From nobody Sat Jun 24 12:55:20 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 4QpDbs1Lr5z4h5Q7 for ; Sat, 24 Jun 2023 12:55:21 +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 4QpDbr2n1Fz3hWB for ; Sat, 24 Jun 2023 12:55:20 +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=1687611320; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=OOuW2ubyN6nVotjXindi44/U9QgK5UjLd8qJPqhiwqs=; b=YjZvyTJ1svtGkrSvF2Ppa3vSmPjoWa1AhBC+vt4Nx74LmOWPaiz8epf4iYPR3UpV2jWWpe x7+pXTDv1znGetdA75ChwaavFKxr7F+wdFVdB+ADqpstj0wCj0WCn+cMt0ehi7YJC+MwYa 9QWl1/sEwRMQSy5LxgmU6u6nyNlcg5zALQsirhCDD8W0ysZwY1BbDsoxmwonkxM3Shb5y9 A/JptqQFUa0NUOUQ4KD/RQe2/odQmoEa7PkK0uTiXVlT74QOuvsuAlcXUYb6AzN+sPVOCU Mge2WKKgZ/FHu1BEksU7scyKphuGxkBnDGTHds4zRqh8fl+rL8FoNpXsOjW+yg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1687611320; a=rsa-sha256; cv=none; b=G5BisSlxnX+IfpbCD9U8bXh2dfsi7kyNAs6E4fn3LnKJ67FT9EQSN0+6umxPknUfNatoSu 4ZR8t9oRqN6irYNxvHGl0PnO1/+Os8rJA6YhFy8MfhcNopZMWVynAHqCX9niOYtYz8QhWa /N9MVKas1ZOkGVDDbEhDU7OpupnXecvvqzjbd3pYIy+qakeIwpOCowh8HHy1EI58JYf/Ov axl0fQ1mYJEYrrDqpEX+KwdNURRVs441YKIUBCrxct4BUfQRVY8YQ+nVMFZ9BYHIt8BI4l CbotWx+wH7eEdNepTMtzcqd8Tp/HtUIywCkR9Uhd+5QeNtRStYiHvK9g946WLw== Received: from beefy8.nyi.freebsd.org (beefy8.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:17]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4QpDbr1rKmzmpt for ; Sat, 24 Jun 2023 12:55:20 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 6592 by beefy8.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy8.nyi.freebsd.org); Sat, 24 Jun 2023 12:55:20 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - main-armv6-default][biology/paml] Failed for paml-4.10.6 in build Date: Sat, 24 Jun 2023 12:55:20 +0000 Message-Id: <6496e7b8.6592.6cd75b3f@beefy8.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: jrm@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy8/data/main-armv6-default/p4785b313b958_s9ead001d5b/logs/paml-4.10.6.log Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=p4785b313b958_s9ead001d5b Log: =>> Building biology/paml build started at Sat Jun 24 12:51:30 UTC 2023 port directory: /usr/ports/biology/paml package name: paml-4.10.6 building for: FreeBSD main-armv6-default-job-04 14.0-CURRENT FreeBSD 14.0-CURRENT 1400092 arm maintained by: jrm@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400088 Jail OSVERSION: 1400092 Job Id: 04 !!! Jail is newer than host. (Jail: 1400092, Host: 1400088) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1400092 UNAME_v=FreeBSD 14.0-CURRENT 1400092 UNAME_r=14.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-armv6-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for paml-4.10.6: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jrm@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/paml/work/.cache HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/paml/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-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/paml/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/paml/work/.cache HOME=/wrkdirs/usr/ports/biology/paml/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/paml/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/paml/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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/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-- PORTDOCS="" PORTEXAMPLES="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/paml" EXAMPLESDIR="share/examples/paml" DATADIR="share/paml" WWWDIR="www/paml" ETCDIR="etc/paml" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/paml DOCSDIR=/usr/local/share/doc/paml EXAMPLESDIR=/usr/local/share/examples/paml WWWDIR=/usr/local/www/paml ETCDIR=/usr/local/etc/paml --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv6 ARCH=${MACHINE_ARCH} #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_53255a77=yes CC_OUTPUT_9d218390_911cfe02=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes CC_OUTPUT_9d218390_af59ad06=yes CC_OUTPUT_9d218390_a15f3fcf=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400092 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> paml-4.10.6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-armv6-default-job-04] Installing pkg-1.19.1_1... [main-armv6-default-job-04] Extracting pkg-1.19.1_1: .......... done ===> paml-4.10.6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of paml-4.10.6 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.10.6 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.10.6 for building => SHA256 Checksum OK for abacus-gene-paml-v4.10.6_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by paml-4.10.6 for building ===> Extracting for paml-4.10.6 => SHA256 Checksum OK for abacus-gene-paml-v4.10.6_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for paml-4.10.6 ===> Converting DOS text files to UNIX text files =========================================================================== =================================================== ===> paml-4.10.6 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-armv6-default-job-04] Installing gmake-4.3_2... [main-armv6-default-job-04] `-- Installing gettext-runtime-0.21.1... [main-armv6-default-job-04] | `-- Installing indexinfo-0.3.1... [main-armv6-default-job-04] | `-- Extracting indexinfo-0.3.1: .... done [main-armv6-default-job-04] `-- Extracting gettext-runtime-0.21.1: .......... done [main-armv6-default-job-04] Extracting gmake-4.3_2: .......... done ===> paml-4.10.6 depends on package: gmake>=4.3 - found ===> Returning to build of paml-4.10.6 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for paml-4.10.6 =========================================================================== =================================================== ===> Building for paml-4.10.6 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/paml/work/paml-4.10.6/src' cc -O3 -Wall -Wno-unused-result -c baseml.c In file included from baseml.c:137: ./treesub.c:2993:19: warning: result of comparison of constant -1 with expression of type 'char' is always false [-Wtautological-constant-out-of-range-compare] if (line[i] == EOF) ~~~~~~~ ^ ~~~ ./treesub.c:4606:8: warning: variable 'step' set but not used [-Wunused-but-set-variable] int step = 0, ntree = 0, nmove = 0, improve = 0, ineighb, i; ^ ./treesub.c:6257:35: warning: variable 'nchange' set but not used [-Wunused-but-set-variable] int nid = tree.nnode - com.ns, nchange; ^ 3 warnings generated. cc -O3 -Wall -Wno-unused-result -c tools.c tools.c:106:8: warning: variable 'i' set but not used [-Wunused-but-set-variable] int i; ^ tools.c:664:27: warning: argument 'pi' of type 'double[4]' with mismatched bound [-Warray-parameter] double rates[], double pi[4], double kappa, int isHKY85) ^ ./paml.h:174:89: note: previously declared as 'double[]' here int EvolveHKY85 (char source[], char target[], int ls, double t, double rates[], double pi[], double kapa, int isHKY85); ^ tools.c:6137:30: warning: variable 'percentUse' set but not used [-Wunused-but-set-variable] double factor = 2, step1, percentUse = 0; ^ 3 warnings generated. cc -O3 -Wall -Wno-unused-result -o baseml baseml.o tools.o -lm cc: error: unable to execute command: Abort trap (core dumped) cc: error: linker command failed due to signal (use -v to see invocation) gmake[1]: *** [Makefile:12: baseml] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/paml/work/paml-4.10.6/src' *** Error code 2 Stop. make: stopped in /usr/ports/biology/paml