From nobody Mon Jan 24 20:57:24 2022 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 427961970FCA for ; Mon, 24 Jan 2022 20:57:25 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4JjMkD4sCNz4fMN for ; Mon, 24 Jan 2022 20:57:24 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (beefy8.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:17]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 624A31CF47 for ; Mon, 24 Jan 2022 20:57:24 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy8.nyi.freebsd.org (localhost [127.0.0.1]) by beefy8.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 20OKvOW1025919 for ; Mon, 24 Jan 2022 20:57:24 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy8.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 20OKvOYu025917; Mon, 24 Jan 2022 20:57:24 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Mon, 24 Jan 2022 20:57:24 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202201242057.20OKvOYu025917@beefy8.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - main-armv6-default][biology/bio-mocha] Failed for bio-mocha-1.14 in stage ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1643057844; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=zuZD3gLEbSuybbyVsVbN5BFGi1DoaOSgCcm0W2Tjnq0=; b=IM+hL+GnUAFccA1CaKFzyjR+REPUQwWpkB0eguB/yF6vkn6xmvzlv1p7NcnSzRE30vxOgs D2hm9TugcDHen53/FnK3uD7mfQVv9OsXEPEpbRIRlHb1hmCEJomQxh3QcCXV8NBP9Cp0zR 3x8QmxnIM8or/jPSuhBHstNQQkG/uVYp/4ydZiAp+N3U8JY5FeAcqUb4fA53nTxcShedJ3 53V53usEYEg+Zg8asPbJd0mZnyT48NN3uv/WHs7YzQ1poi6ZXin7PIp/9T37bp+uM5RQfT QgxEM5pAm99Bi5jc8GosCLSw46Fyq2Y5a26yO7AqdwKuXKxZyuTrMUBqquip+A== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1643057844; a=rsa-sha256; cv=none; b=ox7z/zRJLj7nR64wIejbb410U1tMlWulHU6Qkv+QW635gtmdde03r4goh0ey9YPU4F6eZi 1xymejzNWwhZD7FDvDKGfW7JX5zGHTAl6sUeI+7Na8dOYo+0HXwj7rHCDZ/T1fpUe7qLN+ vgrCL+FrRz6D1Ugi5e9FWh+HRnQFM0EFgMXDHYMZ2XOE3DdvOlTiFNr8GJboLAPiQB43Mv mZIJytlnAIA95NJAXPx+XRLYXNUjnKuFp37GkjxtNNncWS/5t0S0sUzYrittr7oiqYmFAR pRMj4B+LniLvYIAYTh0qWfBEoD4VTae92mZFTncDGsebTh5C5q8uPbJDzcTU/w== ARC-Authentication-Results: i=1; mx1.freebsd.org; none X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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: jwb@FreeBSD.org Log URL: http://beefy8.nyi.freebsd.org/data/main-armv6-default/p7201e24c4c91_scc68614da8/logs/bio-mocha-1.14.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=p7201e24c4c91_scc68614da8 Log: =>> Building biology/bio-mocha build started at Mon Jan 24 20:47:30 UTC 2022 port directory: /usr/ports/biology/bio-mocha package name: bio-mocha-1.14 building for: FreeBSD main-armv6-default-job-08 14.0-CURRENT FreeBSD 14.0-CURRENT 1400047 arm maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1300121 Jail OSVERSION: 1400047 Job Id: 08 !!! Jail is newer than host. (Jail: 1400047, Host: 1300121) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1400047 UNAME_v=FreeBSD 14.0-CURRENT 1400047 UNAME_r=14.0-CURRENT 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 LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/main-armv6-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.8" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work/.cache HOME=/wrkdirs/usr/ports/biology/bio-mocha/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bio-mocha/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin 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-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bio-mocha/work/.cache HOME=/wrkdirs/usr/ports/biology/bio-mocha/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bio-mocha/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.8 PYTHON_LIBDIR=lib/python3.8 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.8/site-packages PYTHON_SUFFIX=38 PYTHON_EXT_SUFFIX=.cpython-38 PYTHON_VER=3.8 PYTHON_VERSION=python3.8 PYTHON2="@comment " PYTHON3="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/bio-mocha" EXAMPLESDIR="share/examples/bio-mocha" DATADIR="share/bio-mocha" WWWDIR="www/bio-mocha" ETCDIR="etc/bio-mocha" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bio-mocha DOCSDIR=/usr/local/share/doc/bio-mocha EXAMPLESDIR=/usr/local/share/examples/bio-mocha WWWDIR=/usr/local/www/bio-mocha ETCDIR=/usr/local/etc/bio-mocha --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/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 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400047 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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) 1024 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-- =================================================== ===> License MIT accepted by the user =========================================================================== =================================================== ===> bio-mocha-1.14 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [main-armv6-default-job-08] Installing pkg-1.17.5... [main-armv6-default-job-08] Extracting pkg-1.17.5: .......... done ===> bio-mocha-1.14 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bio-mocha-1.14 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user => bio-mocha_1.14-20220112.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://software.broadinstitute.org/software/mocha/bio-mocha_1.14-20220112.tar.gz bio-mocha_1.14-20220112.tar.gz 74 kB 3442 kBps 00s ===> Fetching all distfiles required by bio-mocha-1.14 for building =========================================================================== Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem ===> bio-mocha-1.14 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of bio-mocha-1.14 =========================================================================== =================================================== ===> Configuring for bio-mocha-1.14 configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ./../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ./../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ./../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure.ac:94: warning: AC_CONFIG_SUBDIRS: you should use literals ./../lib/autoconf/status.m4:1097: AC_CONFIG_SUBDIRS is expanded from... m4/ax_with_htslib.m4:55: AX_WITH_HTSLIB is expanded from... configure.ac:94: the top level configure: loading site script /usr/ports/Templates/config.site checking for gcc... /nxb-bin/usr/bin/cc 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 we are using the GNU C compiler... yes checking whether /nxb-bin/usr/bin/cc accepts -g... yes checking for /nxb-bin/usr/bin/cc option to accept ISO C89... none needed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for C compiler warning flags... -Wall checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking location of HTSlib source tree... none found checking for htslib/sam.h... yes checking for hts_version in -lhts... yes checking shared library type... plain .so checking for library containing dlopen... none required checking if the compiler accepts -rdynamic... yes checking for zlib.h... (cached) yes checking for inflate in -lz... yes checking for library containing regcomp... none required configure: creating ./config.status config.status: creating config.mk config.status: creating config.h =========================================================================== =================================================== ===> Building for bio-mocha-1.14 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14' echo '#define BCFTOOLS_VERSION "1.14"' > version.h /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o main.o main.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfindex.o vcfindex.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tabix.o tabix.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfstats.o vcfstats.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfisec.o vcfisec.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfmerge.o vcfmerge.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfquery.o vcfquery.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcffilter.o vcffilter.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o filter.o filter.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsom.o vcfsom.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfnorm.o vcfnorm.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfgtcheck.o vcfgtcheck.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfview.o vcfview.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfannotate.o vcfannotate.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfroh.o vcfroh.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconcat.o vcfconcat.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfcall.o vcfcall.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mcall.o mcall.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcmp.o vcmp.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o gvcf.o gvcf.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o reheader.o reheader.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o convert.o convert.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfconvert.o vcfconvert.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o tsv2vcf.o tsv2vcf.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfcnv.o vcfcnv.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o HMM.o HMM.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o consensus.o consensus.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ploidy.o ploidy.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bin.o bin.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o hclust.o hclust.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o version.o version.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o regidx.o regidx.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o smpl_ilist.o smpl_ilist.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o csq.o csq.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfbuf.o vcfbuf.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o mpileup.o mpileup.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf.o bam2bcf.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam2bcf_indel.o bam2bcf_indel.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o bam_sample.o bam_sample.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfsort.o vcfsort.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o cols.o cols.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o extsort.o extsort.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o dist.o dist.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o abuf.o abuf.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o ccall.o ccall.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o em.o em.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o prob1.o prob1.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o kmin.o kmin.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o str_finder.o str_finder.c /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -DPLUGINPATH='"/usr/local/libexec/bcftools"' -c -o vcfplugin.o vcfplugin.c /nxb-bin/usr/bin/cc -rdynamic -fstack-protector-strong -o bcftools main.o vcfindex.o tabix.o vcfstats.o vcfisec.o vcfmerge.o vcfquery.o vcffilter.o filter.o vcfsom.o vcfnorm.o vcfgtcheck.o vcfview.o vcfannotate.o vcfroh.o vcfconcat.o vcfcall.o mcall.o vcmp.o gvcf.o reheader.o convert.o vcfconvert.o tsv2vcf.o vcfcnv.o HMM.o consensus.o ploidy.o bin.o hclust.o version.o regidx.o smpl_ilist.o csq.o vcfbuf.o mpileup.o bam2bcf.o bam2bcf_indel.o bam_sample.o vcfsort.o cols.o extsort.o dist.o abuf.o ccall.o em.o prob1.o kmin.o str_finder.o vcfplugin.o -lhts -lm -lz -L/usr/local/lib -lpthread /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-rbuf.o test/test-rbuf.c /nxb-bin/usr/bin/cc -fstack-protector-strong -o test/test-rbuf test/test-rbuf.o -lz -L/usr/local/lib /nxb-bin/usr/bin/cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o test/test-regidx.o test/test-regidx.c /nxb-bin/usr/bin/cc -fstack-protector-strong -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/GTisec.so version.c plugins/GTisec.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/GTsubset.so version.c plugins/GTsubset.