From nobody Tue May 02 18:45:54 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 4Q9ptp6McBz49Hbj for ; Tue, 2 May 2023 18:45:54 +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 4Q9ptp4g6yz3yKd for ; Tue, 2 May 2023 18:45:54 +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=1683053154; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=WEDDkjoLPXt/U072UKwM3k6ahwoMxoQqnX7Uwa1kaJM=; b=efXij0fSTolGNCxdlt6mERmu0lto3wuzONJUw6++hCNFwrWd8dqrRTcnaGRtoBbG3Rqnpy lgRsZIDGljIvPKCl4qTAlYO3YVb6hXqLyfcNkUHeXLIS2xA2WhcK5v0Fimi3P1lsQCHeSY a2eGpprhOB20YF8HsZAyCwAMBDq77Qp8XuR/rmf5o8GjisUBUBmJbk3sUo7LwgvN97SWw3 wM9f3qLYo/RjFOAIRUS9zrMkc9DNlFy99GLTd4iI/RvcLqo9roVMmRN50MuL58LryYARxn 0lUuq7DGyeWTF8ZL2u1bO7U5GSmccItsNCPaxU5JNi7PKZ5Ms2rkZElVS9sGkw== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1683053154; a=rsa-sha256; cv=none; b=doBAtha3JFu8nHIoAPqjTzI9sX4Emoag3iP+4GvDUrN6njkIIiCuR1R/yr1/dv7XhddMEp c3pqg5a85JHDMajiIgydhG0Rr7kr8w+bxT+NLQJ72U9cC8nxe9rp/x8dbACg5KqUD5efPH OBEKp9xzP2hL6pLknF0crfOuB/TpCr6TtKXaRf/KQxqozKegR/xdt0tvsp/M5s/q0L/L4V TRk3o1+y88pjyyPCop0mKc3ytCzJV1eYmuwSXICZTLOF0OM1YOQttHvphRPoMnh9cZpXqu SK3HWwkNMYclAhKFInj2S+TMy2IVPflM4d6P5NccC+8ZQc6nZmBBzS4iB15OmA== Received: from ampere3.nyi.freebsd.org (ampere3.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:26]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4Q9ptp3jxKz103g for ; Tue, 2 May 2023 18:45:54 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from ampere3.nyi.freebsd.org (localhost [127.0.0.1]) by ampere3.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 342IjsAf044296 for ; Tue, 2 May 2023 18:45:54 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by ampere3.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 342Ijs86044289; Tue, 2 May 2023 18:45:54 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Tue, 2 May 2023 18:45:54 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202305021845.342Ijs86044289@ampere3.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 131releng-armv7-default][biology/seqan-apps] Failed for seqan-apps-2.4.0_11 in configure 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: h2+fbsdports@fsfe.org Log URL: https://pkg-status.freebsd.org/ampere3/data/131releng-armv7-default/8b8e64274fc0/logs/seqan-apps-2.4.0_11.log Build URL: https://pkg-status.freebsd.org/ampere3/build.html?mastername=131releng-armv7-default&build=8b8e64274fc0 Log: =>> Building biology/seqan-apps build started at Tue May 2 18:45:36 UTC 2023 port directory: /usr/ports/biology/seqan-apps package name: seqan-apps-2.4.0_11 building for: FreeBSD 131releng-armv7-default-job-03 13.1-RELEASE-p7 FreeBSD 13.1-RELEASE-p7 1301000 arm maintained by: h2+fbsdports@fsfe.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1301000 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE-p7 1301000 UNAME_r=13.1-RELEASE-p7 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/131releng-armv7-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131releng-armv7-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131releng-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131releng-armv7-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 seqan-apps-2.4.0_11: ====> Options available for the radio ARCH: you can only select none or one of them SSE4=off: Use SSE4 and POPCNT instructions AVX2=off: Use SSE4, AVX2 and POPCNT instructions NATIVE=off: Use all available instruction sets (-march=native) ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- h2+fbsdports@fsfe.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/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/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/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/seqan-apps/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 " 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-- CMAKE_BUILD_TYPE="release" RM_I386="@comment " OSREL=13.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqan-apps" EXAMPLESDIR="share/examples/seqan-apps" DATADIR="share/seqan-apps" WWWDIR="www/seqan-apps" ETCDIR="etc/seqan-apps" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan-apps DOCSDIR=/usr/local/share/doc/seqan-apps EXAMPLESDIR=/usr/local/share/examples/seqan-apps WWWDIR=/usr/local/www/seqan-apps ETCDIR=/usr/local/etc/seqan-apps --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf 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 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: armv7-unknown-freebsd13.1-gnueabihf Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE-p7 OSREL=13.1 OSVERSION=1301000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user =========================================================================== =================================================== ===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [131releng-armv7-default-job-03] Installing pkg-1.19.1_1... [131releng-armv7-default-job-03] Extracting pkg-1.19.1_1: .......... done ===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.4.0_11 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building =========================================================================== =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building => SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building ===> Extracting for