[package - main-i386-default][biology/btllib] Failed for btllib-1.7.0 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Wed, 10 Jan 2024 06:11:47 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/beefy17/data/main-i386-default/pbc67f159e5b6_sdf8a58b17a/logs/btllib-1.7.0.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=pbc67f159e5b6_sdf8a58b17a
Log:
=>> Building biology/btllib
build started at Wed Jan 10 06:11:21 UTC 2024
port directory: /usr/ports/biology/btllib
package name: btllib-1.7.0
building for: FreeBSD main-i386-default-job-04 15.0-CURRENT FreeBSD 15.0-CURRENT 1500008 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 854 Dec 14 01:01 /usr/ports/biology/btllib/Makefile
Ports top last git commit: bc67f159e5b
Ports top unclean checkout: no
Port dir last git commit: e8a2beffcfe
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.0
Host OSVERSION: 1500006
Jail OSVERSION: 1500008
Job Id: 04
!!! Jail is newer than host. (Jail: 1500008, Host: 1500006) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
OSVERSION=1500008
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
UNAME_m=i386
UNAME_p=i386
UNAME_r=15.0-CURRENT
LOCALBASE=/usr/local
UNAME_v=FreeBSD 15.0-CURRENT 1500008
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.0
MASTERMNT=/usr/local/poudriere/data/.m/main-i386-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-i386-default/04/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.0
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--prefix /usr/local --mandir man --infodir share/info --auto-features=enabled -Dpython.bytecompile=-1 -Db_colorout=never --buildtype release --optimization plain --strip _build
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/btllib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/btllib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/btllib/work/.cache HOME=/wrkdirs/usr/ports/biology/btllib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/btllib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/btllib/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8
--End CONFIGURE_ENV--
--MAKE_ENV--
NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/btllib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/btllib/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/btllib/work/.cache HOME=/wrkdirs/usr/ports/biology/btllib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/btllib/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/btllib/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/btllib/work/stage LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 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="i
nstall -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--
PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/btllib" EXAMPLESDIR="share/examples/btllib" DATADIR="share/btllib" WWWDIR="www/btllib" ETCDIR="etc/btllib"
--End PLIST_SUB--
--SUB_LIST--
PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd15 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/btllib DOCSDIR=/usr/local/share/doc/btllib EXAMPLESDIR=/usr/local/share/examples/btllib WWWDIR=/usr/local/www/btllib ETCDIR=/usr/local/etc/btllib
--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
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### ####
# 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) 524288
stack size (kbytes, -s) 65536
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
pseudo-terminals (-p) unlimited
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 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> btllib-1.7.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.9.pkg
[main-i386-default-job-04] Installing pkg-1.20.9...
[main-i386-default-job-04] Extracting pkg-1.20.9: .......... done
===> btllib-1.7.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of btllib-1.7.0
===========================================================================
=======================<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 GPLv3 accepted by the user
===> Fetching all distfiles required by btllib-1.7.0 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License GPLv3 accepted by the user
===> Fetching all distfiles required by btllib-1.7.0 for building
=> SHA256 Checksum OK for bcgsc-btllib-v1.7.0_GH0.tar.gz.
=> SHA256 Checksum OK for p-ranav-argparse-15d745f_GH0.tar.gz.
=> SHA256 Checksum OK for skystrife-cpptoml-fededad_GH0.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 GPLv3 accepted by the user
===> Fetching all distfiles required by btllib-1.7.0 for building
===> Extracting for btllib-1.7.0
=> SHA256 Checksum OK for bcgsc-btllib-v1.7.0_GH0.tar.gz.
=> SHA256 Checksum OK for p-ranav-argparse-15d745f_GH0.tar.gz.
=> SHA256 Checksum OK for skystrife-cpptoml-fededad_GH0.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 btllib-1.7.0
===> Applying FreeBSD patches for btllib-1.7.0 from /usr/ports/biology/btllib/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> btllib-1.7.0 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.2.21.pkg
[main-i386-default-job-04] Installing bash-5.2.21...
[main-i386-default-job-04] `-- Installing gettext-runtime-0.22.3...
[main-i386-default-job-04] | `-- Installing indexinfo-0.3.1...
