=>> Building biology/preseq build started at Tue Mar 17 01:37:30 EDT 2026 port directory: /usr/ports/biology/preseq package name: preseq-3.2.0 building for: FreeBSD pkg.DaveG.ca 15.0-RELEASE-p3 FreeBSD 15.0-RELEASE-p3 1500068 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 639 Nov 29 2024 /usr/ports/biology/preseq/Makefile Ports top last git commit: 8c988f802ea2 Ports top unclean checkout: no Port dir last git commit: 1c58b378342d Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1500068 Job Id: 03 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500068 UNAME_v=FreeBSD 15.0-RELEASE-p3 1500068 UNAME_r=15.0-RELEASE-p3 BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=tmux-256color OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/03/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_15_0_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_15_0_x64-HEAD-ALL/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-- jwb@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=" " 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--- DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### DEFAULT_VERSIONS+=pgsql=15 DEFAULT_VERSIONS+=php=82 DISABLE_LICENSES=yes SELECTED_OPTIONS+=OPENBLAS ARCHDEF=AMD64K10h64SSE3 WITH_CCACHE_BUILD=yes CCACHE_DIR=/root/.ccache #### 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) 33554432 stack size (kbytes, -s) 524288 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 pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 =========================================================================== =================================================== ===== 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-2.6.2.pkg [pkg.DaveG.ca] Installing pkg-2.6.2... [pkg.DaveG.ca] Extracting pkg-2.6.2: .......... done ===> preseq-3.2.0 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of preseq-3.2.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by preseq-3.2.0 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by preseq-3.2.0 for building => SHA256 Checksum OK for preseq-3.2.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> 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. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for preseq-3.2.0 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> preseq-3.2.0 depends on file: /usr/local/bin/ccache - not found ===> Installing existing package /packages/All/ccache-3.7.12_8.pkg [pkg.DaveG.ca] Installing ccache-3.7.12_8... [pkg.DaveG.ca] Extracting ccache-3.7.12_8: ......... done Create compiler links... create symlink for cc create symlink for cc (world) create symlink for c++ create symlink for c++ (world) create symlink for CC create symlink for CC (world) create symlink for clang create symlink for clang (world) create symlink for clang++ create symlink for clang++ (world) ===== Message from ccache-3.7.12_8: -- NOTE: Please read /usr/local/share/doc/ccache/ccache-howto-freebsd.txt for information on using ccache with FreeBSD ports and src. ===> preseq-3.2.0 depends on file: /usr/local/bin/ccache - found ===> Returning to build of preseq-3.2.0 =========================================================================== =================================================== ===== 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-1.22.pkg [pkg.DaveG.ca] Installing htslib-1.22... [pkg.DaveG.ca] `-- Installing curl-8.17.0... [pkg.DaveG.ca] | `-- Installing brotli-1.2.0,1... [pkg.DaveG.ca] | `-- Extracting brotli-1.2.0,1: .......... done [pkg.DaveG.ca] | `-- Installing libidn2-2.3.8... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Installing libunistring-1.4.2... [pkg.DaveG.ca] | | `-- Extracting libunistring-1.4.2: .......... done [pkg.DaveG.ca] | `-- Extracting libidn2-2.3.8: .......... done [pkg.DaveG.ca] | `-- Installing libnghttp2-1.68.0... [pkg.DaveG.ca] | `-- Extracting libnghttp2-1.68.0: ....... done [pkg.DaveG.ca] | `-- Installing libpsl-0.21.5_2... [pkg.DaveG.ca] | `-- Extracting libpsl-0.21.5_2: ........ done [pkg.DaveG.ca] | `-- Installing libssh2-1.11.1,3... [pkg.DaveG.ca] | `-- Extracting libssh2-1.11.1,3: .......... done [pkg.DaveG.ca] | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] `-- Extracting curl-8.17.0: .......... done [pkg.DaveG.ca] `-- Installing libdeflate-1.25... [pkg.DaveG.ca] `-- Extracting libdeflate-1.25: .......... done [pkg.DaveG.ca] Extracting htslib-1.22: .......... 