=>> Building biology/gemma build started at Thu Jan 22 07:09:22 EST 2026 port directory: /usr/ports/biology/gemma package name: gemma-0.98.5_1 building for: FreeBSD pkg.DaveG.ca 14.3-RELEASE-p7 FreeBSD 14.3-RELEASE-p7 1403000 amd64 maintained by: jwb@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1004 Jan 31 2025 /usr/ports/biology/gemma/Makefile Ports top last git commit: 076a295eb33c Ports top unclean checkout: no Port dir last git commit: e54e2c695bbc Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500068 Jail OSVERSION: 1403000 Job Id: 14 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p7 1403000 UNAME_r=14.3-RELEASE-p7 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_14_3_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_14_3_x64-HEAD-ALL/14/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=freebsd_14_3_x64-HEAD-ALL SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/freebsd_14_3_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--- ===> The following configuration options are available for gemma-0.98.5_1: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=/usr/local/bin/gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gemma/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gemma/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gemma/work/.cache HOME=/wrkdirs/usr/ports/biology/gemma/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gemma/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gemma/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" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/gemma/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/gemma/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/gemma/work/.cache HOME=/wrkdirs/usr/ports/biology/gemma/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/gemma/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/gemma/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=" -lopenblas -pthread -L/usr/local/lib -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -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-- PORTEXAMPLES="" OSREL=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/gemma" EXAMPLESDIR="share/examples/gemma" DATADIR="share/gemma" WWWDIR="www/gemma" ETCDIR="etc/gemma" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/gemma DOCSDIR=/usr/local/share/doc/gemma EXAMPLESDIR=/usr/local/share/examples/gemma WWWDIR=/usr/local/www/gemma ETCDIR=/usr/local/etc/gemma --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 ===> gemma-0.98.5_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [pkg.DaveG.ca] Installing pkg-2.5.1... [pkg.DaveG.ca] Extracting pkg-2.5.1: .......... done ===> gemma-0.98.5_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of gemma-0.98.5_1 =========================================================================== =================================================== ===== 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 gemma-0.98.5_1 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by gemma-0.98.5_1 for building => SHA256 Checksum OK for genetics-statistics-GEMMA-v0.98.5_GH0.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 gemma-0.98.5_1 for building ===> Extracting for gemma-0.98.5_1 => SHA256 Checksum OK for genetics-statistics-GEMMA-v0.98.5_GH0.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 gemma-0.98.5_1 ===> Applying FreeBSD patches for gemma-0.98.5_1 from /usr/ports/biology/gemma/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gemma-0.98.5_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - not found ===> Installing existing package /packages/All/eigen-3.4.0_4.pkg [pkg.DaveG.ca] Installing eigen-3.4.0_4... [pkg.DaveG.ca] `-- Installing blas-3.12.1... [pkg.DaveG.ca] | `-- Installing gcc14-14.2.0_4... [pkg.DaveG.ca] | | `-- Installing binutils-2.44,1... [pkg.DaveG.ca] | | `-- Installing indexinfo-0.3.1_1... [pkg.DaveG.ca] | | `-- Extracting indexinfo-0.3.1_1: . done [pkg.DaveG.ca] | | `-- Installing zstd-1.5.7_1... [pkg.DaveG.ca] | | `-- Extracting zstd-1.5.7_1: .......... done [pkg.DaveG.ca] | | `-- Extracting binutils-2.44,1: .......... done [pkg.DaveG.ca] | | `-- Installing gmp-6.3.0... [pkg.DaveG.ca] | | `-- Extracting gmp-6.3.0: .......... done [pkg.DaveG.ca] | | `-- Installing mpc-1.3.1_1... [pkg.DaveG.ca] | | `-- Installing mpfr-4.2.2,1... [pkg.DaveG.ca] | | `-- Extracting mpfr-4.2.2,1: .......... done [pkg.DaveG.ca] | | `-- Extracting mpc-1.3.1_1: ...... done [pkg.DaveG.ca] | `-- Extracting gcc14-14.2.0_4: .......... done [pkg.DaveG.ca] `-- Extracting blas-3.12.1: ..... done [pkg.DaveG.ca] `-- Installing lapack-3.12.1... [pkg.DaveG.ca] `-- Extracting lapack-3.12.1: .......... done [pkg.DaveG.ca] Extracting eigen-3.4.0_4: .......... done ===== Message from gcc14-14.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> gemma-0.98.5_1 depends on file: /usr/local/libdata/pkgconfig/eigen3.pc - found ===> Returning to build of gemma-0.98.5_1 ===> gemma-0.98.5_1 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [pkg.DaveG.ca] Installing gmake-4.4.1... [pkg.DaveG.ca] `-- Installing gettext-runtime-0.26... [pkg.DaveG.ca] `-- Extracting gettext-runtime-0.26: .......... done [pkg.DaveG.ca] Extracting gmake-4.4.1: .......... done ===> gemma-0.98.5_1 depends on package: gmake>=4.4.1 - found ===> Returning to build of gemma-0.98.5_1 ===> gemma-0.98.5_1 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 gcc14 create symlink for gcc14 (world) create symlink for g++14 create symlink for g++14 (world) create symlink for cpp14 create symlink for cpp14 (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. ===> gemma-0.98.5_1 depends on file: /usr/local/bin/ccache - found ===> Returning to build of gemma-0.98.5_1 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> gemma-0.98.5_1 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [pkg.DaveG.ca] Installing gsl-2.7.1_1... [pkg.DaveG.ca] Extracting gsl-2.7.1_1: .......... done ===> gemma-0.98.5_1 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of gemma-0.98.5_1 ===> gemma-0.98.5_1 depends on shared library: libopenblas.so - not found ===> Installing existing package /packages/All/openblas-0.3.30,2.pkg [pkg.DaveG.ca] Installing openblas-0.3.30,2... [pkg.DaveG.ca] Extracting openblas-0.3.30,2: .......... done ===> gemma-0.98.5_1 depends on shared library: libopenblas.so - found (/usr/local/lib/libopenblas.so) ===> Returning to build of gemma-0.98.5_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for gemma-0.98.5_1 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for gemma-0.98.5_1 c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/bslmm.o src/bslmm.