[package - 132releng-armv7-default][biology/mashmap] Failed for mashmap-3.1.1 in build
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Date: Fri, 27 Oct 2023 19:33:36 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/ampere3/data/132releng-armv7-default/08943441f26e/logs/mashmap-3.1.1.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=132releng-armv7-default&build=08943441f26e
Log:
=>> Building biology/mashmap
build started at Fri Oct 27 19:33:18 UTC 2023
port directory: /usr/ports/biology/mashmap
package name: mashmap-3.1.1
building for: FreeBSD 132releng-armv7-default-job-08 13.2-RELEASE-p4 FreeBSD 13.2-RELEASE-p4 1302001 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
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---Begin OPTIONS List---
===> The following configuration options are available for mashmap-3.1.1:
NATIVE=off: Use native optimization (-march=native)
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
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--End CONFIGURE_ARGS--
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=======================<phase: check-sanity >============================
===> License PD accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> mashmap-3.1.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.7.pkg
[132releng-armv7-default-job-08] Installing pkg-1.20.7...
[132releng-armv7-default-job-08] Extracting pkg-1.20.7: .......... done
===> mashmap-3.1.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of mashmap-3.1.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License PD accepted by the user
===> Fetching all distfiles required by mashmap-3.1.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License PD accepted by the user
===> Fetching all distfiles required by mashmap-3.1.1 for building
=> SHA256 Checksum OK for marbl-MashMap-v3.1.1_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License PD accepted by the user
===> Fetching all distfiles required by mashmap-3.1.1 for building
===> Extracting for mashmap-3.1.1
=> SHA256 Checksum OK for marbl-MashMap-v3.1.1_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for mashmap-3.1.1
===========================================================================
=======================<phase: build-depends >============================
===> mashmap-3.1.1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.26.1_3.pkg
[132releng-armv7-default-job-08] Installing cmake-core-3.26.1_3...
[132releng-armv7-default-job-08] `-- Installing expat-2.5.0...
[132releng-armv7-default-job-08] `-- Extracting expat-2.5.0: .......... done
[132releng-armv7-default-job-08] `-- Installing jsoncpp-1.9.5...
[132releng-armv7-default-job-08] `-- Extracting jsoncpp-1.9.5: .......... done
[132releng-armv7-default-job-08] `-- Installing libuv-1.46.0...
[132releng-armv7-default-job-08] `-- Extracting libuv-1.46.0: .......... done
[132releng-armv7-default-job-08] `-- Installing rhash-1.4.4...
[132releng-armv7-default-job-08] | `-- Installing gettext-runtime-0.22_1...
[132releng-armv7-default-job-08] | | `-- Installing indexinfo-0.3.1...
[132releng-armv7-default-job-08] | | `-- Extracting indexinfo-0.3.1: .... done
[132releng-armv7-default-job-08] | `-- Extracting gettext-runtime-0.22_1: .......... done
[132releng-armv7-default-job-08] `-- Extracting rhash-1.4.4: .......... done
[132releng-armv7-default-job-08] Extracting cmake-core-3.26.1_3: .......... done
===> mashmap-3.1.1 depends on file: /usr/local/bin/cmake - found
===> Returning to build of mashmap-3.1.1
===> mashmap-3.1.1 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.11.1,2.pkg
[132releng-armv7-default-job-08] Installing ninja-1.11.1,2...
[132releng-armv7-default-job-08] `-- Installing python39-3.9.18...
[132releng-armv7-default-job-08] | `-- Installing libffi-3.4.4...
[132releng-armv7-default-job-08] | `-- Extracting libffi-3.4.4: .......... done
[132releng-armv7-default-job-08] | `-- Installing mpdecimal-2.5.1...
[132releng-armv7-default-job-08] | `-- Extracting mpdecimal-2.5.1: .......... done
[132releng-armv7-default-job-08] | `-- Installing readline-8.2.1...
[132releng-armv7-default-job-08] | `-- Extracting readline-8.2.1: .......... done
[132releng-armv7-default-job-08] `-- Extracting python39-3.9.18: .......... done
[132releng-armv7-default-job-08] Extracting ninja-1.11.1,2: ........ done
=====
Message from python39-3.9.18:
--
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
===> mashmap-3.1.1 depends on executable: ninja - found
===> Returning to build of mashmap-3.1.1
===========================================================================
=======================<phase: lib-depends >============================
===> mashmap-3.1.1 depends on shared library: libgsl.so - not found
===> Installing existing package /packages/All/gsl-2.7.1.pkg
[132releng-armv7-default-job-08] Installing gsl-2.7.1...