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 =========================================================================== =================================================== ===== 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=amd64-portbld-freebsd15.0' 'build_alias=amd64-portbld-freebsd15.0' 'CXX=c++' 'CXXFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include ' 'LDFLAGS= ' '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 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for preseq-3.2.0 make: /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/Makefile:977: warning: Invalid character " " in variable name "filter-out src/smithlab_cpp, src/smithlab_cpp" --- all --- /usr/bin/make all-recursive make[1]: /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/Makefile:977: warning: Invalid character " " in variable name "filter-out src/smithlab_cpp, src/smithlab_cpp" --- all-recursive --- Making all in src/smithlab_cpp --- all --- /usr/bin/make all-am --- GenomicRegion.o --- --- MappedRead.o --- --- OptionParser.o --- --- QualityScore.o --- --- bisulfite_utils.o --- --- chromosome_utils.o --- --- sim_utils.o --- --- smithlab_os.o --- --- smithlab_utils.o --- --- zlib_wrapper.o --- --- dna_four_bit.o --- --- cigar_utils.o --- --- htslib_wrapper_deprecated.o --- --- sam_record.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 --- 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 --- bisulfite_utils.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT bisulfite_utils.o -MD -MP -MF .deps/bisulfite_utils.Tpo -c -o bisulfite_utils.o bisulfite_utils.cpp --- chromosome_utils.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT chromosome_utils.o -MD -MP -MF .deps/chromosome_utils.Tpo -c -o chromosome_utils.o chromosome_utils.cpp --- sim_utils.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT sim_utils.o -MD -MP -MF .deps/sim_utils.Tpo -c -o sim_utils.o sim_utils.cpp --- smithlab_os.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT smithlab_os.o -MD -MP -MF .deps/smithlab_os.Tpo -c -o smithlab_os.o smithlab_os.cpp --- smithlab_utils.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT smithlab_utils.o -MD -MP -MF .deps/smithlab_utils.Tpo -c -o smithlab_utils.o smithlab_utils.cpp --- zlib_wrapper.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT zlib_wrapper.o -MD -MP -MF .deps/zlib_wrapper.Tpo -c -o zlib_wrapper.o zlib_wrapper.cpp --- dna_four_bit.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT dna_four_bit.o -MD -MP -MF .deps/dna_four_bit.Tpo -c -o dna_four_bit.o dna_four_bit.cpp --- cigar_utils.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT cigar_utils.o -MD -MP -MF .deps/cigar_utils.Tpo -c -o cigar_utils.o cigar_utils.cpp --- htslib_wrapper_deprecated.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT htslib_wrapper_deprecated.o -MD -MP -MF .deps/htslib_wrapper_deprecated.Tpo -c -o htslib_wrapper_deprecated.o htslib_wrapper_deprecated.cpp --- sam_record.o --- c++ -std=c++11 -DHAVE_CONFIG_H -I. -isystem /usr/local/include -O3 -MT sam_record.o -MD -MP -MF .deps/sam_record.Tpo -c -o sam_record.o sam_record.cpp --- dna_four_bit.o --- mv -f .deps/dna_four_bit.Tpo .deps/dna_four_bit.Po --- zlib_wrapper.o --- mv -f .deps/zlib_wrapper.Tpo .deps/zlib_wrapper.Po --- cigar_utils.o --- mv -f .deps/cigar_utils.Tpo .deps/cigar_utils.Po --- sam_record.o --- In file included from sam_record.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 &seqs, | ^ 1 warning generated. mv -f .deps/sam_record.Tpo .deps/sam_record.Po --- 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 &seqs, | ^ 1 warning generated. --- htslib_wrapper_deprecated.o --- In file included from htslib_wrapper_deprecated.cpp:25: In file included from ./htslib_wrapper_deprecated.hpp:23: ./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 &seqs, | ^ htslib_wrapper_deprecated.cpp:210:22: warning: object backing the pointer will be destroyed at the end of the full-expression [-Wdangling-gsl] 210 | const char *temp = meth_call_str.substr(5).c_str(); | ^~~~~~~~~~~~~~~~~~~~~~~ 2 warnings generated. mv -f .deps/htslib_wrapper_deprecated.Tpo .deps/htslib_wrapper_deprecated.Po --- QualityScore.o --- mv -f .deps/QualityScore.Tpo .deps/QualityScore.Po --- 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 &seqs, | ^ 1 