Date: Wed, 31 Aug 2016 00:54:26 GMT From: pkg-fallout@FreeBSD.org To: bacon4000@gmail.com Cc: pkg-fallout@FreeBSD.org Subject: [package - 93amd64-default][biology/ncbi-blast+] Failed for ncbi-blast+-2.2.30_2 in configure Message-ID: <201608310054.u7V0sQ1u032770@beefy2.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: bacon4000@gmail.com Last committer: mat@FreeBSD.org Ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 412344 2016-04-01 13:29:15Z mat $ Log URL: http://beefy2.nyi.freebsd.org/data/93amd64-default/421100/logs/ncbi-blast+-2.2.30_2.log Build URL: http://beefy2.nyi.freebsd.org/build.html?mastername=93amd64-default&build=421100 Log: ====>> Building biology/ncbi-blast+ build started at Wed Aug 31 00:53:58 UTC 2016 port directory: /usr/ports/biology/ncbi-blast+ building for: FreeBSD 93amd64-default-job-23 9.3-RELEASE-p45 FreeBSD 9.3-RELEASE-p45 amd64 maintained by: bacon4000@gmail.com Makefile ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 412344 2016-04-01 13:29:15Z mat $ Poudriere version: 3.1.14 Host OSVERSION: 1200005 Jail OSVERSION: 903000 ---Begin Environment--- SHELL=/bin/csh UNAME_v=FreeBSD 9.3-RELEASE-p45 UNAME_r=9.3-RELEASE-p45 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 OPSYS=FreeBSD ARCH=amd64 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/93amd64-default/ref UID=0 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin _JAVA_VERSION_LIST_REGEXP=1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+ POUDRIERE_BUILD_TYPE=bulk PKGNAME=ncbi-blast+-2.2.30_2 OSREL=9.3 _OSRELEASE=9.3-RELEASE-p45 PYTHONBASE=/usr/local OLDPWD=/ _SMP_CPUS=24 PWD=/usr/local/poudriere/data/.m/93amd64-default/ref/.p/pool HAVE_COMPAT_IA32_KERN=YES LINUX_OSRELEASE=2.6.32 MASTERNAME=93amd64-default SCRIPTPREFIX=/usr/local/share/poudriere _JAVA_VENDOR_LIST_REGEXP=openjdk\|oracle\|sun USER=root HOME=/root POUDRIERE_VERSION=3.1.14 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh CONFIGURE_MAX_CMD_LEN=262144 LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes _JAVA_OS_LIST_REGEXP=native\|linux OSVERSION=903000 ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- AR="ar cr" --without-boost --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ncbi_cv_prog_amq_w=no MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh 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" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work HOME=/wrkdirs/usr/ports/biology/ncbi-blast+/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes 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 LIBDIR="/usr/lib" CC="gcc48" CFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -fno-strict-aliasing" CPP="cpp48" CPPFLAGS="" LDFLAGS=" -fstack-protector -Wl,-rpath=/usr/local/lib/gcc48 -L/usr/local/lib/gcc48" LIBS="" CXX="g++48" CXXFLAGS="-O2 -pipe -fstack-protector -Wl,-rpath=/usr/ local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc48" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 444" 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=freebsd9 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_VER=2.7 PYTHON_VERSION=python2.7 OSREL=9.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.20.3 PERL_VER=5.20 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.20 DOCSDIR="share/doc/blast+" EXAMPLESDIR="share/examples/blast+" DATADIR="share/blast+" WWWDIR="www/blast+" ETCDIR="etc/blast+" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/blast+ DOCSDIR=/usr/local/share/doc/blast+ EXAMPLESDIR=/usr/local/share/examples/blast+ WWWDIR=/usr/local/www/blast+ ETCDIR=/usr/local/etc/blast+ --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /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 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> License PD accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_1.txz [93amd64-default-job-23] Installing pkg-1.8.7_1... [93amd64-default-job-23] Extracting pkg-1.8.7_1: .......... done ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-blast+-2.2.30_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building => SHA256 Checksum OK for ncbi-blast-2.2.30+-src.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building ===> Extracting for ncbi-blast+-2.2.30_2 => SHA256 Checksum OK for ncbi-blast-2.2.30+-src.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for ncbi-blast+-2.2.30_2 ===> Applying FreeBSD patches for ncbi-blast+-2.2.30_2 /usr/bin/sed -i.bak -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' -e '/--infodir=DIR/d' -e '/--mandir=DIR/d' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/configure /usr/bin/sed -i.bak -e 's|@prefix@|/wrkdirs/usr/ports/biology/ncbi-blast+/work/stage@prefix@|g' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top =========================================================================== =======================<phase: build-depends >============================ ===> ncbi-blast+-2.2.30_2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz [93amd64-default-job-23] Installing gmake-4.2.1_1... [93amd64-default-job-23] `-- Installing indexinfo-0.2.4... [93amd64-default-job-23] `-- Extracting indexinfo-0.2.4: .... done [93amd64-default-job-23] `-- Installing libiconv-1.14_9... [93amd64-default-job-23] `-- Extracting libiconv-1.14_9: .......... done [93amd64-default-job-23] `-- Installing gettext-runtime-0.19.8.1... [93amd64-default-job-23] `-- Extracting gettext-runtime-0.19.8.1: .......... done [93amd64-default-job-23] Extracting gmake-4.2.1_1: .......... done ===> ncbi-blast+-2.2.30_2 depends on executable: gmake - found ===> Returning to build of ncbi-blast+-2.2.30_2 ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/python2.7 - not found ===> Installing existing package /packages/All/python27-2.7.12.txz [93amd64-default-job-23] Installing python27-2.7.12... [93amd64-default-job-23] `-- Installing libffi-3.2.1... [93amd64-default-job-23] `-- Extracting libffi-3.2.1: .......... done [93amd64-default-job-23] Extracting python27-2.7.12: .......... done Message from python27-2.7.12: =========================================================================== 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 =========================================================================== ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/python2.7 - found ===> Returning to build of ncbi-blast+-2.2.30_2 ===> ncbi-blast+-2.2.30_2 depends on executable: gcc48 - not found ===> Installing existing package /packages/All/gcc-4.8.5_2.txz [93amd64-default-job-23] Installing gcc-4.8.5_2... [93amd64-default-job-23] `-- Installing mpc-1.0.3... [93amd64-default-job-23] | `-- Installing gmp-5.1.3_3... [93amd64-default-job-23] | `-- Extracting gmp-5.1.3_3: .......... done [93amd64-default-job-23] | `-- Installing mpfr-3.1.4... [93amd64-default-job-23] | `-- Extracting mpfr-3.1.4: .......... done [93amd64-default-job-23] `-- Extracting mpc-1.0.3: ...... done [93amd64-default-job-23] `-- Installing gcc-ecj-4.5... [93amd64-default-job-23] `-- Extracting gcc-ecj-4.5: . done [93amd64-default-job-23] `-- Installing binutils-2.27_1,1... [93amd64-default-job-23] `-- Extracting binutils-2.27_1,1: .......... done [93amd64-default-job-23] Extracting gcc-4.8.5_2: .......... done Message from gcc-4.8.5_2: 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/gcc48 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> ncbi-blast+-2.2.30_2 depends on executable: gcc48 - found ===> Returning to build of ncbi-blast+-2.2.30_2 ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/as - found ===> ncbi-blast+-2.2.30_2 depends on package: perl5>=5.20<5.21 - not found ===> Installing existing package /packages/All/perl5-5.20.3_15.txz [93amd64-default-job-23] Installing perl5-5.20.3_15... [93amd64-default-job-23] Extracting perl5-5.20.3_15: .......... done Message from perl5-5.20.3_15: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> ncbi-blast+-2.2.30_2 depends on package: perl5>=5.20<5.21 - found ===> Returning to build of ncbi-blast+-2.2.30_2 =========================================================================== =======================<phase: lib-depends >============================ ===> ncbi-blast+-2.2.30_2 depends on shared library: libpcre.so - not found ===> Installing existing package /packages/All/pcre-8.39.txz [93amd64-default-job-23] Installing pcre-8.39... [93amd64-default-job-23] Extracting pcre-8.39: .......... done ===> ncbi-blast+-2.2.30_2 depends on shared library: libpcre.so - found (/usr/local/lib/libpcre.so) ===> Returning to build of ncbi-blast+-2.2.30_2 ===> ncbi-blast+-2.2.30_2 depends on shared library: libbz2.so - found (/usr/lib/libbz2.so) =========================================================================== =======================<phase: configure >============================ ===> Configuring for ncbi-blast+-2.2.30_2 configure: loading site script /usr/ports/Templates/config.site configure: creating cache config.cache checking build system type... amd64-portbld-freebsd9.3 checking host system type... amd64-portbld-freebsd9.3 checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... gcc48 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc48 accepts -g... yes checking for gcc48 option to accept ISO C89... none needed checking whether we are using the GNU C++ compiler... yes checking whether g++48 accepts -g... yes adjusted C compiler: /usr/local/bin/gcc48 adjusted C++ compiler: /usr/local/bin/g++48 Using built-in specs. COLLECT_GCC=/usr/local/bin/gcc48 COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc48/gcc/x86_64-portbld-freebsd9.3/4.8.5/lto-wrapper Target: x86_64-portbld-freebsd9.3 Configured with: /wrkdirs/usr/ports/lang/gcc/work/gcc-4.8.5/configure --disable-bootstrap --disable-nls --enable-gnu-indirect-function --libdir=/usr/local/lib/gcc48 --libexecdir=/usr/local/libexec/gcc48 --program-suffix=48 --with-as=/usr/local/bin/as --with-gmp=/usr/local --with-gxx-include-dir=/usr/local/lib/gcc48/include/c++/ --with-ld=/usr/local/bin/ld --with-libiconv-prefix=/usr/local --with-pkgversion='FreeBSD Ports Collection' --with-system-zlib --with-ecj-jar=/usr/local/share/java/ecj-4.5.jar --enable-languages=c,c++,objc,fortran,java --prefix=/usr/local --localstatedir=/var --mandir=/usr/local/man --infodir=/usr/local/info/gcc48 --build=x86_64-portbld-freebsd9.3 Thread model: posix gcc version 4.8.5 (FreeBSD Ports Collection) checking whether /usr/local/bin/gcc48 has an option to export all symbols... -Wl,-export-dynamic checking whether /usr/local/bin/gcc48 supports -Wl,--{en,dis}able-new-dtags... yes checking whether _LIBCPP_VERSION is declared... no checking how to enable C++ '11 features in /usr/local/bin/g++48 ... -std=gnu++11 checking how to enable C '11 or at least '99 features in /usr/local/bin/gcc48 ... -std=gnu11 -fgnu89-inline checking whether ln -s works... yes checking for ranlib... /usr/local/bin/ranlib checking for ar... ar cr checking ranlib's effectiveness... neutral checking for strip... strip checking whether strip loses runtime type information... Segmentation fault yes Do you still want to proceed (at your own risk)? [y/N] configure: error: Configuration has been canceled by user. ===> Script "configure" failed unexpectedly. Please report the problem to bacon4000@gmail.com [maintainer] and attach the "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/config.log" 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). *** [do-configure] Error code 1 Stop in /usr/ports/biology/ncbi-blast+.
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