From nobody Mon Nov 18 17:20:09 2024 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 4XsZBf1T36z5dLwD for ; Mon, 18 Nov 2024 17:20:10 +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 "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4XsZBd6pYfz44fh for ; Mon, 18 Nov 2024 17:20:09 +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=1731950409; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=1xj+4/TqRm78NG5FbHEyzKNTzSZ9To9bWgobTEFCm04=; b=WtgEp0p2rw4SBhVxXONS76qxp6NcX5ZURoEhGOvoMt2R0kZpsKGpAgOeHfVt9aK0ndgceq K7hX1d4ClELz2tgMjTCs3wu7i4xcxAHbx0/u2QwErLGzlc8m0ReP9uwKlj3KgqPdmvB7z1 O7YbfjdS1IwBchOcJNOQxcRBQuRCvS3TfPFg3YH5Y9kmBeI808+1JuZJKrILAfYGA72bdr Fi3XaGmMhQpy7PoB+FiF1uz9nGLukbsL/5BnAhb19os65DMHFH754oeCZWYfESk81n8g0u B9lkFQsRVa3bdal+UjR+iL36uKH0OCl1nHgN+Pbc79I1dHgdGFJRvFmspZzu5g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1731950409; a=rsa-sha256; cv=none; b=VeOpOiu0Hnx0HA3WIzDhAtWInJb6ylhKjBixsTdTMFHdg0BiljwenIyS1YJgVnZaFcMBBm xvXkAGQuzyVP1DDe1QyperyPcvl/a+opiRW/17Oo/nZJnjj19Ckj5GJ5iTEXh+X0fpguGa Newz5K2Y1ukvSKME5luNfbCdcMaTxk342i2xc/pJHGZN6LQ4x6gTks9LQi9+bsx35gySXw 8uXvLV2/HZDPF1mXvnBFfLzmr2A7FCWPp/4jDm7epRgdfkJx2PsBu+/e+F2j/DLJvracV6 lpVCdt7ihViIOz0sJEGBGDQLLF/lcYusCeH8j31z7eOWH1cPKyk45a+bE/6M0Q== Received: from ampere1.nyi.freebsd.org (ampere1.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:23]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4XsZBd5yv8zpDn for ; Mon, 18 Nov 2024 17:20:09 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 924 by ampere1.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere1.nyi.freebsd.org); Mon, 18 Nov 2024 17:20:09 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - 141releng-armv7-quarterly][biology/fastani] Failed for fastani-1.34 in build Date: Mon, 18 Nov 2024 17:20:09 +0000 Message-Id: <673b7749.924.465ebc9a@ampere1.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: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/ampere1/data/141releng-armv7-quarterly/019c097f521d/logs/fastani-1.34.log Build URL: https://pkg-status.freebsd.org/ampere1/build.html?mastername=141releng-armv7-quarterly&build=019c097f521d Log: =>> Building biology/fastani build started at Mon Nov 18 17:19:58 UTC 2024 port directory: /usr/ports/biology/fastani package name: fastani-1.34 building for: FreeBSD 141releng-armv7-quarterly-job-13 14.1-RELEASE-p6 FreeBSD 14.1-RELEASE-p6 1401000 arm maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 597 Oct 15 01:02 /usr/ports/biology/fastani/Makefile Ports top last git commit: 019c097f5 Ports top unclean checkout: no Port dir last git commit: db5128afd Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1401000 Job Id: 13 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1401000 UNAME_v=FreeBSD 14.1-RELEASE-p6 1401000 UNAME_r=14.1-RELEASE-p6 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 MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/141releng-armv7-quarterly/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/141releng-armv7-quarterly/13/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=141releng-armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/141releng-armv7-quarterly/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastani/work/.cache HOME=/wrkdirs/usr/ports/biology/fastani/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastani/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastani/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-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastani/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastani/work/.cache HOME=/wrkdirs/usr/ports/biology/fastani/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastani/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastani/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 DESTDIR=/wrkdirs/usr/ports/biology/fastani/work/stage 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 " BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0 644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=14.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/fastani" EXAMPLESDIR="share/examples/fastani" DATADIR="share/fastani" WWWDIR="www/fastani" ETCDIR="etc/fastani" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fastani DOCSDIR=/usr/local/share/doc/fastani EXAMPLESDIR=/usr/local/share/examples/fastani WWWDIR=/usr/local/www/fastani ETCDIR=/usr/local/etc/fastani --End SUB_LIST-- ---Begin 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 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # 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 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" 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) 524288 stack size (kbytes, -s) 65536 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) 8192 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License APACHE20 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastani-1.34 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [141releng-armv7-quarterly-job-13] Installing pkg-1.21.3... [141releng-armv7-quarterly-job-13] Extracting pkg-1.21.3: .......... done ===> fastani-1.34 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fastani-1.34 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by fastani-1.34 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by fastani-1.34 for building => SHA256 Checksum OK for