[132releng-armv7-default-job-08] Extracting gsl-2.7.1: .......... done
===> mashmap-3.1.1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so)
===> Returning to build of mashmap-3.1.1
===> mashmap-3.1.1 depends on shared library: libhts.so - not found
===> Installing existing package /packages/All/htslib-1.17.pkg
[132releng-armv7-default-job-08] Installing htslib-1.17...
[132releng-armv7-default-job-08] `-- Installing curl-8.3.0_1...
[132releng-armv7-default-job-08] | `-- Installing libnghttp2-1.56.0...
[132releng-armv7-default-job-08] | `-- Extracting libnghttp2-1.56.0: .......... done
[132releng-armv7-default-job-08] | `-- Installing libpsl-0.21.2_3...
[132releng-armv7-default-job-08] | | `-- Installing libidn2-2.3.4...
[132releng-armv7-default-job-08] | | `-- Installing libunistring-1.1...
[132releng-armv7-default-job-08] | | `-- Extracting libunistring-1.1: .......... done
[132releng-armv7-default-job-08] | | `-- Extracting libidn2-2.3.4: .......... done
[132releng-armv7-default-job-08] | `-- Extracting libpsl-0.21.2_3: .......... done
[132releng-armv7-default-job-08] | `-- Installing libssh2-1.11.0,3...
[132releng-armv7-default-job-08] | `-- Extracting libssh2-1.11.0,3: .......... done
[132releng-armv7-default-job-08] `-- Extracting curl-8.3.0_1: .......... done
[132releng-armv7-default-job-08] `-- Installing libdeflate-1.19...
[132releng-armv7-default-job-08] `-- Extracting libdeflate-1.19: .......... done
[132releng-armv7-default-job-08] Extracting htslib-1.17: .......... done
===> mashmap-3.1.1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so)
===> Returning to build of mashmap-3.1.1
===========================================================================
=======================<phase: configure >============================
===> Configuring for mashmap-3.1.1
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/mashmap/work/.build
-- The C compiler identification is Clang 14.0.5
-- The CXX compiler identification is Clang 14.0.5
-- 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
-- CMAKE_BUILD_TYPE: Release
-- Configuring done (0.9s)
-- Generating done (0.0s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_COLOR_MAKEFILE
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
CMAKE_SHARED_LINKER_FLAGS
CMAKE_VERBOSE_MAKEFILE
FETCHCONTENT_FULLY_DISCONNECTED
THREADS_HAVE_PTHREAD_ARG
-- Build files have been written to: /wrkdirs/usr/ports/biology/mashmap/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for mashmap-3.1.1
[ 16% 3/6] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o -MF CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/common/utils.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common/utils.cpp
[ 33% 4/6] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/common/utils.cpp.o -MF CMakeFiles/mashmap.dir/src/common/utils.cpp.o.d -o CMakeFiles/mashmap.dir/src/common/utils.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common/utils.cpp
[ 50% 4/6] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -MF CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o.d -o CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/mash_map.cpp
FAILED: CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o
/usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -MF CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o.d -o CMakeFiles/mashmap.dir/src/map/mash_map.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/mash_map.cpp
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/mash_map.cpp:13:
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/include/map_parameters.hpp:14:
/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common/ALeS.hpp:294:11: fatal error: unknown type name '__uint128_t'
typedef __uint128_t uint128_t;
^
1 error generated.
[ 66% 4/6] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -MF CMakeFiles/mashmap-align.dir/src/align/align.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/align/align.cpp
FAILED: CMakeFiles/mashmap-align.dir/src/align/align.cpp.o
/usr/bin/c++ -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src -I/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -DNDEBUG -std=c++17 -Wfatal-errors -MD -MT CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -MF CMakeFiles/mashmap-align.dir/src/align/align.cpp.o.d -o CMakeFiles/mashmap-align.dir/src/align/align.cpp.o -c /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/align/align.cpp
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/align/align.cpp:18:
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/align/include/parseCmdArgs.hpp:16:
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/include/parseCmdArgs.hpp:16:
In file included from /wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/map/include/map_parameters.hpp:14:
/wrkdirs/usr/ports/biology/mashmap/work/MashMap-3.1.1/src/common/ALeS.hpp:294:11: fatal error: unknown type name '__uint128_t'
typedef __uint128_t uint128_t;
^
1 error generated.
ninja: build stopped: subcommand failed.
===> 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/mashmap