From nobody Wed Dec 22 19:11:55 2021 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 507CB190F6E3 for ; Wed, 22 Dec 2021 19:11:56 +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 4JK2xm00RGz4Vsr for ; Wed, 22 Dec 2021 19:11:56 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere2.nyi.freebsd.org (ampere2.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:24]) (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 C9F882289B for ; Wed, 22 Dec 2021 19:11:55 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere2.nyi.freebsd.org (localhost [127.0.0.1]) by ampere2.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 1BMJBtHJ087131 for ; Wed, 22 Dec 2021 19:11:55 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere2.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 1BMJBto9087129; Wed, 22 Dec 2021 19:11:55 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 22 Dec 2021 19:11:55 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202112221911.1BMJBto9087129@ampere2.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - main-arm64-default][biology/bio-mocha] Failed for bio-mocha-1.13 in run-depends ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1640200316; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=OPAW2Vbq312206pd/e9H3qKzeq1Vomu2T81DJU8VBCE=; b=i1fgsfiLG/F7RvhDDxRLE69TJNtPLJaPqRnlns8op3ofTJcmfHyd7+HQxxRpNWP0tWI/sQ z2fU0gNoXR+v1BHTnMYXewOnrQUuPIPxSudICtPUY1dCOxkXyVKNKHVKqVKfEwbbI2L6KG g5WXyPaAjniYZWOsAbRx/OXFfJQVfQduF5eG8bmnMKRTAMhKi0zLLs/Ayq8Xu9jYrPxYwn lINX+6WxXm7Ebe7/+irVuKa6mnYNM4XSx2YlVALrf6/e+691+9F+nD7aJm/CsKyZ9IGOJv RMDD1bCGyIrrjhqV3E1VdFgdFsGygWxILE0e+PgrYK0YpxZSHCkk7HTixcilug== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1640200316; a=rsa-sha256; cv=none; b=Og76vwkGCat5Rjk1HypkHSPa38DBekuQkSm3TcgUGEwXQfw/ujwu7I5PvwxHHdJueQt1u1 +7UI1BDQP5KE7G5Hy/i9/SKk2PtU4sc8EE2n492kz02i6uhtI5HAveXcyc8ODdKzeS5mH3 tnmOebHQ/Kc1RpCVooBzDpp4WRFHQ0FOP9jKlhN64iePjlgxpFkrv3sODSBdENn3SmwypH RZfrF5bnGgRDVRPvNAVKbjT3RQOtHG+TP3nuzERU8P7RBciA3Zpek4ddArMm0JKp63Issa lpk/DKaxzN9SIW/MRA7IgnhMhcquQogyYbuXvliqNvpbFNL8xy3AdqxfME47Cw== 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://ampere2.nyi.freebsd.org/data/main-arm64-default/p633b51aa6f3e_s623ecf2332/logs/bio-mocha-1.13.log Build URL: http://ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p633b51aa6f3e_s623ecf2332 Log: =>> Building biology/bio-mocha build started at Wed Dec 22 19:10:05 UTC 2021 port directory: /usr/ports/biology/bio-mocha package name: bio-mocha-1.13 building for: FreeBSD main-arm64-default-job-07 14.0-CURRENT FreeBSD 14.0-CURRENT 1400045 arm64 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400008 Jail OSVERSION: 1400045 Job Id: 07 !!! Jail is newer than host. (Jail: 1400045, Host: 1400008) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400045 UNAME_v=FreeBSD 14.0-CURRENT 1400045 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 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-arm64-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="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /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_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400045 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### 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) 1048576 stack size (kbytes, -s) 1048576 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-1.13 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [main-arm64-default-job-07] Installing pkg-1.17.5... [main-arm64-default-job-07] Extracting pkg-1.17.5: .......... done ===> bio-mocha-1.13 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bio-mocha-1.13 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by bio-mocha-1.13 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by bio-mocha-1.13 for building => SHA256 Checksum OK for bio-mocha_1.13-20211015.tar.gz. => SHA256 Checksum OK for samtools-bcftools-1.13_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by bio-mocha-1.13 for building ===> Extracting for bio-mocha-1.13 => SHA256 Checksum OK for bio-mocha_1.13-20211015.tar.gz. => SHA256 Checksum OK for samtools-bcftools-1.13_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bio-mocha-1.13 ===> Applying FreeBSD patches for bio-mocha-1.13 from /usr/ports/biology/bio-mocha/files =========================================================================== =================================================== ===> bio-mocha-1.13 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.1.12.pkg [main-arm64-default-job-07] Installing bash-5.1.12... [main-arm64-default-job-07] `-- Installing gettext-runtime-0.21... [main-arm64-default-job-07] | `-- Installing indexinfo-0.3.1... [main-arm64-default-job-07] | `-- Extracting indexinfo-0.3.1: .... done [main-arm64-default-job-07] `-- Extracting gettext-runtime-0.21: .......... done 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-1.13 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of bio-mocha-1.13 =========================================================================== =================================================== ===> Configuring for bio-mocha-1.13 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... 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 cc accepts -g... yes checking for 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-1.13 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.13' echo '#define BCFTOOLS_VERSION "1.13"' > version.h 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 convert.c:784:15: warning: variable 'sum' set but not used [-Wunused-but-set-variable] float sum = 0, *ptr = (float*)convert->dat + i*n; ^ 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 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 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 1 warning generated. 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 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 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 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 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 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 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 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 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 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 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 mpileup.c:318:16: warning: variable 'tot_ins' set but not used [-Wunused-but-set-variable] int i, tot_ins = 0; ^ mpileup.c:320:13: warning: variable 'p' set but not used [-Wunused-but-set-variable] int p = 0; ^ 2 warnings generated. 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 bam2bcf.c:505:19: warning: variable 'ties' set but not used [-Wunused-but-set-variable] double U = 0, ties = 0; ^ bam2bcf.c:549:19: warning: variable 'ties' set but not used [-Wunused-but-set-variable] double U = 0, ties = 0; ^ 2 warnings generated. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 convert.c:784:15: warning: variable 'sum' set but not used [-Wunused-but-set-variable] float sum = 0, *ptr = (float*)convert->dat + i*n; ^ 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 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 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 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 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 1 warning generated. 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 plugins/missing2ref.c:98:9: warning: variable 'an' set but not used [-Wunused-but-set-variable] int an = 0; ^ 1 warning generated. 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 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 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 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 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 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 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 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 plugins/setGT.c:411:13: warning: variable 'an' set but not used [-Wunused-but-set-variable] int an = 0, maxAC = -1, majorAllele = -1; ^ 1 warning generated. 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 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 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 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 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 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 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 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 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 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 cc -fstack-protector-strong -o test/test-rbuf test/test-rbuf.o -lz -L/usr/local/lib cc -fstack-protector-strong -o test/test-regidx test/test-regidx.o regidx.o -lhts -lpthread -lz -L/usr/local/lib 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 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bio-mocha/work/bcftools-1.13' =========================================================================== =================================================== ===> bio-mocha-1.13 depends on package: bcftools==1.13 - not found ===> Installing existing package /packages/All/bcftools-1.14.pkg [main-arm64-default-job-07] Installing bcftools-1.14... [main-arm64-default-job-07] `-- Installing gsl-2.7... [main-arm64-default-job-07] `-- Extracting gsl-2.7: .......... done [main-arm64-default-job-07] Extracting bcftools-1.14: .......... done ===> bio-mocha-1.13 depends on package: bcftools==1.13 - not found *** Error code 1 Stop. make: stopped in /usr/ports/biology/bio-mocha