warning generated. mv -f .deps/MappedRead.Tpo .deps/MappedRead.Po --- bisulfite_utils.o --- mv -f .deps/bisulfite_utils.Tpo .deps/bisulfite_utils.Po --- smithlab_utils.o --- In file included from smithlab_utils.cpp:23: ./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 &seqs, | ^ 1 warning generated. mv -f .deps/smithlab_utils.Tpo .deps/smithlab_utils.Po --- chromosome_utils.o --- In file included from chromosome_utils.cpp:23: In file included from ./chromosome_utils.hpp:37: 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 &seqs, | ^ chromosome_utils.cpp:108:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 108 | char buffer[region_size + 1]; | ^~~~~~~~~~~~~~~ chromosome_utils.cpp:108:17: note: initializer of 'region_size' is not a constant expression chromosome_utils.cpp:103:18: note: declared here 103 | const size_t region_size = adjust_region_size( | ^ chromosome_utils.cpp:112:5: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result] 112 | std::remove_if(buffer, buffer + region_size, | ^~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 113 | [](const char x) {return x == '\n';}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ chromosome_utils.cpp:145:17: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension] 145 | char buffer[region_size + 1]; | ^~~~~~~~~~~~~~~ chromosome_utils.cpp:145:17: note: initializer of 'region_size' is not a constant expression chromosome_utils.cpp:140:18: note: declared here 140 | const size_t region_size = adjust_region_size( | ^ chromosome_utils.cpp:149:5: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result] 149 | std::remove_if(buffer, buffer + region_size, | ^~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 150 | [](const char x) {return x == '\n';}); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 warnings generated. mv -f .deps/chromosome_utils.Tpo .deps/chromosome_utils.Po --- sim_utils.o --- In file included from sim_utils.cpp:25: ./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 &seqs, | ^ 1 warning generated. mv -f .deps/sim_utils.Tpo .deps/sim_utils.Po --- smithlab_os.o --- In file included from smithlab_os.cpp:29: ./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 &seqs, | ^ 1 warning generated. mv -f .deps/smithlab_os.Tpo .deps/smithlab_os.Po --- 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 &seqs, | ^ 1 warning generated. mv -f .deps/GenomicRegion.Tpo .deps/GenomicRegion.Po --- 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 &seqs, | ^ 1 warning generated. mv -f .deps/OptionParser.Tpo .deps/OptionParser.Po --- libsmithlab_cpp.a --- rm -f libsmithlab_cpp.a ar cru libsmithlab_cpp.a GenomicRegion.o MappedRead.o OptionParser.o QualityScore.o bisulfite_utils.o chromosome_utils.o sim_utils.o smithlab_os.o smithlab_utils.o zlib_wrapper.o dna_four_bit.o cigar_utils.o htslib_wrapper_deprecated.o sam_record.o ranlib libsmithlab_cpp.a make[2]: /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/Makefile:977: warning: Invalid character " " in variable name "filter-out src/smithlab_cpp, src/smithlab_cpp" --- src/.dirstamp --- --- src/.deps/.dirstamp --- --- src/preseq.o --- --- src/continued_fraction.o --- --- src/load_data_for_complexity.o --- --- src/moment_sequence.o --- --- src/to-mr.o --- --- src/preseq.o --- depbase=`echo src/preseq.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -std=c++11 -DHAVE_CONFIG_H -I. -I ./src/smithlab_cpp -DHAVE_HTSLIB -isystem /usr/local/include -O2 -MT src/preseq.o -MD -MP -MF $depbase.Tpo -c -o src/preseq.o src/preseq.cpp && mv -f $depbase.Tpo $depbase.Po --- src/continued_fraction.o --- depbase=`echo src/continued_fraction.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -std=c++11 -DHAVE_CONFIG_H -I. -I ./src/smithlab_cpp -DHAVE_HTSLIB -isystem /usr/local/include -O2 -MT src/continued_fraction.o -MD -MP -MF $depbase.Tpo -c -o src/continued_fraction.o src/continued_fraction.cpp && mv -f $depbase.Tpo $depbase.Po --- src/moment_sequence.o --- depbase=`echo src/moment_sequence.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -std=c++11 -DHAVE_CONFIG_H -I. -I ./src/smithlab_cpp -DHAVE_HTSLIB -isystem /usr/local/include -O2 -MT src/moment_sequence.o -MD -MP -MF $depbase.Tpo -c -o src/moment_sequence.o src/moment_sequence.cpp && mv -f $depbase.Tpo $depbase.Po --- src/load_data_for_complexity.o --- depbase=`echo src/load_data_for_complexity.