From owner-freebsd-pkg-fallout@freebsd.org Fri Feb 21 22:32:18 2020 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id C3106245BD0 for ; Fri, 21 Feb 2020 22:32:18 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (mailman.nyi.freebsd.org [IPv6:2610:1c1:1:606c::50:13]) by mx1.freebsd.org (Postfix) with ESMTP id 48PR6B4013z4X23 for ; Fri, 21 Feb 2020 22:32:18 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 7CDBD245BCF; Fri, 21 Feb 2020 22:32:18 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 7B15B245BCE for ; Fri, 21 Feb 2020 22:32:18 +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) server-signature RSA-PSS (4096 bits) client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 48PR6B12DDz4X1J for ; Fri, 21 Feb 2020 22:32:18 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from pylon.nyi.freebsd.org (pylon.nyi.freebsd.org [IPv6:2610:1c1:1:6082::16:fc]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 1B45F19C6F for ; Fri, 21 Feb 2020 22:32:18 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from pylon.nyi.freebsd.org (localhost [127.0.0.1]) by pylon.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 01LMWIn6055800 for ; Fri, 21 Feb 2020 22:32:18 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by pylon.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 01LMWHVq055797; Fri, 21 Feb 2020 22:32:17 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Fri, 21 Feb 2020 22:32:17 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202002212232.01LMWHVq055797@pylon.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - head-powerpc64-default][biology/kallisto] Failed for kallisto-0.46.2 in build X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 21 Feb 2020 22:32:18 -0000 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 Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/kallisto/Makefile 526244 2020-02-15 23:09:19Z jwb $ Log URL: http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p526244_s356047/logs/kallisto-0.46.2.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p526244_s356047 Log: =>> Building biology/kallisto build started at Fri Feb 21 22:31:01 UTC 2020 port directory: /usr/ports/biology/kallisto package name: kallisto-0.46.2 building for: FreeBSD head-powerpc64-default-job-09 13.0-CURRENT FreeBSD 13.0-CURRENT 1300068 powerpc maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/kallisto/Makefile 526244 2020-02-15 23:09:19Z jwb $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300047 Jail OSVERSION: 1300068 Job Id: 09 !!! Jail is newer than host. (Jail: 1300068, Host: 1300047) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300068 UNAME_v=FreeBSD 13.0-CURRENT 1300068 UNAME_r=13.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root 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=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-powerpc64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-powerpc64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-powerpc64-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 kallisto-0.46.2: EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/kallisto/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/kallisto/work HOME=/wrkdirs/usr/ports/biology/kallisto/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/kallisto/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc9" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp9" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstac k-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 -L/usr/local/lib " LIBS="" CXX="g++9" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 -isystem /usr/local/include " 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-- PORTEXAMPLES="" CMAKE_BUILD_TYPE="release" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/kallisto" EXAMPLESDIR="share/examples/kallisto" DATADIR="share/kallisto" WWWDIR="www/kallisto" ETCDIR="etc/kallisto" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/kallisto DOCSDIR=/usr/local/share/doc/kallisto EXAMPLESDIR=/usr/local/share/examples/kallisto WWWDIR=/usr/local/www/kallisto ETCDIR=/usr/local/etc/kallisto --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=4 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 PPC_ABI=ELFv1 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300068 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---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 =========================================================================== =================================================== ===> kallisto-0.46.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.13.1.txz [head-powerpc64-default-job-09] Installing pkg-1.13.1... [head-powerpc64-default-job-09] Extracting pkg-1.13.1: .......... done ===> kallisto-0.46.