[package - 132arm64-quarterly][biology/seqwish] Failed for seqwish-0.7.9 in build
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Date: Thu, 01 Feb 2024 19:24:49 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/ampere1/data/132arm64-quarterly/68593b1d8800/logs/seqwish-0.7.9.log
Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=132arm64-quarterly&build=68593b1d8800
Log:
=>> Building biology/seqwish
build started at Thu Feb 1 19:22:56 UTC 2024
port directory: /usr/ports/biology/seqwish
package name: seqwish-0.7.9
building for: FreeBSD 132arm64-quarterly-job-10 13.2-RELEASE-p9 FreeBSD 13.2-RELEASE-p9 arm64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 839 Jan 16 01:02 /usr/ports/biology/seqwish/Makefile
Ports top last git commit: 68593b1d8
Ports top unclean checkout: no
Port dir last git commit: 72cbe1a32
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.1
Host OSVERSION: 1500006
Jail OSVERSION: 1302001
Job Id: 10
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PORT_FLAGS=
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---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
===> The following configuration options are available for seqwish-0.7.9:
OPENMP=on: Parallel processing support via OpenMP
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/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--
XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqwish/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqwish/work/.cache HOME=/wrkdirs/usr/ports/biology/seqwish/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqwish/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqwish/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 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 -fopenmp " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_
INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
CMAKE_BUILD_TYPE="release" OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqwish" EXAMPLESDIR="share/examples/seqwish" DATADIR="share/seqwish" WWWDIR="www/seqwish" ETCDIR="etc/seqwish"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqwish DOCSDIR=/usr/local/share/doc/seqwish EXAMPLESDIR=/usr/local/share/examples/seqwish WWWDIR=/usr/local/www/seqwish ETCDIR=/usr/local/etc/seqwish
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 1048576
stack size (kbytes, -s) 1048576
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
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kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> seqwish-0.7.9 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9.pkg
[132arm64-quarterly-job-10] Installing pkg-1.20.9...
[132arm64-quarterly-job-10] Extracting pkg-1.20.9: .......... done
===> seqwish-0.7.9 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of seqwish-0.7.9
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
=> SHA256 Checksum OK for seqwish-v0.7.9.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License MIT accepted by the user
===> Fetching all distfiles required by seqwish-0.7.9 for building
===> Extracting for seqwish-0.7.9
=> SHA256 Checksum OK for seqwish-v0.7.9.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for seqwish-0.7.9
===> Applying FreeBSD patches for seqwish-0.7.9 from /usr/ports/biology/seqwish/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> seqwish-0.7.9 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.28.1.pkg
[132arm64-quarterly-job-10] Installing cmake-core-3.28.1...
[132arm64-quarterly-job-10] `-- Installing expat-2.5.0...
[132arm64-quarterly-job-10] `-- Extracting expat-2.5.0: .......... done
[132arm64-quarterly-job-10] `-- Installing jsoncpp-1.9.5...
[132arm64-quarterly-job-10] `-- Extracting jsoncpp-1.9.5: .......... done
[132arm64-quarterly-job-10] `-- Installing libuv-1.47.0...
[132arm64-quarterly-job-10] `-- Extracting libuv-1.47.0: .......... done
[132arm64-quarterly-job-10] `-- Installing rhash-1.4.4...
[132arm64-quarterly-job-10] | `-- Installing gettext-runtime-0.22.3...
[132arm64-quarterly-job-10] | | `-- Installing indexinfo-0.3.1...
