From nobody Mon Jun 26 15:43:44 2023 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 4QqXFF1ml6z4kj8d for ; Mon, 26 Jun 2023 15:43:45 +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 4QqXFD2sJDz3hyl for ; Mon, 26 Jun 2023 15:43:44 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1687794224; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=xCw/iivt6jd4ZRpYJ2pYvc7ovP64/NsjjOpCPYQ5ze4=; b=yY6uSjC1K9TsghNaCfIU+z9bRzzxUB5OPD3WiRB3kdqRhjShXzthHdHedY+Hn0dwQz6PEx p1t2F/ojeCHgVnvRrfa3jp5IlrVppjmfdovobngsTXl9vyv7PQSGkXu1g6et5jmiJkVAU1 VL1ZnOt23teX+bIURwaqe44LP/GTRBqWy2eT1MOdYAHQvwe8ExZeMBV4BUpB+KjRUYGEsC VNgX9bnO5n2ewEBliHGkWMv2wco22CZa1Yo+0oFRyJ8bZ2zHZp+h5a8zzfcQqyMblbsjn4 s3xKKbB/5krfJUs7ZvI6+vM8qkmG/3MEEuzYy5O+CKyv6GDiAoXa9bbQni2/zA== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1687794224; a=rsa-sha256; cv=none; b=uPKsLNTu6J2Q9S2zhvj8m6NmOvCJSW3WqpBJjOeKqJUEQmqjb1PqrMB8LoUg2XRI2bnGBv vQbZHTN6CJ6sHEBwlcsbNZC8bnrL1mUqfIfNN3bS4F8t54szu3EJhgkwiXr9V54KDa97i8 jzaNHX6cyM1HcKC9SDkf907ASCmMwB887Mt1OyyquyDBXmv22GUj/hBxBLRKARtBigjlWZ Qm44uduIqvCb/VPl4oqzx3PtGpEpV8RvOCgsSLqvGV//vekHtadOMh7uWOAwZI+dABsleI wpt4LOtVwxvAgvJHzkDl/gojyvERi2ZKnc/5rKQpAcjo4IIZN06bwy3xzQYQqQ== Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:21]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4QqXFD1y2vzGJq for ; Mon, 26 Jun 2023 15:43:44 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 2499 by beefy18.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy18.nyi.freebsd.org); Mon, 26 Jun 2023 15:43:44 +0000 To: jwb@FreeBSD.org Subject: [package - main-amd64-default][biology/bcf-score] Failed for bcf-score-1.16 in build Cc: pkg-fallout@FreeBSD.org Date: Mon, 26 Jun 2023 15:43:44 +0000 Message-Id: <6499b230.2499.766d81ed@beefy18.nyi.freebsd.org> From: 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: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p4785b313b958_se8efee297c/logs/bcf-score-1.16.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p4785b313b958_se8efee297c Log: =>> Building biology/bcf-score build started at Mon Jun 26 15:42:59 UTC 2023 port directory: /usr/ports/biology/bcf-score package name: bcf-score-1.16 building for: FreeBSD main-amd64-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400091 amd64 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1400091 Job Id: 05 !!! Jail is newer than host. (Jail: 1400091, Host: 1400089) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400091 UNAME_v=FreeBSD 14.0-CURRENT 1400091 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=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-amd64-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/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/bcf-score/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcf-score/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bcf-score/work/.cache HOME=/wrkdirs/usr/ports/biology/bcf-score/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bcf-score/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bcf-score/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.71 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/bcf-score/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/bcf-score/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/bcf-score/work/.cache HOME=/wrkdirs/usr/ports/biology/bcf-score/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/bcf-score/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/bcf-score/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 DEFAULT_AUTOCONF=2.71 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 -is ystem /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/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 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/bcf-score" EXAMPLESDIR="share/examples/bcf-score" DATADIR="share/bcf-score" WWWDIR="www/bcf-score" ETCDIR="etc/bcf-score" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/bcf-score DOCSDIR=/usr/local/share/doc/bcf-score EXAMPLESDIR=/usr/local/share/examples/bcf-score WWWDIR=/usr/local/www/bcf-score ETCDIR=/usr/local/etc/bcf-score --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 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/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_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_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400091 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES 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) 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 =========================================================================== =================================================== ===> bcf-score-1.16 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-amd64-default-job-05] Installing pkg-1.19.1_1... [main-amd64-default-job-05] Extracting pkg-1.19.1_1: .......... done ===> bcf-score-1.16 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of bcf-score-1.16 =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by bcf-score-1.16 for building =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by bcf-score-1.16 for building => SHA256 Checksum OK for score_1.16-20221221.tar.gz. => SHA256 Checksum OK for samtools-bcftools-1.16-1.17_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License MIT accepted by the user ===> Fetching all distfiles required by bcf-score-1.16 for building ===> Extracting for bcf-score-1.16 => SHA256 Checksum OK for score_1.16-20221221.tar.gz. => SHA256 Checksum OK for samtools-bcftools-1.16-1.17_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for bcf-score-1.16 ===> Applying FreeBSD patches for bcf-score-1.16 from /usr/ports/biology/bcf-score/files =========================================================================== =================================================== ===> bcf-score-1.16 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.2.15.pkg configure.ac:94: warning: _AC_CONFIG_SUBDIRS: you should use literals ./lib/autoconf/status.m4:1096: 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 the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... 