[package - 133amd64-default][science/dssp] Failed for dssp-4.4.2_1 in configure
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Date: Mon, 16 Sep 2024 07:10:17 UTC
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/beefy16/data/133amd64-default/14728ba1fb78/logs/dssp-4.4.2_1.log Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=133amd64-default&build=14728ba1fb78 Log: =>> Building science/dssp build started at Mon Sep 16 07:09:40 UTC 2024 port directory: /usr/ports/science/dssp package name: dssp-4.4.2_1 building for: FreeBSD 133amd64-default-job-09 13.3-RELEASE-p6 FreeBSD 13.3-RELEASE-p6 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 646 Aug 1 01:01 /usr/ports/science/dssp/Makefile Ports top last git commit: 14728ba1fb7 Ports top unclean checkout: no Port dir last git commit: b4d3bbb5d13 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1303001 Job Id: 09 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1303001 UNAME_v=FreeBSD 13.3-RELEASE-p6 UNAME_r=13.3-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/133amd64-default/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/133amd64-default/09/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=133amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/133amd64-default/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/science/dssp/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/dssp/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/dssp/work/.cache HOME=/wrkdirs/usr/ports/science/dssp/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/dssp/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/dssp/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/science/dssp/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/dssp/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/dssp/work/.cache HOME=/wrkdirs/usr/ports/science/dssp/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/dssp/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/dssp/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 " 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="i nstall -m 444" --End MAKE_ENV-- --PLIST_SUB-- CMAKE_BUILD_TYPE="release" OSREL=13.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/dssp" EXAMPLESDIR="share/examples/dssp" DATADIR="share/dssp" WWWDIR="www/dssp" ETCDIR="etc/dssp" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/dssp DOCSDIR=/usr/local/share/doc/dssp EXAMPLESDIR=/usr/local/share/examples/dssp WWWDIR=/usr/local/www/dssp ETCDIR=/usr/local/etc/dssp --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 #### #### # 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) 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) 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-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD2CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> dssp-4.4.2_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [133amd64-default-job-09] Installing pkg-1.21.3... [133amd64-default-job-09] Extracting pkg-1.21.3: .......... done ===> dssp-4.4.2_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of dssp-4.4.2_1 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by dssp-4.4.2_1 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by dssp-4.4.2_1 for building => SHA256 Checksum OK for PDB-REDO-dssp-v4.4.2_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by dssp-4.4.2_1 for building ===> Extracting for dssp-4.4.2_1 => SHA256 Checksum OK for PDB-REDO-dssp-v4.4.2_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for dssp-4.4.2_1 =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> dssp-4.4.2_1 depends on package: libmcfp>0 - not found ===> Installing existing package /packages/All/libmcfp-1.3.3.pkg [133amd64-default-job-09] Installing libmcfp-1.3.3... [133amd64-default-job-09] Extracting libmcfp-1.3.3: .......... done ===> dssp-4.4.2_1 depends on package: libmcfp>0 - found ===> Returning to build of dssp-4.4.2_1 ===> dssp-4.4.2_1 depends on executable: mrc - not found ===> Installing existing package /packages/All/mrc-1.3.13.pkg [133amd64-default-job-09] Installing mrc-1.3.13... [133amd64-default-job-09] Extracting mrc-1.3.13: ...... done ===> dssp-4.4.2_1 depends on executable: mrc - found ===> Returning to build of dssp-4.4.2_1 ===> dssp-4.4.2_1 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-core-3.30.3_1.pkg [133amd64-default-job-09] Installing cmake-core-3.30.3_1... [133amd64-default-job-09] `-- Installing expat-2.6.2... [133amd64-default-job-09] `-- Extracting