ParBLiSS-FastANI-v1.34_GH0.tar.gz. => SHA256 Checksum OK for catchorg-Catch2-359542d_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License APACHE20 accepted by the user ===> Fetching all distfiles required by fastani-1.34 for building ===> Extracting for fastani-1.34 => SHA256 Checksum OK for ParBLiSS-FastANI-v1.34_GH0.tar.gz. => SHA256 Checksum OK for catchorg-Catch2-359542d_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for fastani-1.34 ===> Applying FreeBSD patches for fastani-1.34 from /usr/ports/biology/fastani/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastani-1.34 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.30.5.pkg [141releng-armv7-quarterly-job-13] Installing cmake-core-3.30.5... [141releng-armv7-quarterly-job-13] `-- Installing expat-2.6.3... [141releng-armv7-quarterly-job-13] `-- Extracting expat-2.6.3: .......... done [141releng-armv7-quarterly-job-13] `-- Installing jsoncpp-1.9.6_1... [141releng-armv7-quarterly-job-13] `-- Extracting jsoncpp-1.9.6_1: .......... done [141releng-armv7-quarterly-job-13] `-- Installing libuv-1.49.0... [141releng-armv7-quarterly-job-13] `-- Extracting libuv-1.49.0: .......... done [141releng-armv7-quarterly-job-13] `-- Installing rhash-1.4.4_1... [141releng-armv7-quarterly-job-13] | `-- Installing gettext-runtime-0.22.5... [141releng-armv7-quarterly-job-13] | | `-- Installing indexinfo-0.3.1... [141releng-armv7-quarterly-job-13] | | `-- Extracting indexinfo-0.3.1: .... done [141releng-armv7-quarterly-job-13] | `-- Extracting gettext-runtime-0.22.5: .......... done [141releng-armv7-quarterly-job-13] `-- Extracting rhash-1.4.4_1: .......... done [141releng-armv7-quarterly-job-13] Extracting cmake-core-3.30.5: .......... done ===> fastani-1.34 depends on file: /usr/local/bin/cmake - found ===> Returning to build of fastani-1.34 ===> fastani-1.34 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,4.pkg [141releng-armv7-quarterly-job-13] Installing ninja-1.11.1,4... [141releng-armv7-quarterly-job-13] `-- Installing python311-3.11.10... [141releng-armv7-quarterly-job-13] | `-- Installing libffi-3.4.6... [141releng-armv7-quarterly-job-13] | `-- Extracting libffi-3.4.6: .......... done [141releng-armv7-quarterly-job-13] | `-- Installing mpdecimal-4.0.0... [141releng-armv7-quarterly-job-13] | `-- Extracting mpdecimal-4.0.0: .......... done [141releng-armv7-quarterly-job-13] | `-- Installing readline-8.2.13_1... [141releng-armv7-quarterly-job-13] | `-- Extracting readline-8.2.13_1: .......... done [141releng-armv7-quarterly-job-13] `-- Extracting python311-3.11.10: .......... done [141releng-armv7-quarterly-job-13] Extracting ninja-1.11.1,4: ........ done ===== Message from python311-3.11.10: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py311-gdbm databases/py-gdbm@py311 py311-sqlite3 databases/py-sqlite3@py311 py311-tkinter x11-toolkits/py-tkinter@py311 ===> fastani-1.34 depends on executable: ninja - found ===> Returning to build of fastani-1.34 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> fastani-1.34 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [141releng-armv7-quarterly-job-13] Installing gsl-2.7.1_1... [141releng-armv7-quarterly-job-13] Extracting gsl-2.7.1_1: .......... done ===> fastani-1.34 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of fastani-1.34 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for fastani-1.34 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/fastani/work/.build -- The CXX compiler identification is Clang 18.1.5 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found ZLIB: /usr/lib/libz.so (found suitable version "1.3.1", minimum required is "1.1") Using zlib library v1.3.1 -- Could NOT find OpenMP_CXX (missing: OpenMP_CXX_FLAGS OpenMP_CXX_LIB_NAMES) -- Could NOT find OpenMP (missing: OpenMP_CXX_FOUND) NOTE: OpenMP not found; Compiling as a single threaded app... -- Found GSL: /usr/local/include (found suitable version "2.7.1", minimum required is "1.6") GSL v2.7.1 Found: -- Configuring done (1.2s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_COLOR_MAKEFILE CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE FETCHCONTENT_FULLY_DISCONNECTED THREADS_HAVE_PTHREAD_ARG -- Build files have been written to: /wrkdirs/usr/ports/biology/fastani/work/.build =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Building for fastani-1.34 [ 33% 2/3] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/main.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/main.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/main.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/main.cpp [ 66% 2/3] /usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp FAILED: CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o /usr/bin/c++ -I/wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src -I/usr/local/include -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -MD -MT CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -MF CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o.d -o CMakeFiles/fastANI.dir/src/cgi/core_genome_identity.cpp.o -c /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp /wrkdirs/usr/ports/biology/fastani/work/FastANI-1.34/src/cgi/core_genome_identity.cpp:11:10: fatal error: 'omp.h' file not found 11 | #include | ^~~~~~~ 1 error generated. ninja: build stopped: subcommand failed. ===> 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/fastani