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 bcf-score-1.16 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.17' echo '#define BCFTOOLS_VERSION "1.17"' > 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 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 cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o vcfhead.o vcfhead.c 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 vcfbuf.c:249:32: warning: implicit truncation from 'int' to a one-bit wide bit-field changes value from 1 to -1 [-Wsingle-bit-bitfield-constant-conversion] buf->vcf[i].af_set = 1; ^ ~ 1 warning generated. 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 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 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 bam2bcf_iaux.o bam2bcf_iaux.c cc -Wall -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I. -isystem /usr/local/include -c -o read_consensus.o read_consensus.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 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/blupx.so version.c plugins/blupx.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 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/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/liftover.so version.c plugins/liftover.c -L/usr/local/lib plugins/liftover.c:1106:9: warning: absolute value function 'abs' given an argument of type 'hts_pos_t' (aka 'long') but has parameter of type 'int' which may cause truncation of value [-Wabsolute-value] if (abs(right_pos - left_pos) > indel_win) return -1; ^ plugins/liftover.c:1106:9: note: use function 'labs' instead if (abs(right_pos - left_pos) > indel_win) return -1; ^~~ labs 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/mendelian2.so version.c plugins/mendelian2.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/metal.so version.c plugins/metal.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/missing2ref.so version.c plugins/missing2ref.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/munge.so version.c plugins/munge.c -L/usr/local/lib plugins/munge.c:123:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] static const int (*tsv_setters[])(tsv_t *tsv, bcf1_t *rec, void *usr) = {tsv_setter_id_flexible, // SNP ^~~~~~~~~~~~~~~~~~~~~~ plugins/munge.c:124:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_setter_pos_flexible, // BP ^~~~~~~~~~~~~~~~~~~~~~~ plugins/munge.c:125:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_setter_chrom_flexible, // CHR ^~~~~~~~~~~~~~~~~~~~~~~~~ plugins/munge.c:126:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_allele, // A1 ^~~~~~~~~~~~~~~ plugins/munge.c:127:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_allele, // A2 ^~~~~~~~~~~~~~~ plugins/munge.c:128:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float_and_minus_log10, // P ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ plugins/munge.c:129:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // Z ^~~~~~~~~~~~~~ plugins/munge.c:130:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float_and_log, // OR ^~~~~~~~~~~~~~~~~~~~~~ plugins/munge.c:131:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // BETA ^~~~~~~~~~~~~~ plugins/munge.c:132:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // N ^~~~~~~~~~~~~~ plugins/munge.c:133:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // N_CAS ^~~~~~~~~~~~~~ plugins/munge.c:134:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // N_CON ^~~~~~~~~~~~~~ plugins/munge.c:135:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // INFO ^~~~~~~~~~~~~~ plugins/munge.c:136:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // FRQ ^~~~~~~~~~~~~~ plugins/munge.c:137:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_allele, // A0 ^~~~~~~~~~~~~~~ plugins/munge.c:138:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // SE ^~~~~~~~~~~~~~ plugins/munge.c:139:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // LP ^~~~~~~~~~~~~~ plugins/munge.c:140:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // AC ^~~~~~~~~~~~~~ plugins/munge.c:141:74: error: incompatible function pointer types initializing 'const int (*)(tsv_t *, bcf1_t *, void *)' (aka 'const int (*)(struct _tsv_t *, struct bcf1_t *, void *)') with an expression of type 'int (tsv_t *, bcf1_t *, void *)' (aka 'int (struct _tsv_t *, struct bcf1_t *, void *)') [-Wincompatible-function-pointer-types] tsv_read_float, // NEFF ^~~~~~~~~~~~~~ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. gmake[1]: *** [Makefile:200: plugins/munge.so] Error 1 gmake[1]: *** Waiting for unfinished jobs.... gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/bcf-score/work/bcftools-1.17' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/bcf-score