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -std=c++11 -DHAVE_CONFIG_H -I. -I ./src/smithlab_cpp -DHAVE_HTSLIB -isystem /usr/local/include -O2 -MT src/load_data_for_complexity.o -MD -MP -MF $depbase.Tpo -c -o src/load_data_for_complexity.o src/load_data_for_complexity.cpp && mv -f $depbase.Tpo $depbase.Po --- src/to-mr.o --- depbase=`echo src/to-mr.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; c++ -std=c++11 -DHAVE_CONFIG_H -I. -I ./src/smithlab_cpp -DHAVE_HTSLIB -isystem /usr/local/include -O2 -MT src/to-mr.o -MD -MP -MF $depbase.Tpo -c -o src/to-mr.o src/to-mr.cpp && mv -f $depbase.Tpo $depbase.Po In file included from src/to-mr.cpp:31: ./src/smithlab_cpp/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]; | ^~~~~~~~~~~~~~~~~~~~ ./src/smithlab_cpp/smithlab_utils.hpp:399:14: note: function parameter 'seqs' with unknown value cannot be used in a constant expression ./src/smithlab_cpp/smithlab_utils.hpp:390:52: note: declared here 390 | inline kmer_counts(const std::vector &seqs, | ^ 1 warning generated. --- to-mr --- c++ -std=c++11 -O2 -o to-mr src/to-mr.o src/smithlab_cpp/libsmithlab_cpp.a -lhts -L/usr/local/lib --- src/load_data_for_complexity.o --- In file included from src/load_data_for_complexity.cpp:28: In file included from ./src/smithlab_cpp/GenomicRegion.hpp:27: ./src/smithlab_cpp/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]; | ^~~~~~~~~~~~~~~~~~~~ ./src/smithlab_cpp/smithlab_utils.hpp:399:14: note: function parameter 'seqs' with unknown value cannot be used in a constant expression ./src/smithlab_cpp/smithlab_utils.hpp:390:52: note: declared here 390 | inline kmer_counts(const std::vector &seqs, | ^ 1 warning generated. --- src/preseq.o --- In file included from src/preseq.cpp:38: ./src/smithlab_cpp/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]; | ^~~~~~~~~~~~~~~~~~~~ ./src/smithlab_cpp/smithlab_utils.hpp:399:14: note: function parameter 'seqs' with unknown value cannot be used in a constant expression ./src/smithlab_cpp/smithlab_utils.hpp:390:52: note: declared here 390 | inline kmer_counts(const std::vector &seqs, | ^ 1 warning generated. --- preseq --- c++ -std=c++11 -O2 -o preseq src/preseq.o src/continued_fraction.o src/load_data_for_complexity.o src/moment_sequence.o src/smithlab_cpp/libsmithlab_cpp.a -lhts -L/usr/local/lib =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for preseq-3.2.0 ===> Generating temporary packing list make: /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/Makefile:977: warning: Invalid character " " in variable name "filter-out src/smithlab_cpp, src/smithlab_cpp" Making install in src/smithlab_cpp /bin/mkdir -p '/wrkdirs/usr/ports/biology/preseq/work/stage/usr/local/lib' install -m 0644 libsmithlab_cpp.a '/wrkdirs/usr/ports/biology/preseq/work/stage/usr/local/lib' ( cd '/wrkdirs/usr/ports/biology/preseq/work/stage/usr/local/lib' && ranlib libsmithlab_cpp.a ) /bin/mkdir -p '/wrkdirs/usr/ports/biology/preseq/work/stage/usr/local/include' install -m 0644 GenomicRegion.hpp MappedRead.hpp OptionParser.hpp QualityScore.hpp bisulfite_utils.hpp chromosome_utils.hpp sim_utils.hpp smithlab_os.hpp smithlab_utils.hpp zlib_wrapper.hpp dna_four_bit.hpp cigar_utils.hpp htslib_wrapper_deprecated.hpp sam_record.hpp '/wrkdirs/usr/ports/biology/preseq/work/stage/usr/local/include' make[1]: /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/Makefile:977: warning: Invalid character " " in variable name "filter-out src/smithlab_cpp, src/smithlab_cpp" make[2]: /wrkdirs/usr/ports/biology/preseq/work/preseq-3.2.0/Makefile:977: warning: Invalid character " " in variable name "filter-out src/smithlab_cpp, src/smithlab_cpp" /bin/mkdir -p '/wrkdirs/usr/ports/biology/preseq/work/stage/usr/local/bin' install -s -m 555 preseq to-mr '/wrkdirs/usr/ports/biology/preseq/work/stage/usr/local/bin' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2026-03-17T05:37:30+0000' 'PKG_NOTE_ports_top_git_hash=8c988f802ea2' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=1c58b378342d' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.2' NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building packages for preseq-3.2.0 ===> Building preseq-3.2.0 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for preseq-3.2.0 build of biology/preseq | preseq-3.2.0 ended at Tue Mar 17 01:38:11 EDT 2026 build time: 00:00:49