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Maintainer: j...@freebsd.org Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p6df70458f823_se0bf7bc3b2b/logs/preseq-3.2.0.log Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p6df70458f823_se0bf7bc3b2b Log: =>> Building biology/preseq build started at Sun Nov 24 05:16:59 UTC 2024 port directory: /usr/ports/biology/preseq package name: preseq-3.2.0 building for: FreeBSD main-i386-default-job-08 15.0-CURRENT FreeBSD 15.0-CURRENT 1500027 i386 maintained by: j...@freebsd.org Makefile datestamp: -rw-r--r-- 1 root wheel 508 Nov 23 01:01 /usr/ports/biology/preseq/Makefile Ports top last git commit: 6df70458f82 Ports top unclean checkout: no Port dir last git commit: af7a74db000 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1500027 Job Id: 08 !!! Jail is newer than host. (Jail: 1500027, Host: 1500023) !!! !!! 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=1500027 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 1500027 USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 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/08/.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-3.4.2 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-- j...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --enable-hts --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/preseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/preseq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/preseq/work/.cache HOME=/wrkdirs/usr/ports/biology/preseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/preseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/preseq/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/preseq/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/preseq/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/preseq/work/.cache HOME=/wrkdirs/usr/ports/biology/preseq/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/preseq/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/preseq/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 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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-- OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/preseq" EXAMPLESDIR="share/examples/preseq" DATADIR="share/preseq" WWWDIR="www/preseq" ETCDIR="etc/preseq" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/preseq DOCSDIR=/usr/local/share/doc/preseq EXAMPLESDIR=/usr/local/share/examples/preseq WWWDIR=/usr/local/www/preseq ETCDIR=/usr/local/etc/preseq --End SUB_LIST-- ---Begin make.conf--- # 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 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-- ulimit: can't get limit: Invalid argument 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 ===> preseq-3.2.0 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [main-i386-default-job-08] Installing pkg-1.21.3... [main-i386-default-job-08] Extracting pkg-1.21.3: .......... done ===> preseq-3.2.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of preseq-3.2.0 =========================================================================== =======================<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 => preseq-3.2.0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://github.com/smithlabcode/preseq/releases/download/v3.2.0/preseq-3.2.0.tar.gz preseq-3.2.0.tar.gz 6336 kB 23 MBps 01s ===> Fetching all distfiles required by preseq-3.2.0 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 preseq-3.2.0 for building => SHA256 Checksum OK for preseq-3.2.0.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 preseq-3.2.0 for building ===> Extracting for preseq-3.2.0 => SHA256 Checksum OK for preseq-3.2.0.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 preseq-3.2.0 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> preseq-3.2.0 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.21.pkg [main-i386-default-job-08] Installing htslib-1.21... [main-i386-default-job-08] `-- Installing curl-8.11.0_1... [main-i386-default-job-08] | `-- Installing brotli-1.1.0,1... [main-i386-default-job-08] | `-- Extracting brotli-1.1.0,1: .......... done [main-i386-default-job-08] | `-- Installing libidn2-2.3.7... [main-i386-default-job-08] | | `-- Installing indexinfo-0.3.1... [main-i386-default-job-08] | | `-- Extracting indexinfo-0.3.1: .... done [main-i386-default-job-08] | | `-- Installing libunistring-1.2... [main-i386-default-job-08] | | `-- Extracting libunistring-1.2: .......... done [main-i386-default-job-08] | `-- Extracting libidn2-2.3.7: .......... done [main-i386-default-job-08] | `-- Installing libnghttp2-1.64.0... [main-i386-default-job-08] | `-- Extracting libnghttp2-1.64.0: .......... done [main-i386-default-job-08] | `-- Installing libpsl-0.21.5_1... [main-i386-default-job-08] | `-- Extracting libpsl-0.21.5_1: .......... done [main-i386-default-job-08] | `-- Installing libssh2-1.11.1,3... [main-i386-default-job-08] | `-- Extracting libssh2-1.11.1,3: .......... done [main-i386-default-job-08] | `-- Installing zstd-1.5.6... [main-i386-default-job-08] | | `-- Installing liblz4-1.10.0,1... [main-i386-default-job-08] | | `-- Extracting liblz4-1.10.0,1: .......... done [main-i386-default-job-08] | `-- Extracting zstd-1.5.6: .......... done [main-i386-default-job-08] `-- Extracting curl-8.11.0_1: .......... done [main-i386-default-job-08] `-- Installing libdeflate-1.22... [main-i386-default-job-08] `-- Extracting libdeflate-1.22: .......... done [main-i386-default-job-08] Extracting htslib-1.21: .......... done ===> preseq-3.2.0 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of preseq-3.2.0 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for preseq-3.2.0 configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking whether c++ supports C++11 features with -std=c++11... yes checking for ranlib... ranlib checking for hts_version in -lhts... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in src/smithlab_cpp (/wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/src/smithlab_cpp) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local' '--enable-hts' '--localstatedir=/var' '--mandir=/usr/local/share/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=i386-portbld-freebsd15.0' 'build_alias=i386-portbld-freebsd15.0' 'CXX=c++' 'CXXFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include ' 'LDFLAGS= -fstack-protector-strong ' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether make supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking whether c++ supports C++11 features with -std=c++11... yes checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for ar... ar checking the archiver (ar) interface... ar checking for ranlib... ranlib checking for hts_version in -lhts... yes checking for zlibVersion in -lz... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands =========================================================================== =======================<phase: build >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for preseq-3.2.0 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in src/smithlab_cpp --- all --- /usr/bin/make all-am --- GenomicRegion.o --- --- MappedRead.o --- --- OptionParser.o --- --- GenomicRegion.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT GenomicRegion.o -MD -MP -MF .deps/GenomicRegion.Tpo -c -o GenomicRegion.o GenomicRegion.cpp --- MappedRead.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT MappedRead.o -MD -MP -MF .deps/MappedRead.Tpo -c -o MappedRead.o MappedRead.cpp --- OptionParser.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT OptionParser.o -MD -MP -MF .deps/OptionParser.Tpo -c -o OptionParser.o OptionParser.cpp --- GenomicRegion.o --- In file included from GenomicRegion.cpp:23: In file included from ./GenomicRegion.hpp:27: ./smithlab_utils.hpp:399:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 399 | char seq[seqs[i].length() + 1]; | ^~~~~~~~~~~~~~~~~~~~ ./smithlab_utils.hpp:399:14: note: function parameter 'seqs' with unknown value cannot be used in a constant expression ./smithlab_utils.hpp:390:52: note: declared here 390 | inline kmer_counts(const std::vector<std::string> &seqs, | ^ --- MappedRead.o --- In file included from MappedRead.cpp:23: In file included from ./MappedRead.hpp:26: In file included from ./GenomicRegion.hpp:27: ./smithlab_utils.hpp:399:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 399 | char seq[seqs[i].length() + 1]; | ^~~~~~~~~~~~~~~~~~~~ ./smithlab_utils.hpp:399:14: note: function parameter 'seqs' with unknown value cannot be used in a constant expression ./smithlab_utils.hpp:390:52: note: declared here 390 | inline kmer_counts(const std::vector<std::string> &seqs, | ^ 1 warning generated. mv -f .deps/MappedRead.Tpo .deps/MappedRead.Po --- QualityScore.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT QualityScore.o -MD -MP -MF .deps/QualityScore.Tpo -c -o QualityScore.o QualityScore.cpp --- OptionParser.o --- In file included from OptionParser.cpp:38: ./smithlab_utils.hpp:399:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 399 | char seq[seqs[i].length() + 1]; | ^~~~~~~~~~~~~~~~~~~~ ./smithlab_utils.hpp:399:14: note: function parameter 'seqs' with unknown value cannot be used in a constant expression ./smithlab_utils.hpp:390:52: note: declared here 390 | inline kmer_counts(const std::vector<std::string> &seqs, | ^ OptionParser.cpp:521:26: error: no matching function for call to 'min' 521 | for (size_t i = 0; i < std::min(2ul, options.size()); ++i) | ^~~~~~~~ /usr/include/c++/v1/__algorithm/min.h:35:1: note: candidate template ignored: deduced conflicting types for parameter '_Tp' ('unsigned long' vs. 'size_type' (aka 'unsigned int')) 35 | min(_LIBCPP_LIFETIMEBOUND const _Tp& __a, _LIBCPP_LIFETIMEBOUND const _Tp& __b) { | ^ /usr/include/c++/v1/__algorithm/min.h:43:1: note: candidate template ignored: could not match 'initializer_list<_Tp>' against 'unsigned long' 43 | min(initializer_list<_Tp> __t, _Compare __comp) { | ^ /usr/include/c++/v1/__algorithm/min.h:48:82: note: candidate function template not viable: requires single argument '__t', but 2 arguments were provided 48 | _LIBCPP_NODISCARD inline _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX14 _Tp min(initializer_list<_Tp> __t) { | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/v1/__algorithm/min.h:29:1: note: candidate function template not viable: requires 3 arguments, but 2 were provided 29 | min(_LIBCPP_LIFETIMEBOUND const _Tp& __a, _LIBCPP_LIFETIMEBOUND const _Tp& __b, _Compare __comp) { | ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1 warning and 1 error generated. *** [OptionParser.o] Error code 1 make[3]: stopped making "all-am" in /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/src/smithlab_cpp --- QualityScore.o --- In file included from QualityScore.cpp:26: ./smithlab_utils.hpp:399:14: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 399 | char seq[seqs[i].length() + 1]; | ^~~~~~~~~~~~~~~~~~~~ ./smithlab_utils.hpp:399:14: note: function parameter 'seqs' with unknown value cannot be used in a constant expression ./smithlab_utils.hpp:390:52: note: declared here 390 | inline kmer_counts(const std::vector<std::string> &seqs, | ^ 1 warning generated. mv -f .deps/QualityScore.Tpo .deps/QualityScore.Po --- GenomicRegion.o --- 1 warning generated. mv -f .deps/GenomicRegion.Tpo .deps/GenomicRegion.Po make[3]: 1 error make[3]: stopped making "all-am" in /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/src/smithlab_cpp make[2]: stopped making "all" in /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/src/smithlab_cpp make[1]: stopped making "all-recursive" in /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0 make: stopped making "all" in /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0 ===> 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 making "build" in /usr/ports/biology/preseq