expat-2.6.2: .......... done [133amd64-default-job-09] `-- Installing jsoncpp-1.9.6_1... [133amd64-default-job-09] `-- Extracting jsoncpp-1.9.6_1: .......... done [133amd64-default-job-09] `-- Installing libuv-1.48.0... [133amd64-default-job-09] `-- Extracting libuv-1.48.0: .......... done [133amd64-default-job-09] `-- Installing rhash-1.4.4_1... [133amd64-default-job-09] | `-- Installing gettext-runtime-0.22.5... [133amd64-default-job-09] | | `-- Installing indexinfo-0.3.1... [133amd64-default-job-09] | | `-- Extracting indexinfo-0.3.1: .... done [133amd64-default-job-09] | `-- Extracting gettext-runtime-0.22.5: .......... done [133amd64-default-job-09] `-- Extracting rhash-1.4.4_1: .......... done [133amd64-default-job-09] Extracting cmake-core-3.30.3_1: .......... done ===> dssp-4.4.2_1 depends on file: /usr/local/bin/cmake - found ===> Returning to build of dssp-4.4.2_1 =========================================================================== =======================<phase: lib-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> dssp-4.4.2_1 depends on shared library: libboost_iostreams.so - not found ===> Installing existing package /packages/All/boost-libs-1.84.0.pkg [133amd64-default-job-09] Installing boost-libs-1.84.0... [133amd64-default-job-09] `-- Installing icu-74.2_1,1... [133amd64-default-job-09] `-- Extracting icu-74.2_1,1: .......... done [133amd64-default-job-09] Extracting boost-libs-1.84.0: .......... done ===== Message from boost-libs-1.84.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> dssp-4.4.2_1 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so) ===> Returning to build of dssp-4.4.2_1 ===> dssp-4.4.2_1 depends on shared library: libcifpp.so - not found ===> Installing existing package /packages/All/libcifpp-7.0.5.pkg [133amd64-default-job-09] Installing libcifpp-7.0.5... [133amd64-default-job-09] `-- Installing bash-5.2.32... [133amd64-default-job-09] | `-- Installing readline-8.2.13... [133amd64-default-job-09] | `-- Extracting readline-8.2.13: .......... done [133amd64-default-job-09] `-- Extracting bash-5.2.32: .......... done [133amd64-default-job-09] Extracting libcifpp-7.0.5: .......... done ===> dssp-4.4.2_1 depends on shared library: libcifpp.so - found (/usr/local/lib/libcifpp.so) ===> Returning to build of dssp-4.4.2_1 =========================================================================== =======================<phase: configure >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Configuring for dssp-4.4.2_1 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/science/dssp/work/.build -- The CXX compiler identification is Clang 17.0.6 -- 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 CMake Warning (dev) at CMakeLists.txt:37 (include): Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run "cmake --help-policy CMP0145" for policy details. Use the cmake_policy command to set the policy and suppress this warning. This warning is for project developers. Use -Wno-dev to suppress it. CMake Warning (dev) at /usr/local/share/cmake/Modules/Dart.cmake:47 (message): Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run "cmake --help-policy CMP0145" for policy details. Use the cmake_policy command to set the policy and suppress this warning. Call Stack (most recent call first): CMakeLists.txt:37 (include) This warning is for project developers. Use -Wno-dev to suppress it. -- Looking for C++ include filesystem -- Looking for C++ include filesystem - found -- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED -- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED - Success -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found ZLIB: /usr/lib/libz.so (found version "1.3.1") -- Configuring done (10.1s) CMake Error at /usr/local/lib/cmake/cifpp/cifpp-targets.cmake:61 (set_target_properties): The link interface of target "cifpp::cifpp" contains: std::atomic but the target was not found. Possible reasons include: * There is a typo in the target name. * A find_package call is missing for an IMPORTED target. * An ALIAS target is missing. Call Stack (most recent call first): /usr/local/lib/cmake/cifpp/cifpp-config.cmake:27 (include) CMakeLists.txt:108 (find_package) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_C_COMPILER CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS FETCHCONTENT_FULLY_DISCONNECTED CMake Generate step failed. Build files cannot be regenerated correctly. *** Error code 1 Stop. make: stopped in /usr/ports/science/dssp