Date: Tue, 16 Apr 2019 14:29:32 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120armv7-quarterly][biology/unanimity] Failed for unanimity-3.4.1 in configure Message-ID: <201904161429.x3GETWhi015912@beefy13.nyi.freebsd.org>
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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: branches/2019Q2/biology/unanimity/Makefile 493769 2019-02-24 16:04:58Z jwb $ Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/499069/logs/unanimity-3.4.1.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=499069 Log: =>> Building biology/unanimity build started at Tue Apr 16 14:28:35 UTC 2019 port directory: /usr/ports/biology/unanimity package name: unanimity-3.4.1 building for: FreeBSD 120armv7-quarterly-job-16 12.0-RELEASE-p3 FreeBSD 12.0-RELEASE-p3 1200086 arm maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q2/biology/unanimity/Makefile 493769 2019-02-24 16:04:58Z jwb $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300009 Jail OSVERSION: 1200086 Job Id: 16 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p3 1200086 UNAME_r=12.0-RELEASE-p3 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-3-g02cc9753 MASTERMNT=/usr/local/poudriere/data/.m/120armv7-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120armv7-quarterly/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--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix /usr/local --mandir man --infodir share/info --buildtype release --strip _build --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/unanimity/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" LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/unanimity/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 DESTDIR=/wrkdirs/usr/ports/biology/unanimity/work/stage LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -lexecinfo " LIBS="-L/usr/local/lib" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -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_INST ALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd12 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/unanimity" EXAMPLESDIR="share/examples/unanimity" DATADIR="share/unanimity" WWWDIR="www/unanimity" ETCDIR="etc/unanimity" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/unanimity DOCSDIR=/usr/local/share/doc/unanimity EXAMPLESDIR=/usr/local/share/examples/unanimity WWWDIR=/usr/local/www/unanimity ETCDIR=/usr/local/etc/unanimity --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=armv7 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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-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_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p3 OSREL=12.0 OSVERSION=1200086 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--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as 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-- =======================<phase: check-sanity >============================ ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> unanimity-3.4.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120armv7-quarterly-job-16] Installing pkg-1.10.5_5... [120armv7-quarterly-job-16] Extracting pkg-1.10.5_5: .......... done ===> unanimity-3.4.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of unanimity-3.4.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user => PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz fetch: https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz: size unknown fetch: https://codeload.github.com/PacificBiosciences/unanimity/tar.gz/v3.4.1?dummy=/PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz: size of remote file is not known PacificBiosciences-unanimity-v3.4.1_GH0.tar.gz 6341 kB 9053 kBps 00s ===> Fetching all distfiles required by unanimity-3.4.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-3.4.1 for building <snip> The cblas port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from python27-2.7.16: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from metis-5.1.0_7: ===> NOTICE: The metis port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> unanimity-3.4.1 depends on package: py27-numpy>0 - found ===> Returning to build of unanimity-3.4.1 ===> unanimity-3.4.1 depends on executable: meson - not found ===> Installing existing package /packages/All/meson-0.49.2.txz [120armv7-quarterly-job-16] Installing meson-0.49.2... [120armv7-quarterly-job-16] `-- Installing ninja-1.8.2_1,2... [120armv7-quarterly-job-16] `-- Extracting ninja-1.8.2_1,2: ......... done [120armv7-quarterly-job-16] `-- Installing py36-setuptools-40.8.0... [120armv7-quarterly-job-16] | `-- Installing python36-3.6.8_1... [120armv7-quarterly-job-16] | `-- Extracting python36-3.6.8_1: .......... done [120armv7-quarterly-job-16] `-- Extracting py36-setuptools-40.8.0: .......... done [120armv7-quarterly-job-16] Extracting meson-0.49.2: .......... done Message from python36-3.6.8_1: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: py36-gdbm databases/py-gdbm@py36 py36-sqlite3 databases/py-sqlite3@py36 py36-tkinter x11-toolkits/py-tkinter@py36 =========================================================================== Message from py36-setuptools-40.8.0: ******************************************************************* Only /usr/local/bin/easy_install-3.6 script has been installed since Python 3.6 is not the default Python version. ******************************************************************* ===> unanimity-3.4.1 depends on executable: meson - found ===> Returning to build of unanimity-3.4.1 ===> unanimity-3.4.1 depends on executable: ninja - found ===> unanimity-3.4.1 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.6.0,1.txz [120armv7-quarterly-job-16] Installing pkgconf-1.6.0,1... [120armv7-quarterly-job-16] Extracting pkgconf-1.6.0,1: .......... done ===> unanimity-3.4.1 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of unanimity-3.4.1 ===> unanimity-3.4.1 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =======================<phase: lib-depends >============================ ===> unanimity-3.4.1 depends on shared library: libhts.so - not found ===> Installing existing package /packages/All/htslib-1.9.txz [120armv7-quarterly-job-16] Installing htslib-1.9... [120armv7-quarterly-job-16] `-- Installing curl-7.64.1_1... [120armv7-quarterly-job-16] | `-- Installing ca_root_nss-3.43... [120armv7-quarterly-job-16] | `-- Extracting ca_root_nss-3.43: ........ done [120armv7-quarterly-job-16] | `-- Installing libnghttp2-1.37.0... [120armv7-quarterly-job-16] | `-- Extracting libnghttp2-1.37.0: .......... done [120armv7-quarterly-job-16] `-- Extracting curl-7.64.1_1: .......... done [120armv7-quarterly-job-16] Extracting htslib-1.9: .......... done Message from ca_root_nss-3.43: ********************************* WARNING ********************************* 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. *********************************** NOTE ********************************** 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 *************************************************************************** ===> unanimity-3.4.1 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> Returning to build of unanimity-3.4.1 ===> unanimity-3.4.1 depends on shared library: libboost_regex.so - not found ===> Installing existing package /packages/All/boost-libs-1.69.0_2.txz [120armv7-quarterly-job-16] Installing boost-libs-1.69.0_2... [120armv7-quarterly-job-16] `-- Installing icu-64.1,1... [120armv7-quarterly-job-16] `-- Extracting icu-64.1,1: .......... done [120armv7-quarterly-job-16] Extracting boost-libs-1.69.0_2: .......... done Message from boost-libs-1.69.0_2: You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> unanimity-3.4.1 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) ===> Returning to build of unanimity-3.4.1 ===> unanimity-3.4.1 depends on shared library: libpbbam.so.0.18.0 - not found ===> Installing existing package /packages/All/pbbam-0.18.0.txz [120armv7-quarterly-job-16] Installing pbbam-0.18.0... [120armv7-quarterly-job-16] Extracting pbbam-0.18.0: .......... done ===> unanimity-3.4.1 depends on shared library: libpbbam.so.0.18.0 - found (/usr/local/lib/libpbbam.so.0.18.0) ===> Returning to build of unanimity-3.4.1 ===> unanimity-3.4.1 depends on shared library: libpbcopper.so.0.4.1 - not found ===> Installing existing package /packages/All/pbcopper-0.4.1.txz [120armv7-quarterly-job-16] Installing pbcopper-0.4.1... [120armv7-quarterly-job-16] Extracting pbcopper-0.4.1: .......... done ===> unanimity-3.4.1 depends on shared library: libpbcopper.so.0.4.1 - found (/usr/local/lib/libpbcopper.so.0.4.1) ===> Returning to build of unanimity-3.4.1 =========================================================================== =======================<phase: configure >============================ ===> Configuring for unanimity-3.4.1 The Meson build system Version: 0.49.2 Source dir: /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.4.1 Build dir: /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.4.1/_build Build type: native build Project name: UNANIMITY Project version: 3.0.0 Appending CFLAGS from environment: '-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing ' Appending LDFLAGS from environment: ' -lexecinfo ' Appending CPPFLAGS from environment: '-isystem /usr/local/include' Native C compiler: /nxb-bin/usr/bin/cc (clang 6.0.1 "FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1)") Appending CXXFLAGS from environment: '-O2 -pipe -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include ' Appending LDFLAGS from environment: ' -lexecinfo ' Appending CPPFLAGS from environment: '-isystem /usr/local/include' Native C++ compiler: /nxb-bin/usr/bin/c++ (clang 6.0.1 "FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1)") Build machine cpu family: arm Build machine cpu: arm Compiler for C++ supports arguments -Wno-unused-parameter: YES Compiler for C++ supports arguments -Wno-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-unused-variable: YES Compiler for C++ supports arguments -Wno-sign-compare: YES Compiler for C++ supports arguments -Wno-unused-local-typedef: YES Compiler for C++ supports arguments -Wno-delete-non-virtual-dtor: YES Compiler for C++ supports arguments -Wno-dynamic-class-memaccess: YES Dependency threads found: YES Dependency Boost found: YES 1.69 Found pkg-config: /usr/local/bin/pkgconf (1.6.0) Dependency pbbam found: YES 0.18.0 Dependency pbcopper found: YES 0.4.1 Dependency zlib found: YES 1.2.10 Dependency seqan-2 found: YES 2.4.0 Configuring UnanimityVersion.cpp using configuration Configuring ModelInternalInitializer.cpp using configuration Program python2.7 found: YES (/usr/local/bin/python2.7) Program swig3.0 found: YES (/usr/local/bin/swig3.0) Message: Python version: 2.7 Configuring python_sitedir.py using configuration Message: Python modules will be installed into: /usr/local/lib/python2.7/site-packages Dependency python-2.7 found: YES 2.7 swig/meson.build:4:2: ERROR: Problem encountered: Could not determine NumPy includedir! A full log can be found at /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.4.1/_build/meson-logs/meson-log.txt ===> Script "configure" failed unexpectedly. Please report the problem to jwb@FreeBSD.org [maintainer] and attach the "/wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.4.1/_build/meson-logs/meson-log.txt" including the output of the failure of your make command. Also, it might be a good idea to provide an overview of all packages installed on your system (e.g. a /usr/local/sbin/pkg-static info -g -Ea). *** Error code 1 Stop. make: stopped in /usr/ports/biology/unanimity
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