From nobody Sun Oct 29 17:45:26 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 4SJP1y6C2kz4y07T for ; Sun, 29 Oct 2023 17:45:26 +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 4SJP1y2bS0z4HBb for ; Sun, 29 Oct 2023 17:45:26 +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=1698601526; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=WKXm6sfTL2zRRD95KzvEReWOT3BsMqw18qc14LRkSpg=; b=WCEBzi3VFioCAEJ+/oGOPm73Blyal55IxVEc0Du59MYPwMqNU8sNArEipA50oa3ckdQTLa LSZmMSnOS4sk+wbjZPu7LOjTAI88UJePcK4gtBiehKYP+gkpgQwSBTvhq0SePwjVcQAeQ+ 6S5iDVbCk5jifLRqUql3NtZr+Sqhu42J3RqdjQptu6PToOeLSByHgoaPnQmBbpCGMbnpf3 t5PWUXuo7SXpqb3MiijnrIK1dcvVKuNPuDprZAO44d5NGDp8wcZCeKtZB6l/ZbtHmTo5gR Il4n1V4G0wrCaQBOLa/cSloDIq4k320Nbm6FUK8SHPRQWoQbjYJtsSPUFRX2bg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1698601526; a=rsa-sha256; cv=none; b=mxV1Um+vyHIdHQ5fCrrFdfceKbgB2DH0V3jfTbNpq4lqEe0ny/c6Xqlbv6ASz1RN7rjewd c5v9UuYbSVduWwEq6XQFm0pbWKq/C+6n71zLhgHNqQt0tTIuDQcaHUsIr7h+pZPhhObE59 fB/2rZXKL7qSf3lQo+E9cT5Z5c52/N5hzldQs3PbQYCyESFZZtImQIlCRBQQnpPpAENSqV d0+1N7nDvc56XHCjIpwCtbPLy3u43k+WfjPXAJmqZ3rRCPlSiTkjrQVSLSoaXfUIemUUTq g1EBS/0Ta1nEUmB/OKLYvMTNixdYrWJVa1C7N+vnRjhWqdoYOnHd9/Vfnwib0Q== Received: from beefy16.nyi.freebsd.org (beefy16.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:1f]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4SJP1y1TJ0zns9 for ; Sun, 29 Oct 2023 17:45:26 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 1270 by beefy16.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy16.nyi.freebsd.org); Sun, 29 Oct 2023 17:45:26 +0000 To: jwb@FreeBSD.org Subject: [package - 132amd64-default][biology/biolibc-tools] Failed for biolibc-tools-0.1.4.9 in build Cc: pkg-fallout@FreeBSD.org Date: Sun, 29 Oct 2023 17:45:26 +0000 Message-Id: <653e9a36.1270.7cd21959@beefy16.nyi.freebsd.org> From: 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/beefy16/data/132amd64-default/7190d05ec515/logs/biolibc-tools-0.1.4.9.log Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=132amd64-default&build=7190d05ec515 Log: =>> Building biology/biolibc-tools build started at Sun Oct 29 17:45:21 UTC 2023 port directory: /usr/ports/biology/biolibc-tools package name: biolibc-tools-0.1.4.9 building for: FreeBSD 132amd64-default-job-11 13.2-RELEASE-p4 FreeBSD 13.2-RELEASE-p4 amd64 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1500000 Jail OSVERSION: 1302001 Job Id: 11 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1302001 UNAME_v=FreeBSD 13.2-RELEASE-p4 UNAME_r=13.2-RELEASE-p4 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/132amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/132amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=132amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/132amd64-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-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biolibc-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biolibc-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biolibc-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/biolibc-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/biolibc-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biolibc-tools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- VERSION=0.1.4.9 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/biolibc-tools/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/biolibc-tools/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/biolibc-tools/work/.cache HOME=/wrkdirs/usr/ports/biology/biolibc-tools/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/biolibc-tools/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/biolibc-tools/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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-- OSREL=13.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/biolibc-tools" EXAMPLESDIR="share/examples/biolibc-tools" DATADIR="share/biolibc-tools" WWWDIR="www/biolibc-tools" ETCDIR="etc/biolibc-tools" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biolibc-tools DOCSDIR=/usr/local/share/doc/biolibc-tools EXAMPLESDIR=/usr/local/share/examples/biolibc-tools WWWDIR=/usr/local/www/biolibc-tools ETCDIR=/usr/local/etc/biolibc-tools --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 3 jobs MAKE_JOBS_NUMBER=3 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: x86_64-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: x86_64-unknown-freebsd13.2 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 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: x86_64-unknown-freebsd13.2 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.2-RELEASE-p4 OSREL=13.2 OSVERSION=1302001 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 BSD2CLAUSE accepted by the user =========================================================================== =================================================== ===> biolibc-tools-0.1.4.9 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.8.pkg [132amd64-default-job-11] Installing pkg-1.20.8... [132amd64-default-job-11] Extracting pkg-1.20.8: .......... done ===> biolibc-tools-0.1.4.9 