seqan-apps-2.4.0_11 => SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for seqan-apps-2.4.0_11 =========================================================================== =================================================== ===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.81.0_1.pkg [131releng-armv7-default-job-03] Installing boost-libs-1.81.0_1... [131releng-armv7-default-job-03] `-- Installing icu-73.1,1... [131releng-armv7-default-job-03] `-- Extracting icu-73.1,1: .......... done [131releng-armv7-default-job-03] Extracting boost-libs-1.81.0_1: .......... done ===== Message from boost-libs-1.81.0_1: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - found ===> Returning to build of seqan-apps-2.4.0_11 ===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.26.1.pkg [131releng-armv7-default-job-03] Installing cmake-core-3.26.1... [131releng-armv7-default-job-03] `-- Installing expat-2.5.0... [131releng-armv7-default-job-03] `-- Extracting expat-2.5.0: .......... done [131releng-armv7-default-job-03] `-- Installing jsoncpp-1.9.5... [131releng-armv7-default-job-03] `-- Extracting jsoncpp-1.9.5: .......... done [131releng-armv7-default-job-03] `-- Installing libuv-1.44.2... [131releng-armv7-default-job-03] `-- Extracting libuv-1.44.2: .......... done [131releng-armv7-default-job-03] `-- Installing rhash-1.4.3... [131releng-armv7-default-job-03] | `-- Installing gettext-runtime-0.21.1... [131releng-armv7-default-job-03] | | `-- Installing indexinfo-0.3.1... [131releng-armv7-default-job-03] | | `-- Extracting indexinfo-0.3.1: .... done [131releng-armv7-default-job-03] | `-- Extracting gettext-runtime-0.21.1: .......... done [131releng-armv7-default-job-03] `-- Extracting rhash-1.4.3: .......... done [131releng-armv7-default-job-03] Extracting cmake-core-3.26.1: .......... done ===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/cmake - found ===> Returning to build of seqan-apps-2.4.0_11 ===> seqan-apps-2.4.0_11 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.11.1,2.pkg [131releng-armv7-default-job-03] Installing ninja-1.11.1,2... [131releng-armv7-default-job-03] `-- Installing python39-3.9.16_2... [131releng-armv7-default-job-03] | `-- Installing libffi-3.4.4... [131releng-armv7-default-job-03] | `-- Extracting libffi-3.4.4: .......... done [131releng-armv7-default-job-03] | `-- Installing mpdecimal-2.5.1... [131releng-armv7-default-job-03] | `-- Extracting mpdecimal-2.5.1: .......... done [131releng-armv7-default-job-03] | `-- Installing readline-8.2.1... [131releng-armv7-default-job-03] | `-- Extracting readline-8.2.1: .......... done [131releng-armv7-default-job-03] `-- Extracting python39-3.9.16_2: .......... done [131releng-armv7-default-job-03] Extracting ninja-1.11.1,2: ........ done ===== Message from python39-3.9.16_2: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py39-gdbm databases/py-gdbm@py39 py39-sqlite3 databases/py-sqlite3@py39 py39-tkinter x11-toolkits/py-tkinter@py39 ===> seqan-apps-2.4.0_11 depends on executable: ninja - found ===> Returning to build of seqan-apps-2.4.0_11 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for seqan-apps-2.4.0_11 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/seqan-apps/work/.build CMake Warning (dev) at CMakeLists.txt:9 (project): cmake_minimum_required() should be called prior to this top-level project() call. Please see the cmake-commands(7) manual for usage documentation of both commands. This warning is for project developers. Use -Wno-dev to suppress it. -- The CXX compiler identification is Clang 13.0.0 -- 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 -- Initializing SeqAn Build System... -- Selected repository dir: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0 -- No revision system found. -- Repository date not determined. -- Repository revision not determined. -- Configuring apps -- Configuring apps/alf -- Performing Test CXX14_BUILTIN -- Performing Test CXX14_BUILTIN - Success -- Looking for C++ include execinfo.h -- Looking for C++ include execinfo.h - found -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") -- Configuring apps/bs_tools -- Found ZLIB: /usr/lib/libz.so (found version "1.2.12") -- Found Boost: /usr/local/include (found version "1.81.0") -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/dfi -- Found Seqan: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include (found version "2.4.0") -- Could NOT find PythonInterp (missing: PYTHON_EXECUTABLE) (Required is at least version "2.7") -- Configuring apps/fiona CMake Error at /usr/local/share/cmake/Modules/FindOpenMP.cmake:266 (try_compile): The test project needs language C which is not enabled. Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindOpenMP.cmake:534 (_OPENMP_GET_FLAGS) apps/fiona/CMakeLists.txt:21 (find_package) CMake Error: CMAKE_C_COMPILER not set, after EnableLanguage CMake Error: CMAKE_CXX_COMPILER not set, after EnableLanguage CMake Error at /usr/local/share/cmake/Modules/FindOpenMP.cmake:266 (try_compile): Failed to configure test project build system. Call Stack (most recent call first): /usr/local/share/cmake/Modules/FindOpenMP.cmake:534 (_OPENMP_GET_FLAGS) apps/fiona/CMakeLists.txt:21 (find_package) -- Configuring incomplete, errors occurred! *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqan-apps