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/bslmmdap.o src/bslmmdap.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/debug.o src/debug.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/fastblas.o src/fastblas.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/gemma.o src/gemma.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/gemma_io.o src/gemma_io.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/gzstream.o src/gzstream.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/lapack.o src/lapack.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/ldr.o src/ldr.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/lm.o src/lm.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/lmm.o src/lmm.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/logistic.o src/logistic.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/main.o src/main.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/mathfunc.o src/mathfunc.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/mvlmm.o src/mvlmm.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/param.o src/param.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/prdt.o src/prdt.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/varcov.o src/varcov.cpp c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -isystem /usr/local/include -c -o src/vc.o src/vc.cpp src/lapack.cpp:265:7: warning: variable 'count_negative_eigenvalues' set but not used [-Wunused-but-set-variable] 265 | int count_negative_eigenvalues = 0; | ^ 1 warning generated. src/varcov.cpp:378:18: warning: variable 'inc' set but not used [-Wunused-but-set-variable] 378 | size_t t2 = 0, inc; | ^ 1 warning generated. src/vc.cpp:661:10: warning: variable 'ns_test' set but not used [-Wunused-but-set-variable] 661 | size_t ns_test = 0, ns_total = 0; | ^ src/vc.cpp:661:23: warning: variable 'ns_total' set but not used [-Wunused-but-set-variable] 661 | size_t ns_test = 0, ns_total = 0; | ^ src/vc.cpp:813:10: warning: variable 'ns_test' set but not used [-Wunused-but-set-variable] 813 | size_t ns_test = 0; | ^ src/vc.cpp:1220:25: warning: variable 'var_y' set but not used [-Wunused-but-set-variable] 1220 | double a, b, x, y, n, var_y, var_x, mean_y, mean_x, cov_xy, crt_factor; | ^ 4 warnings generated. src/gemma_io.cpp:1862:21: warning: variable 'c_snp' set but not used [-Wunused-but-set-variable] 1862 | size_t c_idv = 0, c_snp = 0; | ^ src/gemma_io.cpp:2114:21: warning: variable 'c_snp' set but not used [-Wunused-but-set-variable] 2114 | size_t c_idv = 0, c_snp = 0, c = 0; | ^ src/gemma_io.cpp:2785:10: warning: variable 'ns_test' set but not used [-Wunused-but-set-variable] 2785 | size_t ns_test = 0; | ^ src/gemma_io.cpp:2965:10: warning: variable 'ns_test' set but not used [-Wunused-but-set-variable] 2965 | size_t ns_test = 0; | ^ src/gemma_io.cpp:3674:9: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign] 3674 | z = z; | ~ ^ ~ src/gemma_io.cpp:3556:24: warning: variable 'ns_total' set but not used [-Wunused-but-set-variable] 3556 | size_t ni_total = 0, ns_total = 0, ns_test = 0; | ^ src/gemma_io.cpp:3556:38: warning: variable 'ns_test' set but not used [-Wunused-but-set-variable] 3556 | size_t ni_total = 0, ns_total = 0, ns_test = 0; | ^ 7 warnings generated. c++ -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/eigen3 -DOPENBLAS -pthread -isystem /usr/local/include -DHAVE_INLINE -Wall -std=gnu++11 -DNDEBUG -Icontrib/catch-1.9.7 -Isrc -o gemma src/bslmm.o src/bslmmdap.o src/debug.o src/fastblas.o src/gemma.o src/gemma_io.o src/gzstream.o src/lapack.o src/ldr.o src/lm.o src/lmm.o src/logistic.o src/main.o src/mathfunc.o src/mvlmm.o src/param.o src/prdt.o src/varcov.o src/vc.o -lopenblas -pthread -L/usr/local/lib -L/usr/local/lib -lgsl -lz =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Staging for gemma-0.98.5_1 ===> Generating temporary packing list mkdir -p /wrkdirs/usr/ports/biology/gemma/work/stage/usr/local/bin install -s -c gemma /wrkdirs/usr/ports/biology/gemma/work/stage/usr/local/bin (cd /wrkdirs/usr/ports/biology/gemma/work/GEMMA-0.98.5/example && /bin/sh -c '(/usr/bin/find -Ed $1 $3 | /usr/bin/cpio -dumpl $2 >/dev/null 2>&1) && /usr/bin/find -Ed $1 $3 \( -type d -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 755 "$@"'\'' . {} + -o -type f -exec /bin/sh -c '\''cd '\''$2'\'' && chmod 0644 "$@"'\'' . {} + \)' COPYTREE_SHARE . /wrkdirs/usr/ports/biology/gemma/work/stage/usr/local/share/examples/gemma) ====> 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=2026-01-22T12:09:22+0000' 'PKG_NOTE_ports_top_git_hash=076a295eb33c' 'PKG_NOTE_ports_top_checkout_unclean=no' 'PKG_NOTE_port_git_hash=e54e2c695bbc' '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 gemma-0.98.5_1 ===> Building gemma-0.98.5_1 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for gemma-0.98.5_1 build of biology/gemma | gemma-0.98.5_1 ended at Thu Jan 22 07:10:38 EST 2026 build time: 00:01:16