Date: Thu, 11 Jun 2020 20:20:43 GMT From: pkg-fallout@FreeBSD.org To: mauricio@arareko.net Cc: pkg-fallout@FreeBSD.org Subject: [package - 113amd64-default][biology/py-biopython] Failed for py27-biopython-1.77 in configure Message-ID: <202006112020.05BKKhpT022599@beefy9.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: mauricio@arareko.net Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/py-biopython/Makefile 536875 2020-05-29 02:03:29Z jwb $ Log URL: http://beefy9.nyi.freebsd.org/data/113amd64-default/538447/logs/py27-biopython-1.77.log Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=113amd64-default&build=538447 Log: =>> Building biology/py-biopython build started at Thu Jun 11 20:20:23 UTC 2020 port directory: /usr/ports/biology/py-biopython package name: py27-biopython-1.77 building for: FreeBSD 113amd64-default-job-12 11.3-RELEASE-p10 FreeBSD 11.3-RELEASE-p10 amd64 maintained by: mauricio@arareko.net Makefile ident: $FreeBSD: head/biology/py-biopython/Makefile 536875 2020-05-29 02:03:29Z jwb $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300089 Jail OSVERSION: 1103000 Job Id: 12 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1103000 UNAME_v=FreeBSD 11.3-RELEASE-p10 UNAME_r=11.3-RELEASE-p10 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/113amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/113amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=113amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/113amd64-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=py27 DEPENDS_ARGS= MAKE_ARGS= FLAVOR=py27 ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for py27-biopython-1.77: REPORTLAB=on: PDF support in Bio.Graphics module ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- mauricio@arareko.net --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biopython/work-py27/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 HOME=/wrkdirs/usr/ports/biology/py-biopython/work-py27 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-biopython/work-py27/.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 LDSHARED="cc -shared" PYTHONDONTWRITEBYTECODE= PYTHONOPTIMIZE= 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-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd11 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=11.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/biopython" EXAMPLESDIR="share/examples/biopython" DATADIR="share/biopython" WWWDIR="www/biopython" ETCDIR="etc/biopython" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/biopython DOCSDIR=/usr/local/share/doc/biopython EXAMPLESDIR=/usr/local/share/examples/biopython WWWDIR=/usr/local/www/biopython ETCDIR=/usr/local/etc/biopython --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 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: x86_64-unknown-freebsd11.3 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: x86_64-unknown-freebsd11.3 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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: x86_64-unknown-freebsd11.3 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=11.3-RELEASE-p10 OSREL=11.3 OSVERSION=1103000 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 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-- =======================<phase: check-sanity >============================ ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. ===> License BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> py27-biopython-1.77 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.4.txz [113amd64-default-job-12] Installing pkg-1.14.4... [113amd64-default-job-12] Extracting pkg-1.14.4: .......... done ===> py27-biopython-1.77 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of py27-biopython-1.77 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-biopython-1.77 for building =========================================================================== =======================<phase: checksum >============================ ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-biopython-1.77 for building => SHA256 Checksum OK for biopython-1.77.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by py27-biopython-1.77 for building ===> Extracting for py27-biopython-1.77 => SHA256 Checksum OK for biopython-1.77.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for py27-biopython-1.77 =========================================================================== =======================<phase: build-depends >============================ ===> py27-biopython-1.77 depends on package: py27-numpy>=1.16,1<1.19,1 - not found ===> Installing existing package /packages/All/py27-numpy-1.16.6,1.txz [113amd64-default-job-12] Installing py27-numpy-1.16.6,1... [113amd64-default-job-12] `-- Installing gcc9-9.3.0_1... [113amd64-default-job-12] | `-- Installing binutils-2.33.1_2,1... [113amd64-default-job-12] | | `-- Installing gettext-runtime-0.20.2... [113amd64-default-job-12] | | `-- Installing indexinfo-0.3.1... [113amd64-default-job-12] | | `-- Extracting indexinfo-0.3.1: .... done [113amd64-default-job-12] | | `-- Extracting gettext-runtime-0.20.2: .......... done [113amd64-default-job-12] | `-- Extracting binutils-2.33.1_2,1: .......... done [113amd64-default-job-12] | `-- Installing gmp-6.2.0... [113amd64-default-job-12] | `-- Extracting gmp-6.2.0: .......... done [113amd64-default-job-12] | `-- Installing mpc-1.1.0_2... [113amd64-default-job-12] | | `-- Installing mpfr-4.0.2... [113amd64-default-job-12] | | `-- Extracting mpfr-4.0.2: .......... done [113amd64-default-job-12] | `-- Extracting mpc-1.1.0_2: ......... done [113amd64-default-job-12] `-- Extracting gcc9-9.3.0_1: .......... done [113amd64-default-job-12] `-- Installing openblas-0.3.9_2,1... [113amd64-default-job-12] `-- Extracting openblas-0.3.9_2,1: .......... done [113amd64-default-job-12] `-- Installing py27-setuptools-44.0.0... [113amd64-default-job-12] | `-- Installing python27-2.7.18... [113amd64-default-job-12] | | `-- Installing libffi-3.2.1_3... [113amd64-default-job-12] | | `-- Extracting libffi-3.2.1_3: .......... done [113amd64-default-job-12] | | `-- Installing readline-8.0.4... [113amd64-default-job-12] | | `-- Extracting readline-8.0.4: .......... done [113amd64-default-job-12] | `-- Extracting python27-2.7.18: .......... done [113amd64-default-job-12] `-- Extracting py27-setuptools-44.0.0: .......... done [113amd64-default-job-12] `-- Installing suitesparse-5.7.2_1... [113amd64-default-job-12] | `-- Installing metis-5.1.0_8... [113amd64-default-job-12] | `-- Extracting metis-5.1.0_8: .......... done [113amd64-default-job-12] | `-- Installing tbb-2020.2... [113amd64-default-job-12] | `-- Extracting tbb-2020.2: .......... done [113amd64-default-job-12] `-- Extracting suitesparse-5.7.2_1: .......... done [113amd64-default-job-12] Extracting py27-numpy-1.16.6,1: .......... done ===== Message from gcc9-9.3.0_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. ===== Message from python27-2.7.18: -- 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 -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: EOLed upstream. It is scheduled to be removed on or after 2020-12-31. ===== Message from py27-setuptools-44.0.0: -- Only /usr/local/bin/easy_install-2.7 script has been installed since Python 2.7 is not the default Python version. -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. ===== Message from py27-numpy-1.16.6,1: -- ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses Python 2.7 which is EOLed upstream. It is scheduled to be removed on or after 2020-12-31. ===> py27-biopython-1.77 depends on package: py27-numpy>=1.16,1<1.19,1 - found ===> Returning to build of py27-biopython-1.77 ===> py27-biopython-1.77 depends on package: py27-setuptools>0 - found ===> py27-biopython-1.77 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for py27-biopython-1.77 Biopython requires Python 3.6 or later. Python 2.7 detected. *** Error code 1 Stop. make: stopped in /usr/ports/biology/py-biopython
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