[package - 131releng-armv7-default][biology/seqan-apps] Failed for seqan-apps-2.4.0_11 in configure
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Date: Tue, 02 May 2023 18:45:54 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: h2+fbsdports@fsfe.org
Log URL: https://pkg-status.freebsd.org/ampere3/data/131releng-armv7-default/8b8e64274fc0/logs/seqan-apps-2.4.0_11.log
Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=131releng-armv7-default&build=8b8e64274fc0
Log:
=>> Building biology/seqan-apps
build started at Tue May 2 18:45:36 UTC 2023
port directory: /usr/ports/biology/seqan-apps
package name: seqan-apps-2.4.0_11
building for: FreeBSD 131releng-armv7-default-job-03 13.1-RELEASE-p7 FreeBSD 13.1-RELEASE-p7 1301000 arm
maintained by: h2+fbsdports@fsfe.org
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---Begin OPTIONS List---
===> The following configuration options are available for seqan-apps-2.4.0_11:
====> Options available for the radio ARCH: you can only select none or one of them
SSE4=off: Use SSE4 and POPCNT instructions
AVX2=off: Use SSE4, AVX2 and POPCNT instructions
NATIVE=off: Use all available instruction sets (-march=native)
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
h2+fbsdports@fsfe.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DESTDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555
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PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan-apps DOCSDIR=/usr/local/share/doc/seqan-apps EXAMPLESDIR=/usr/local/share/examples/seqan-apps WWWDIR=/usr/local/www/seqan-apps ETCDIR=/usr/local/etc/seqan-apps
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=======================<phase: check-sanity >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[131releng-armv7-default-job-03] Installing pkg-1.19.1_1...
[131releng-armv7-default-job-03] Extracting pkg-1.19.1_1: .......... done
===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of seqan-apps-2.4.0_11
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user
===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building
===> Extracting for seqan-apps-2.4.0_11
=> SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for seqan-apps-2.4.0_11
===========================================================================
=======================<phase: build-depends >============================
===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - not found
===> Installing existing package /packages/All/boost-libs-1.81.0_1.pkg
[131releng-armv7-default-job-03] Installing boost-libs-1.81.0_1...
[131releng-armv7-default-job-03] `-- Installing icu-73.1,1...
[131releng-armv7-default-job-03] `-- Extracting icu-73.1,1: .......... done
[131releng-armv7-default-job-03] Extracting boost-libs-1.81.0_1: .......... done
=====
Message from boost-libs-1.81.0_1:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - found
===> Returning to build of seqan-apps-2.4.0_11
===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.26.1.pkg
[131releng-armv7-default-job-03] Installing cmake-core-3.26.1...
[131releng-armv7-default-job-03] `-- Installing expat-2.5.0...
[131releng-armv7-default-job-03] `-- Extracting expat-2.5.0: .......... done
[131releng-armv7-default-job-03] `-- Installing jsoncpp-1.9.5...
[131releng-armv7-default-job-03] `-- Extracting jsoncpp-1.9.5: .......... done
[131releng-armv7-default-job-03] `-- Installing libuv-1.44.2...
[131releng-armv7-default-job-03] `-- Extracting libuv-1.44.2: .......... done
[131releng-armv7-default-job-03] `-- Installing rhash-1.4.3...
[131releng-armv7-default-job-03] | `-- Installing gettext-runtime-0.21.1...
[131releng-armv7-default-job-03] | | `-- Installing indexinfo-0.3.1...
[131releng-armv7-default-job-03] | | `-- Extracting indexinfo-0.3.1: .... done
[131releng-armv7-default-job-03] | `-- Extracting gettext-runtime-0.21.1: .......... done
[131releng-armv7-default-job-03] `-- Extracting rhash-1.4.3: .......... done
[131releng-armv7-default-job-03] Extracting cmake-core-3.26.1: .......... done
===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/cmake - found
===> Returning to build of seqan-apps-2.4.0_11
===> seqan-apps-2.4.0_11 depends on executable: ninja - not found
===> Installing existing package /packages/All/ninja-1.11.1,2.pkg
[131releng-armv7-default-job-03] Installing ninja-1.11.1,2...
[131releng-armv7-default-job-03] `-- Installing python39-3.9.16_2...
[131releng-armv7-default-job-03] | `-- Installing libffi-3.4.4...
[131releng-armv7-default-job-03] | `-- Extracting libffi-3.4.4: .......... done
[131releng-armv7-default-job-03] | `-- Installing mpdecimal-2.5.1...
[131releng-armv7-default-job-03] | `-- Extracting mpdecimal-2.5.1: .......... done
[131releng-armv7-default-job-03] | `-- Installing readline-8.2.1...
[131releng-armv7-default-job-03] | `-- Extracting readline-8.2.1: .......... done
[131releng-armv7-default-job-03] `-- Extracting python39-3.9.16_2: .......... done
[131releng-armv7-default-job-03] Extracting ninja-1.11.1,2: ........ 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
===> seqan-apps-2.4.0_11 depends on executable: ninja - found
===> Returning to build of seqan-apps-2.4.0_11
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for seqan-apps-2.4.0_11
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build
CMake Warning (dev) at CMakeLists.txt:9 (project):
cmake_minimum_required() should be called prior to this top-level project()
call. Please see the cmake-commands(7) manual for usage documentation of
both commands.
This warning is for project developers. Use -Wno-dev to suppress it.
-- The CXX compiler identification is Clang 13.0.0
-- 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
-- Initializing SeqAn Build System...
-- Selected repository dir: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0
-- No revision system found.
-- Repository date not determined.
-- Repository revision not determined.
-- Configuring apps
-- Configuring apps/alf
-- Performing Test CXX14_BUILTIN
-- Performing Test CXX14_BUILTIN - Success
-- Looking for C++ include execinfo.h
-- Looking for C++ include execinfo.h - found
-- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0")
-- Configuring apps/bs_tools
-- Found ZLIB: /usr/lib/libz.so (found version "1.2.12")
-- Found Boost: /usr/local/include (found version "1.81.0")
-- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0")
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Configuring apps/dfi
-- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0")
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7")
-- Configuring apps/fiona
CMake Error at /usr/local/share/cmake/Modules/FindOpenMP.cmake:266 (try_compile):
The test project needs language C which is not enabled.
Call Stack (most recent call first):
/usr/local/share/cmake/Modules/FindOpenMP.cmake:534 (_OPENMP_GET_FLAGS)
apps/fiona/CMakeLists.txt:21 (find_package)
CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage
CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage
CMake Error at /usr/local/share/cmake/Modules/FindOpenMP.cmake:266 (try_compile):
Failed to configure test project build system.
Call Stack (most recent call first):
/usr/local/share/cmake/Modules/FindOpenMP.cmake:534 (_OPENMP_GET_FLAGS)
apps/fiona/CMakeLists.txt:21 (find_package)
-- Configuring incomplete, errors occurred!
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/seqan-apps