[132arm64-quarterly-job-10] | | `-- Extracting indexinfo-0.3.1: .... done
[132arm64-quarterly-job-10] | `-- Extracting gettext-runtime-0.22.3: .......... done
[132arm64-quarterly-job-10] `-- Extracting rhash-1.4.4: .......... done
[132arm64-quarterly-job-10] Extracting cmake-core-3.28.1: .......... done
===> seqwish-0.7.9 depends on file: /usr/local/bin/cmake - found
===> Returning to build of seqwish-0.7.9
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: configure >============================
<snip>
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Performing Test HAVE_INLINE
-- Performing Test HAVE_INLINE - Success
-- Performing Test HAVE___INLINE
-- Performing Test HAVE___INLINE - Success
-- Performing Test HAVE___INLINE__
-- Performing Test HAVE___INLINE__ - Success
-- Performing Test HAVE___DECLSPEC_DLLEXPORT_
-- Performing Test HAVE___DECLSPEC_DLLEXPORT_ - Failed
-- Performing Test HAVE___DECLSPEC_DLLIMPORT_
-- Performing Test HAVE___DECLSPEC_DLLIMPORT_ - Failed
-- Check size of uint8_t
-- Check size of uint8_t - done
-- Check size of int32_t
-- Check size of int32_t - done
-- Looking for PRId32
-- Looking for PRId32 - found
-- Check size of int64_t
-- Check size of int64_t - done
-- Looking for PRId64
-- Looking for PRId64 - found
CMake Warning (dev) at external/googletest/googletest/CMakeLists.txt:47 (project):
Policy CMP0048 is not set: project() command manages VERSION variables.
Run "cmake --help-policy CMP0048" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
The following variable(s) would be set to empty:
PROJECT_VERSION
PROJECT_VERSION_MAJOR
PROJECT_VERSION_MINOR
PROJECT_VERSION_PATCH
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Deprecation Warning at external/googletest/googletest/CMakeLists.txt:48 (cmake_minimum_required):
Compatibility with CMake < 3.5 will be removed from a future version of
CMake.
Update the VERSION argument <min> value or use a ...<max> suffix to tell
CMake that the project does not need compatibility with older versions.
CMake Warning (dev) at external/googletest/googletest/cmake/internal_utils.cmake:211 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed. Run "cmake --help-policy CMP0148" for policy details. Use
the cmake_policy command to set the policy and suppress this warning.
Call Stack (most recent call first):
external/googletest/googletest/CMakeLists.txt:60 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE)
-- 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
-- Looking for C++ include cstdio
-- Looking for C++ include cstdio - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Configuring done (22.5s)
-- Generating done (0.5s)
-- Build files have been written to: /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-configure
--- sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-build ---
[ 80%] Performing build step for 'sdsl-lite'
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/bin/make
[ 0%] Building C object external/libdivsufsort/lib/CMakeFiles/divsufsort.dir/divsufsort.o
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[ 10%] Building C object external/libdivsufsort/lib/CMakeFiles/divsufsort64.dir/sssort.o
[ 10%] Building C object external/libdivsufsort/lib/CMakeFiles/divsufsort.dir/sssort.o
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[ 20%] Building C object external/libdivsufsort/lib/CMakeFiles/divsufsort.dir/trsort.o
[ 20%] Building C object external/libdivsufsort/lib/CMakeFiles/divsufsort.dir/utils.o
[ 20%] Building C object external/libdivsufsort/lib/CMakeFiles/divsufsort64.dir/utils.o
[ 20%] Linking C static library libdivsufsort.a
[ 20%] Linking C static library libdivsufsort64.a
[ 20%] Built target divsufsort64
[ 20%] Built target divsufsort
[ 20%] Building CXX object lib/CMakeFiles/sdsl.dir/bits.cpp.o
[ 20%] Building CXX object lib/CMakeFiles/sdsl.dir/bp_support_algorithm.cpp.o
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[ 30%] Building CXX object lib/CMakeFiles/sdsl.dir/coder_fibonacci.cpp.o
[ 30%] Building CXX object lib/CMakeFiles/sdsl.dir/config.cpp.o
[ 30%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_config.cpp.o
[ 40%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_isa.cpp.o
[ 40%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp.cpp.o
[ 40%] Linking CXX static library libgtest.a
[ 40%] Built target gtest
[ 40%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_lcp_helper.cpp.o
In file included from /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/sdsl-lite/lib/construct_lcp.cpp:6:
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/lib/../include/sdsl/construct_lcp.hpp:130:53: warning: instantiation of variable 'sdsl::key_text_trait<'\b'>::KEY_TEXT' required here, but no definition is available [-Wundefined-var-template]
const char* KEY_TEXT = key_text_trait<t_width>::KEY_TEXT;
^
/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/sdsl-lite/lib/construct_lcp.cpp:209:25: note: in instantiation of function template specialization 'sdsl::construct_lcp_PHI<(unsigned char)'\b'>' requested here
construct_lcp_PHI<8>(config);
^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/lib/../include/sdsl/config.hpp:51:24: note: forward declaration of template entity is here
static const char* KEY_TEXT;
^
/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/lib/../include/sdsl/construct_lcp.hpp:130:53: note: add an explicit instantiation declaration to suppress this warning if 'sdsl::key_text_trait<'\b'>::KEY_TEXT' is explicitly instantiated in another translation unit
const char* KEY_TEXT = key_text_trait<t_width>::KEY_TEXT;
^
[ 40%] Building CXX object external/googletest/googletest/CMakeFiles/gtest_main.dir/src/gtest_main.cc.o
[ 50%] Linking CXX static library libgtest_main.a
[ 50%] Built target gtest_main
[ 50%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa.cpp.o
[ 60%] Building CXX object lib/CMakeFiles/sdsl.dir/construct_sa_se.cpp.o
1 warning generated.