[main-i386-default-job-04] | `-- Extracting indexinfo-0.3.1: .... done
[main-i386-default-job-04] `-- Extracting gettext-runtime-0.22.3: .......... done
<snip>
Host machine cpu: i386
Configuring config.hpp using configuration
Run-time dependency threads found: YES
Run-time dependency OpenMP found: YES 5.1
Executing subproject cpptoml method cmake
cpptoml| Found CMake: /usr/local/bin/cmake (3.28.1)
| Configuring the build directory with CMake version 3.28.1
| Running CMake with: -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local
| - build directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/_build/subprojects/cpptoml/__CMake_build
| - source directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/subprojects/cpptoml
| - toolchain file: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/_build/subprojects/cpptoml/__CMake_build/CMakeMesonToolchainFile.cmake
| - preload file: /usr/local/lib/python3.9/site-packages/mesonbuild/cmake/data/preload.cmake
| - trace args: --trace-expand --trace-format=json-v1 --no-warn-unused-cli --trace-redirect=cmake_trace.txt
| - disabled policy warnings: [CMP0025, CMP0047, CMP0056, CMP0060, CMP0065, CMP0066, CMP0067, CMP0082, CMP0089, CMP0102]
| CMake Deprecation Warning at CMakeLists.txt:1 (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.
| Put cmake in trace mode, but with variables expanded.
| Put cmake in trace mode and sets the trace output format.
| Not searching for unused variables given on the command line.
| Put cmake in trace mode and redirect trace output to a file instead of stderr.
| Trace will be written to cmake_trace.txt
| -- The C compiler identification is Clang 17.0.6
| -- The CXX compiler identification is Clang 17.0.6
| CMake Warning (dev) at /usr/local/share/cmake/Modules/CMakeFindBinUtils.cmake:224 (find_program):
| Policy CMP0126 is not set: set(CACHE) does not remove a normal variable of
| the same name. Run "cmake --help-policy CMP0126" for policy details. Use
| the cmake_policy command to set the policy and suppress this warning.
| For compatibility with older versions of CMake, normal variable
| "CMAKE_TAPI" will be removed from the current scope.
| Call Stack (most recent call first):
| /usr/local/share/cmake/Modules/CMakeDetermineCXXCompiler.cmake:202 (include)
| CMakeLists.txt:2 (project)
| This warning is for project developers. Use -Wno-dev to suppress it.
| -- 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
| -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
| -- Configuring done (1.2s)
| -- Generating done (0.0s)
| -- Build files have been written to: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/_build/subprojects/cpptoml/__CMake_build
cpptoml| CMake configuration: SUCCEEDED
cpptoml| CMake project cpptoml has 1 build targets.
cpptoml| Generated Meson AST: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/_build/subprojects/cpptoml/meson.build
cpptoml| Project name: cpptoml
cpptoml| Project version: undefined
cpptoml| Build targets in project: 0
cpptoml| Subproject cpptoml finished.
Found pkg-config: YES (/usr/local/bin/pkgconf) 2.0.3
Run-time dependency sdsl-lite found: YES 2.1.0
Executing subproject argparse method cmake
| Configuring the build directory with CMake version 3.28.1
| Running CMake with: -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local
| - build directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/_build/subprojects/argparse/__CMake_build
| - source directory: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/subprojects/argparse
| - toolchain file: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/_build/subprojects/argparse/__CMake_build/CMakeMesonToolchainFile.cmake
| - preload file: /usr/local/lib/python3.9/site-packages/mesonbuild/cmake/data/preload.cmake
| - trace args: --trace-expand --trace-format=json-v1 --no-warn-unused-cli --trace-redirect=cmake_trace.txt
| - disabled policy warnings: [CMP0025, CMP0047, CMP0056, CMP0060, CMP0065, CMP0066, CMP0067, CMP0082, CMP0089, CMP0102]
| Put cmake in trace mode, but with variables expanded.
| Put cmake in trace mode and sets the trace output format.
| Not searching for unused variables given on the command line.
| Put cmake in trace mode and redirect trace output to a file instead of stderr.
| Trace will be written to cmake_trace.txt
| -- The CXX compiler identification is Clang 17.0.6
| -- 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
| -- Configuring done (0.8s)
| -- Generating done (0.0s)
| -- Build files have been written to: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/_build/subprojects/argparse/__CMake_build
argparse| CMake configuration: SUCCEEDED
argparse| CMake project argparse has 1 build targets.
argparse| Generated Meson AST: /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/_build/subprojects/argparse/meson.build
argparse| Project name: argparse
argparse| Project version: undefined
argparse| Build targets in project: 0
argparse| Subproject argparse finished.
Program samtools found: YES (/usr/local/bin/samtools)
Program gzip found: YES (/usr/bin/gzip)
Program xz found: YES (/usr/bin/xz)
Program bzip2 found: YES (/usr/bin/bzip2)
Program tar found: YES (/usr/bin/tar)
Program gcovr found: NO
Program swig found: NO
Program doxygen found: NO
WARNING: You should add the boolean check kwarg to the run_command call.
It currently defaults to false,
but it will default to true in future releases of meson.