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/ad-bias.so convert.c version.c plugins/ad-bias.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/add-variantkey.so version.c plugins/add-variantkey.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/af-dist.so bin.c version.c plugins/af-dist.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/allele-length.so version.c plugins/allele-length.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/check-ploidy.so version.c plugins/check-ploidy.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/check-sparsity.so version.c plugins/check-sparsity.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/color-chrs.so HMM.c version.c plugins/color-chrs.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/contrast.so version.c plugins/contrast.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/counts.so version.c plugins/counts.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/dosage.so version.c plugins/dosage.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/extendFMT.so version.c plugins/extendFMT.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-AN-AC.so version.c plugins/fill-AN-AC.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-from-fasta.so filter.c version.c plugins/fill-from-fasta.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fill-tags.so version.c plugins/fill-tags.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fixploidy.so ploidy.c regidx.c version.c plugins/fixploidy.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/fixref.so version.c plugins/fixref.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/frameshifts.so version.c plugins/frameshifts.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/guess-ploidy.so version.c plugins/guess-ploidy.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/gvcfz.so version.c plugins/gvcfz.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/impute-info.so version.c plugins/impute-info.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/indel-stats.so version.c plugins/indel-stats.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/isecGT.so smpl_ilist.c version.c plugins/isecGT.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/mendelian.so version.c plugins/mendelian.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/missing2ref.so version.c plugins/missing2ref.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/mocha.so version.c plugins/mocha.c -L/usr/local/lib plugins/mocha.c:3524:39: warning: passing 'const char *' to parameter of type 'char *' discards qualifiers [-Wincompatible-pointer-types-discards-qualifiers] set_wmode(wmode, output_type, output_fname, clevel); ^~~~~~~~~~~~ ./bcftools.h:54:50: note: passing argument to parameter 'fname' here void set_wmode(char dst[8], int file_type, char *fname, int compression_level); // clevel: 0-9 with or zb type, -1 unset ^ 1 warning generated. /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/mochatools.so version.c plugins/mochatools.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/parental-origin.so version.c plugins/parental-origin.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/prune.so version.c plugins/prune.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/remove-overlaps.so version.c plugins/remove-overlaps.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/scatter.so version.c plugins/scatter.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/score.so version.c plugins/score.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/setGT.so version.c plugins/setGT.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/smpl-stats.so version.c plugins/smpl-stats.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/split-vep.so version.c plugins/split-vep.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/split.so version.c plugins/split.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/tag2tag.so version.c plugins/tag2tag.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/trio-dnm2.so version.c plugins/trio-dnm2.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/trio-phase.so version.c plugins/trio-phase.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/trio-stats.so version.c plugins/trio-stats.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/trio-switch-rate.so version.c plugins/trio-switch-rate.c -L/usr/local/lib /nxb-bin/usr/bin/cc -fPIC -shared -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -fstack-protector-strong -o plugins/variantkey-hex.so version.c plugins/variantkey-hex.c -L/usr/local/lib gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14' =========================================================================== =================================================== ===> bio-mocha-1.14 depends on package: bcftools>=1.14 - not found ===> Installing existing package /packages/All/bcftools-1.14_1.pkg [main-armv6-default-job-08] Installing bcftools-1.14_1... [main-armv6-default-job-08] `-- Installing gsl-2.7.1... [main-armv6-default-job-08] `-- Extracting gsl-2.7.1: .......... done [main-armv6-default-job-08] Extracting bcftools-1.14_1: .......... done ===> bio-mocha-1.14 depends on package: bcftools>=1.14 - found ===> Returning to build of bio-mocha-1.14 =========================================================================== =================================================== ===> Staging for bio-mocha-1.14 ===> Generating temporary packing list /bin/mkdir -p /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/extendFMT.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/mocha.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/mochatools.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/score.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools install -s -m 555 /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/plugins/trio-phase.so /wrkdirs/usr/ports/biology/bio-mocha/work/stage/usr/local/libexec/bcftools (cd /wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.14/MoCha && /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/bio-mocha/work/stage/usr/local/share/bio-mocha) *** Error code 1 Stop. make: stopped in /usr/ports/biology/bio-mocha