[ 60%] Building CXX object lib/CMakeFiles/sdsl.dir/csa_alphabet_strategy.cpp.o
[ 60%] Building CXX object lib/CMakeFiles/sdsl.dir/io.cpp.o
[ 60%] Building CXX object lib/CMakeFiles/sdsl.dir/lcp_support_tree.cpp.o
[ 70%] Building CXX object lib/CMakeFiles/sdsl.dir/louds_tree.cpp.o
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[ 80%] Building CXX object lib/CMakeFiles/sdsl.dir/sfstream.cpp.o
[ 90%] Building CXX object lib/CMakeFiles/sdsl.dir/structure_tree.cpp.o
[ 90%] Building CXX object lib/CMakeFiles/sdsl.dir/uint128_t.cpp.o
[ 90%] Building CXX object lib/CMakeFiles/sdsl.dir/uint256_t.cpp.o
[ 90%] Building CXX object lib/CMakeFiles/sdsl.dir/util.cpp.o
[100%] Building CXX object lib/CMakeFiles/sdsl.dir/wt_helper.cpp.o
[100%] Linking CXX static library libsdsl.a
[100%] Built target sdsl
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-build
--- sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-install ---
[ 81%] No install step for 'sdsl-lite'
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/local/bin/cmake -E echo_append
cd /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build && /usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-install
--- CMakeFiles/sdsl-lite-complete ---
[ 82%] Completed 'sdsl-lite'
/usr/local/bin/cmake -E make_directory /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/sdsl-lite-complete
/usr/local/bin/cmake -E touch /wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-stamp/sdsl-lite-done
[ 82%] Built target sdsl-lite
--- CMakeFiles/seqwish.dir/all ---
/usr/bin/make -f CMakeFiles/seqwish.dir/build.make CMakeFiles/seqwish.dir/depend
--- CMakeFiles/seqwish.dir/depend ---
cd /wrkdirs/usr/ports/biology/seqwish/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9 /wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9 /wrkdirs/usr/ports/biology/seqwish/work/.build /wrkdirs/usr/ports/biology/seqwish/work/.build /wrkdirs/usr/ports/biology/seqwish/work/.build/CMakeFiles/seqwish.dir/DependInfo.cmake
/usr/bin/make -f CMakeFiles/seqwish.dir/build.make CMakeFiles/seqwish.dir/build
--- CMakeFiles/seqwish.dir/src/utils.cpp.o ---
--- CMakeFiles/seqwish.dir/src/tempfile.cpp.o ---
--- CMakeFiles/seqwish.dir/src/main.cpp.o ---
--- CMakeFiles/seqwish.dir/src/utils.cpp.o ---
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/usr/bin/c++ -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9 -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/include -I/wrkdirs/usr/ports/biology/seqwish/work/.build/sdsl-lite-prefix/src/sdsl-lite-build/external/libdivsufsort/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/args -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/gzip_reader -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/ips4o -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/mmmulti/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/iitii/src -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/BBHash -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomicbitvector/include -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/atomic_queue/include/atomic_queue -I/wrkdirs/usr/ports/biology/seqwish/work/seqwish-v0.7.9/deps/flat_hash_map -I/wrkdirs/usr/ports/biol
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