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of kallisto-0.46.2 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user => pachterlab-kallisto-v0.46.2_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.46.2?dummy=/pachterlab-kallisto-v0.46.2_GH0.tar.gz fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.46.2?dummy=/pachterlab-kallisto-v0.46.2_GH0.tar.gz: size unknown fetch: https://codeload.github.com/pachterlab/kallisto/tar.gz/v0.46.2?dummy=/pachterlab-kallisto-v0.46.2_GH0.tar.gz: size of remote file is not known pachterlab-kallisto-v0.46.2_GH0.tar.gz 2630 kB 4306 kBps 01s => Fetched file size mismatch (expected 2693857, actual 2693869) => Trying next site => Attempting to fetch http://distcache.FreeBSD.org/ports-distfiles/pachterlab-kallisto-v0.46.2_GH0.tar.gz pachterlab-kallisto-v0.46.2_GH0.tar.gz 2630 kB 29 MBps 00s ===> Fetching all distfiles required by kallisto-0.46.2 for building =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.46.2 for building => SHA256 Checksum OK for pachterlab-kallisto-v0.46.2_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD2CLAUSE accepted by the user ===> Fetching all distfiles required by kallisto-0.46.2 for building ===> Extracting for kallisto-0.46.2 => SHA256 Checksum OK for pachterlab-kallisto-v0.46.2_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for kallisto-0.46.2 ===> Applying FreeBSD patches for kallisto-0.46.2 =========================================================================== =================================================== ===> kallisto-0.46.2 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.16.4.txz [head-powerpc64-default-job-09] Installing cmake-3.16.4... [head-powerpc64-default-job-09] `-- Installing curl-7.68.0... [head-powerpc64-default-job-09] | `-- Installing ca_root_nss-3.50... [head-powerpc64-default-job-09] | `-- Extracting ca_root_nss-3.50: ........ done [head-powerpc64-default-job-09] | `-- Installing libnghttp2-1.40.0... [head-powerpc64-default-job-09] | | `-- Installing gcc9-9.2.0_1... [head-powerpc64-default-job-09] | | `-- Installing binutils-2.33.1_2,1... [head-powerpc64-default-job-09] | | | `-- Installing gettext-runtime-0.20.1... [head-powerpc64-default-job-09] | | | `-- Installing indexinfo-0.3.1... [head-powerpc64-default-job-09] | | | `-- Extracting indexinfo-0.3.1: .... done [head-powerpc64-default-job-09] | | | `-- Extracting gettext-runtime-0.20.1: .......... done [head-powerpc64-default-job-09] | | `-- Extracting binutils-2.33.1_2,1: .......... done [head-powerpc64-default-job-09] | | `-- Installing gcc8-8.3.0_3... [head-powerpc64-default-job-09] | | | `-- Installing gmp-6.1.2_1... [head-powerpc64-default-job-09] | | | `-- Extracting gmp-6.1.2_1: .......... done [head-powerpc64-default-job-09] | | | `-- Installing mpc-1.1.0_2... [head-powerpc64-default-job-09] | | | `-- Installing mpfr-4.0.2... [head-powerpc64-default-job-09] | | | `-- Extracting mpfr-4.0.2: .......... done [head-powerpc64-default-job-09] | | | `-- Extracting mpc-1.1.0_2: ......... done [head-powerpc64-default-job-09] | | `-- Extracting gcc8-8.3.0_3: .......... done [head-powerpc64-default-job-09] | | `-- Extracting gcc9-9.2.0_1: .......... done [head-powerpc64-default-job-09] | `-- Extracting libnghttp2-1.40.0: .......... done [head-powerpc64-default-job-09] `-- Extracting curl-7.68.0: .......... done [head-powerpc64-default-job-09] `-- Installing expat-2.2.8... [head-powerpc64-default-job-09] `-- Extracting expat-2.2.8: .......... done [head-powerpc64-default-job-09] `-- Installing jsoncpp-1.9.2... [head-powerpc64-default-job-09] `-- Extracting jsoncpp-1.9.2: .......... done [head-powerpc64-default-job-09] `-- Installing libarchive-3.4.0,1... [head-powerpc64-default-job-09] | `-- Installing liblz4-1.9.2_1,1... [head-powerpc64-default-job-09] | `-- Extracting liblz4-1.9.2_1,1: .......... done [head-powerpc64-default-job-09] | `-- Installing lzo2-2.10_1... [head-powerpc64-default-job-09] | `-- Extracting lzo2-2.10_1: .......... done [head-powerpc64-default-job-09] `-- Extracting libarchive-3.4.0,1: .......... done [head-powerpc64-default-job-09] `-- Installing libuv-1.34.2... [head-powerpc64-default-job-09] `-- Extracting libuv-1.34.2: .......... done [head-powerpc64-default-job-09] `-- Installing rhash-1.3.5... [head-powerpc64-default-job-09] `-- Extracting rhash-1.3.5: .......... done [head-powerpc64-default-job-09] Extracting cmake-3.16.4: .......... done ===== Message from ca_root_nss-3.50: -- FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem ===== Message from gcc8-8.3.0_3: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc8 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===== Message from gcc9-9.2.0_1: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc9 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> kallisto-0.46.2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of kallisto-0.46.2 ===> kallisto-0.46.2 depends on executable: gcc9 - found ===> kallisto-0.46.2 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== ===> kallisto-0.46.2 depends on shared library: libhdf5.so - not found ===> Installing