See also: https://github.com/mesonbuild/meson/issues/9300
Program python3 found: YES (/wrkdirs/usr/ports/biology/btllib/work/.bin/python3)
Program python3-config found: NO
Message: python3-config not found, skipping Python wrappers.
Build targets in project: 11
btllib 1.7.0
Subprojects
argparse : YES
cpptoml : YES
User defined options
auto_features : enabled
buildtype : release
infodir : share/info
mandir : man
optimization : plain
prefix : /usr/local
strip : true
python.bytecompile: -1
b_colorout : never
Found ninja-1.11.1 at /usr/local/bin/ninja
WARNING: Need gcovr or lcov/genhtml to generate any coverage reports
WARNING: Running the setup command as `meson [options]` instead of `meson setup [options]` is ambiguous and deprecated.
===========================================================================
=======================<phase: build >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Building for btllib-1.7.0
[ 4% 3/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_fasta_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_fasta_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_fasta_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/seq_reader_fasta_module.cpp
[ 8% 4/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_multiline_fasta_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_multiline_fasta_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_multiline_fasta_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/seq_reader_multiline_fasta_module.cpp
[ 12% 5/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/seq.cpp
[ 16% 6/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_sam_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_sam_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_sam_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/seq_reader_sam_module.cpp
[ 20% 7/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_aahash.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_aahash.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_aahash.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/aahash.cpp
[ 25% 8/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_writer.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_writer.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_writer.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/seq_writer.cpp
[ 29% 9/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_randseq.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_randseq.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_randseq.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/randseq.cpp
[ 33% 10/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/seq_reader.cpp
[ 37% 11/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_data_stream.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_data_stream.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_data_stream.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/data_stream.cpp
[ 41% 12/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_multiline_fastq_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_multiline_fastq_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_multiline_fastq_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/seq_reader_multiline_fastq_module.cpp
[ 45% 13/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_util.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_util.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_util.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/util.cpp
[ 50% 14/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_fastq_module.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_fastq_module.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_seq_reader_fastq_module.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/seq_reader_fastq_module.cpp
[ 54% 15/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_bloom_filter.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_bloom_filter.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_bloom_filter.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/bloom_filter.cpp
FAILED: libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_bloom_filter.cpp.o
c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_bloom_filter.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_bloom_filter.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_bloom_filter.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/bloom_filter.cpp
/wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/bloom_filter.cpp:250:10: error: call to constructor of 'NtHash' is ambiguous
250 | NtHash nthash(seq, seq_len, get_hash_num(), get_k());
| ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/btllib/nthash_kmer.hpp:248:3: note: candidate constructor
248 | NtHash(const char* seq,
| ^
../include/btllib/nthash_kmer.hpp:278:3: note: candidate constructor
278 | NtHash(const std::string& seq,
| ^
/wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/bloom_filter.cpp:260:10: error: call to constructor of 'NtHash' is ambiguous
260 | NtHash nthash(seq, seq_len, get_hash_num(), get_k());
| ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/btllib/nthash_kmer.hpp:248:3: note: candidate constructor
248 | NtHash(const char* seq,
| ^
../include/btllib/nthash_kmer.hpp:278:3: note: candidate constructor
278 | NtHash(const std::string& seq,
| ^
/wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/bloom_filter.cpp:273:10: error: call to constructor of 'NtHash' is ambiguous
273 | NtHash nthash(seq, seq_len, get_hash_num(), get_k());
| ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
../include/btllib/nthash_kmer.hpp:248:3: note: candidate constructor
248 | NtHash(const char* seq,
| ^
../include/btllib/nthash_kmer.hpp:278:3: note: candidate constructor
278 | NtHash(const std::string& seq,
| ^
3 errors generated.
[ 58% 15/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_status.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_status.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_status.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/status.cpp
[ 62% 15/24] c++ -Ilibbtllib.so.p -I. -I.. -Iinclude -I../include -I../subprojects/cpptoml/include -Isubprojects/cpptoml/__CMake_build -I../subprojects/cpptoml/__CMake_build -Isubprojects/cpptoml -I../subprojects/cpptoml -I/usr/local/include -fdiagnostics-color=never --coverage -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -Wextra -Wpedantic -std=c++17 -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -fopenmp -pthread -MD -MQ libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_process_pipeline.cpp.o -MF libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_process_pipeline.cpp.o.d -o libbtllib.so.p/_wrkdirs_usr_ports_biology_btllib_work_btllib-1.7.0_src_btllib_process_pipeline.cpp.o -c /wrkdirs/usr/ports/biology/btllib/work/btllib-1.7.0/src/btllib/process_pipeline.cpp
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/btllib