/examples/kallisto WWWDIR=/usr/local/www/kallisto ETCDIR=/usr/local/etc/kallisto
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=======================<phase: check-sanity >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> kallisto-0.50.0,1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.4.pkg
[main-armv7-default-job-06] Installing pkg-1.20.4...
[main-armv7-default-job-06] Extracting pkg-1.20.4: .......... done
===> kallisto-0.50.0,1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of kallisto-0.50.0,1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
=> SHA256 Checksum OK for pachterlab-kallisto-v0.50.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by kallisto-0.50.0,1 for building
===> Extracting for kallisto-0.50.0,1
=> SHA256 Checksum OK for pachterlab-kallisto-v0.50.0_GH0.tar.gz.
/bin/rm -f -rf /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/htslib
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for kallisto-0.50.0,1
===> Applying FreeBSD patches for kallisto-0.50.0,1 from /usr/ports/biology/kallisto/files
===========================================================================
=======================<phase: build-depends >============================
===> kallisto-0.50.0,1 depends on file: /usr/local/bin/cmake - not found
<snip>
[main-armv7-default-job-06] | `-- Installing binutils-2.40_4,1...
[main-armv7-default-job-06] | | `-- Installing zstd-1.5.5...
[main-armv7-default-job-06] | | `-- Installing liblz4-1.9.4,1...
[main-armv7-default-job-06] | | `-- Extracting liblz4-1.9.4,1: .......... done
[main-armv7-default-job-06] | | `-- Extracting zstd-1.5.5: .......... done
[main-armv7-default-job-06] | `-- Extracting binutils-2.40_4,1: .......... done
[main-armv7-default-job-06] | `-- Installing gmp-6.2.1...
[main-armv7-default-job-06] | `-- Extracting gmp-6.2.1: .......... done
[main-armv7-default-job-06] | `-- Installing mpc-1.3.1_1...
[main-armv7-default-job-06] | | `-- Installing mpfr-4.2.0_1,1...
[main-armv7-default-job-06] | | `-- Extracting mpfr-4.2.0_1,1: .......... done
[main-armv7-default-job-06] | `-- Extracting mpc-1.3.1_1: ......... done
[main-armv7-default-job-06] `-- Extracting gcc12-12.2.0_6: .......... done
[main-armv7-default-job-06] `-- Installing libaec-1.0.6...
[main-armv7-default-job-06] `-- Extracting libaec-1.0.6: .......... done
[main-armv7-default-job-06] Extracting hdf5-1.12.2_2,1: .......... done
=====
Message from gcc12-12.2.0_6:
--
To ensure binaries built with this toolchain find appropriate versions
of the necessary run-time libraries, you may want to link using
-Wl,-rpath=/usr/local/lib/gcc12
For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens
transparently.
===> kallisto-0.50.0,1 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so)
===> Returning to build of kallisto-0.50.0,1
===> kallisto-0.50.0,1 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so)
===> kallisto-0.50.0,1 depends on shared library: libhts.so - not found
===> Installing existing package /packages/All/htslib-1.17.pkg
[main-armv7-default-job-06] Installing htslib-1.17...
[main-armv7-default-job-06] `-- Installing curl-8.1.2...
[main-armv7-default-job-06] | `-- Installing ca_root_nss-3.91...
[main-armv7-default-job-06] | `-- Extracting ca_root_nss-3.91: .......... done
[main-armv7-default-job-06] | `-- Installing libnghttp2-1.54.0...
[main-armv7-default-job-06] | `-- Extracting libnghttp2-1.54.0: .......... done
[main-armv7-default-job-06] | `-- Installing libpsl-0.21.2_3...
[main-armv7-default-job-06] | | `-- Installing libidn2-2.3.4...
[main-armv7-default-job-06] | | `-- Installing libunistring-1.1...
[main-armv7-default-job-06] | | `-- Extracting libunistring-1.1: .......... done
[main-armv7-default-job-06] | | `-- Extracting libidn2-2.3.4: .......... done
[main-armv7-default-job-06] | `-- Extracting libpsl-0.21.2_3: .......... done
[main-armv7-default-job-06] | `-- Installing libssh2-1.11.0,3...
[main-armv7-default-job-06] | `-- Extracting libssh2-1.11.0,3: .......... done
[main-armv7-default-job-06] `-- Extracting curl-8.1.2: .......... done
[main-armv7-default-job-06] `-- Installing libdeflate-1.18...
[main-armv7-default-job-06] `-- Extracting libdeflate-1.18: .......... done
[main-armv7-default-job-06] Extracting htslib-1.17: .......... done
=====
Message from ca_root_nss-3.91:
--
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
===> kallisto-0.50.0,1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of kallisto-0.50.0,1
===========================================================================
=======================<phase: configure >============================
===> Configuring for kallisto-0.50.0,1
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/kallisto/work/.build
-- The C compiler identification is Clang 16.0.6
-- The CXX compiler identification is Clang 16.0.6
-- 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
-- Performing Test COMPILER_SUPPORTS_CXX17
-- Performing Test COMPILER_SUPPORTS_CXX17 - Success
shared build
-- 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
-- Found HDF5: hdf5-shared (found version "1.12.2")
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.13")
-- Configuring done (2.4s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_CXX_FLAGS_DEBUG
CMAKE_C_FLAGS_DEBUG
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for kallisto-0.50.0,1
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
/usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0 -B/wrkdirs/usr/ports/biology/kallisto/work/.build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/kallisto/work/.build//CMakeFiles/progress.marks
gmake -f CMakeFiles/Makefile2 all
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/depend
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
cd /wrkdirs/usr/ports/biology/kallisto/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0 /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles/bifrost.dir/DependInfo.cmake
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake -f CMakeFiles/bifrost.dir/build.make CMakeFiles/bifrost.dir/build
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
[ 3%] Creating directories for 'bifrost'
/usr/local/bin/cmake -Dcfgdir= -P /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/tmp/bifrost-mkdirs.cmake
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-mkdir
[ 7%] No download step for 'bifrost'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-download
[ 11%] No update step for 'bifrost'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-update
[ 15%] No patch step for 'bifrost'
/usr/local/bin/cmake -E echo_append
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-patch
[ 19%] Performing configure step for 'bifrost'
cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost && mkdir -p build && cd build && cmake .. -DCMAKE_INSTALL_PREFIX= "-DCMAKE_CXX_FLAGS=-Wno-subobject-linkage -Wno-return-type"
-- The C compiler identification is Clang 16.0.6
-- The CXX compiler identification is Clang 16.0.6
-- 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
-- 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
Compilation architecture: native
Build type: Release
Maximum k-mer size: 31
Maximum g-mer size: 31
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.13")
-- Configuring done (2.0s)
-- Generating done (0.0s)
-- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build
cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-configure
[ 23%] Performing build step for 'bifrost'
cd /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost && cd build && gmake
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[6]: Entering directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
[ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o
c++: error: unsupported argument 'native' to option '-march='
gmake[6]: *** [src/CMakeFiles/bifrost_static.dir/build.make:76: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[5]: *** [CMakeFiles/Makefile2:102: src/CMakeFiles/bifrost_static.dir/all] Error 2
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[4]: *** [Makefile:136: all] Error 2
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/build'
gmake[3]: *** [CMakeFiles/bifrost.dir/build.make:89: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.50.0/ext/bifrost/src/bifrost-stamp/bifrost-build] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake[2]: *** [CMakeFiles/Makefile2:105: CMakeFiles/bifrost.dir/all] Error 2
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
gmake[1]: *** [Makefile:139: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/kallisto/work/.build'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/kallisto