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of biolibc-tools-0.1.4.9 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by biolibc-tools-0.1.4.9 for building =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by biolibc-tools-0.1.4.9 for building => SHA256 Checksum OK for auerlab-biolibc-tools-0.1.4-9-g6d96043_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by biolibc-tools-0.1.4.9 for building ===> Extracting for biolibc-tools-0.1.4.9 => SHA256 Checksum OK for auerlab-biolibc-tools-0.1.4-9-g6d96043_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for biolibc-tools-0.1.4.9 =========================================================================== =================================================== ===> biolibc-tools-0.1.4.9 depends on package: uthash>0 - not found ===> Installing existing package /packages/All/uthash-2.3.0.pkg [132amd64-default-job-11] Installing uthash-2.3.0... [132amd64-default-job-11] Extracting uthash-2.3.0: .......... done ===> biolibc-tools-0.1.4.9 depends on package: uthash>0 - found ===> Returning to build of biolibc-tools-0.1.4.9 =========================================================================== =================================================== ===> biolibc-tools-0.1.4.9 depends on shared library: libbiolibc.so - not found ===> Installing existing package /packages/All/biolibc-0.2.6.pkg [132amd64-default-job-11] Installing biolibc-0.2.6... [132amd64-default-job-11] `-- Installing libxtend-0.2.0... [132amd64-default-job-11] `-- Extracting libxtend-0.2.0: .......... done [132amd64-default-job-11] Extracting biolibc-0.2.6: .......... done ===> biolibc-tools-0.1.4.9 depends on shared library: libbiolibc.so - found (/usr/local/lib/libbiolibc.so) ===> Returning to build of biolibc-tools-0.1.4.9 ===> biolibc-tools-0.1.4.9 depends on shared library: libxtend.so - found (/usr/local/lib/libxtend.so) ===> biolibc-tools-0.1.4.9 depends on shared library: libxxhash.so - not found ===> Installing existing package /packages/All/xxhash-0.8.2.pkg [132amd64-default-job-11] Installing xxhash-0.8.2... [132amd64-default-job-11] Extracting xxhash-0.8.2: .......... done ===> biolibc-tools-0.1.4.9 depends on shared library: libxxhash.so - found (/usr/local/lib/libxxhash.so) ===> Returning to build of biolibc-tools-0.1.4.9 =========================================================================== =================================================== ===> Configuring for biolibc-tools-0.1.4.9 =========================================================================== =================================================== ===> Building for biolibc-tools-0.1.4.9 (cd /wrkdirs/usr/ports/biology/biolibc-tools/work/biolibc-tools-0.1.4-9-g6d96043 && /usr/bin/make LOCALBASE=/usr/local depend) rm -f Makefile.depend for file in *.c; do cc -isystem ../local/include -isystem /usr/local/include -MM ${file} >> Makefile.depend; printf "\t\${CC} -c \${CFLAGS} ${file}\n\n" >> Makefile.depend; done --- fastx2tsv.o --- --- fastx-derep.o --- --- vcf-search.o --- --- fastx2tsv.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include fastx2tsv.c --- fastx-derep.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include fastx-derep.c --- vcf-search.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include vcf-search.c --- fasta2seq.o --- --- fastx2tsv.o --- fastx2tsv.c:42:2: warning: implicit declaration of function 'strtr' is invalid in C99 [-Wimplicit-function-declaration] strtr(bl_fastx_desc(&rec), "\t", " ", 0); ^ 1 warning generated. --- find-orfs.o --- --- fasta2seq.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include fasta2seq.c --- gff3-to-bed.o --- --- find-orfs.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include find-orfs.c --- gff3-to-bed.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include gff3-to-bed.c --- extract-seq.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include extract-seq.c --- chrom-lens.o --- --- fastx-stats.o --- --- chrom-lens.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include chrom-lens.c --- fastx-stats.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include fastx-stats.c --- ensemblid2gene.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include ensemblid2gene.c --- vcf-downsample.o --- cc -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DLIBEXECDIR=\"/usr/local/libexec/biolibc-tools\" -DXXH_INLINE_ALL -DVERSION=\"`./version.sh`\" -Wno-char-subscripts -isystem /usr/local/include -isystem /usr/local/include vcf-downsample.c --- ensemblid2gene.o --- ensemblid2gene.c:51:82: error: use of undeclared identifier 'strptrcmp' qsort(id_list, id_count, sizeof(*id_list), (int(*)(const void *,const void*))strptrcmp); ^ ensemblid2gene.c:77:44: error: use of undeclared identifier 'strptrcasecmp' (int (*)(const void *, const void *))strptrcasecmp); ^ 2 errors generated. *** [ensemblid2gene.o] Error code 1 make[1]: stopped in /wrkdirs/usr/ports/biology/biolibc-tools/work/biolibc-tools-0.1.4-9-g6d96043 1 error make[1]: stopped in /wrkdirs/usr/ports/biology/biolibc-tools/work/biolibc-tools-0.1.4-9-g6d96043 ===> 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/biolibc-tools