existing package /packages/All/hdf5-1.10.6.txz [head-powerpc64-default-job-09] Installing hdf5-1.10.6... [head-powerpc64-default-job-09] `-- Installing hdf-szip-2.1.1... [head-powerpc64-default-job-09] `-- Extracting hdf-szip-2.1.1: .......... done [head-powerpc64-default-job-09] Extracting hdf5-1.10.6: .......... done ===> kallisto-0.46.2 depends on shared library: libhdf5.so - found (/usr/local/lib/libhdf5.so) ===> Returning to build of kallisto-0.46.2 ===> kallisto-0.46.2 depends on shared library: libsz.so - found (/usr/local/lib/libsz.so) ===> kallisto-0.46.2 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.9.txz [head-powerpc64-default-job-09] Installing htslib-1.9... [head-powerpc64-default-job-09] Extracting htslib-1.9: .......... done ===> kallisto-0.46.2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of kallisto-0.46.2 =========================================================================== =================================================== ===> Configuring for kallisto-0.46.2 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/kallisto/work/.build -- The C compiler identification is GNU 9.2.0 -- The CXX compiler identification is GNU 9.2.0 -- Check for working C compiler: /usr/local/bin/gcc9 -- Check for working C compiler: /usr/local/bin/gcc9 -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Check for working CXX compiler: /usr/local/bin/g++9 -- Check for working CXX compiler: /usr/local/bin/g++9 -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done shared build -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- HDF5: Using hdf5 compiler wrapper to determine C configuration -- Found HDF5: /usr/local/lib/libhdf5.so;/usr/local/lib/libsz.so;/usr/lib/libz.so;/usr/lib/libdl.so;/usr/lib/libm.so (found version "1.10.6") -- Found ZLIB: /usr/lib/libz.so (found version "1.2.11") -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_DEBUG CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS -- Build files have been written to: /wrkdirs/usr/ports/biology/kallisto/work/.build =========================================================================== =================================================== ===> Building for kallisto-0.46.2 /usr/local/bin/cmake -S/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2 -B/wrkdirs/usr/ports/biology/kallisto/work/.build --check-build-system CMakeFiles/Makefile.cmake 0 /usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles /wrkdirs/usr/ports/biology/kallisto/work/.build/CMakeFiles/progress.marks /usr/bin/make -f CMakeFiles/Makefile2 all /usr/bin/make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/depend cd /wrkdirs/usr/ports/biology/kallisto/work/.build && /usr/local/bin/cmake -E cmake_depends "Unix Makefiles" /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2 /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src /wrkdirs/usr/ports/biology/kallisto/work/.build /wrkdirs/usr/ports/biology/kallisto/work/.build/src /wrkdirs/usr/ports/biology/kallisto/work/.build/src/CMakeFiles/kallisto_core.dir/DependInfo.cmake Scanning dependencies of target kallisto_core /usr/bin/make -f src/CMakeFiles/kallisto_core.dir/build.make src/CMakeFiles/kallisto_core.dir/build [ 4%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSData.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/bin/g++9 -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 -isystem /usr/local/include -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSData.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src/BUSData.cpp [ 9%] Building CXX object src/CMakeFiles/kallisto_core.dir/BUSTools.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/bin/g++9 -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 -isystem /usr/local/include -std=c++11 -o CMakeFiles/kallisto_core.dir/BUSTools.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src/BUSTools.cpp [ 14%] Building CXX object src/CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o cd /wrkdirs/usr/ports/biology/kallisto/work/.build/src && /usr/local/bin/g++9 -DUSE_HDF5=ON -I/wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 -isystem /usr/local/include -std=c++11 -o CMakeFiles/kallisto_core.dir/Bootstrap.cpp.o -c /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src/Bootstrap.cpp In file included from /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src/Bootstrap.cpp:1: /wrkdirs/usr/ports/biology/kallisto/work/kallisto-0.46.2/src/Bootstrap.h:57:106: error: 'uint' has not been declared 57 | const std::vector& fld, const std::vector& preBias, const std::vector& postBias, uint compression, size_t index_version, | ^~~~ *** Error code 1 Stop. make[3]: stopped in /wrkdirs/usr/ports/biology/kallisto/work/.build *** Error code 1 Stop. make[2]: stopped in /wrkdirs/usr/ports/biology/kallisto/work/.build *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/kallisto/work/.build *** Error code 1 Stop. make: stopped in /usr/ports/biology/kallisto