Date: Mon, 27 Apr 2015 13:47:03 GMT From: pkg-fallout@FreeBSD.org To: jwbacon@tds.net Cc: pkg-fallout@FreeBSD.org Subject: [package - 93amd64-default][biology/ncbi-blast+] Failed for ncbi-blast+-2.2.30_2 in configure Message-ID: <201504271347.t3RDl3s4030131@beefy2.isc.freebsd.org>
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Maintainer: jwbacon@tds.net Last committer: marino@FreeBSD.org Ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 384733 2015-04-25 14:21:58Z marino $ Log URL: http://beefy2.isc.freebsd.org/data/93amd64-default/384800/logs/ncbi-blast+-2.2.30_2.log Build URL: http://beefy2.isc.freebsd.org/build.html?mastername=93amd64-default&build=384800 Log: ====>> Building biology/ncbi-blast+ build started at Mon Apr 27 13:46:40 UTC 2015 port directory: /usr/ports/biology/ncbi-blast+ building for: FreeBSD 93amd64-default-job-22 9.3-RELEASE-p13 FreeBSD 9.3-RELEASE-p13 amd64 maintained by: jwbacon@tds.net Makefile ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 384733 2015-04-25 14:21:58Z marino $ Poudriere version: 3.1.4 Host OSVERSION: 1100064 Jail OSVERSION: 903000 ---Begin Environment--- OSVERSION=903000 UNAME_v=FreeBSD 9.3-RELEASE-p13 UNAME_r=9.3-RELEASE-p13 BLOCKSIZE=K MAIL=/var/mail/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin STATUS=1 SAVED_TERM=screen MASTERMNT=/usr/local/poudriere/data/.m/93amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PKGNAME=ncbi-blast+-2.2.30_2 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/93amd64-default/ref/.p/pool MASTERNAME=93amd64-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.4 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---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 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=/us r/local/lib/gcc48" MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -o root -g wheel -m 555" BSD_INSTALL_LIB="install -s -o root -g wheel -m 444" BSD_INSTALL_SCRIPT="install -o root -g wheel -m 555" BSD_INSTALL_DATA="install -o root -g wheel -m 0644" BSD_INSTALL_MAN="install -o root -g wheel -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_VERSION=python2.7 PYTHON_VER=2.7 OSREL=9.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.18.4 PERL_VER=5.18 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.18 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 #### MASTER_SITE_FREEBSD=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- =======================<phase: check-sanity >============================ ===> License Public_domain accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> ncbi-blast+-2.2.30_2 depends on file: /usr/local/sbin/pkg - not found ===> Verifying install for /usr/local/sbin/pkg in /usr/ports/ports-mgmt/pkg ===> Installing existing package /packages/All/pkg-1.5.1.txz [93amd64-default-job-22] Installing pkg-1.5.1... [93amd64-default-job-22] Extracting pkg-1.5.1... done Message for pkg-1.5.1: If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of ncbi-blast+-2.2.30_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License Public_domain accepted by the user ===> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License Public_domain 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 Public_domain 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 /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 ===> Verifying install for gmake in /usr/ports/devel/gmake ===> Installing existing package /packages/All/gmake-4.1_1.txz [93amd64-default-job-22] Installing gmake-4.1_1... [93amd64-default-job-22] `-- Installing gettext-runtime-0.19.4... [93amd64-default-job-22] | `-- Installing indexinfo-0.2.3... [93amd64-default-job-22] | `-- Extracting indexinfo-0.2.3... done [93amd64-default-job-22] | `-- Installing libiconv-1.14_8... [93amd64-default-job-22] | `-- Extracting libiconv-1.14_8... done [93amd64-default-job-22] `-- Extracting gettext-runtime-0.19.4... done [93amd64-default-job-22] Extracting gmake-4.1_1... done ===> 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 ===> Verifying install for /usr/local/bin/python2.7 in /usr/ports/lang/python27 ===> Installing existing package /packages/All/python27-2.7.9_1.txz [93amd64-default-job-22] Installing python27-2.7.9_1... [93amd64-default-job-22] `-- Installing libffi-3.2.1... [93amd64-default-job-22] `-- Extracting libffi-3.2.1... done [93amd64-default-job-22] Extracting python27-2.7.9_1... done Message for python27-2.7.9_1: ===================================================================== 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 ===================================================================== ===> Returning to build of ncbi-blast+-2.2.30_2 ===> ncbi-blast+-2.2.30_2 depends on executable: gcc48 - not found ===> Verifying install for gcc48 in /usr/ports/lang/gcc ===> Installing existing package /packages/All/gcc-4.8.4_1.txz [93amd64-default-job-22] Installing gcc-4.8.4_1... [93amd64-default-job-22] `-- Installing binutils-2.25... [93amd64-default-job-22] `-- Extracting binutils-2.25... done [93amd64-default-job-22] `-- Installing gcc-ecj-4.5... [93amd64-default-job-22] `-- Extracting gcc-ecj-4.5... done [93amd64-default-job-22] `-- Installing gmp-5.1.3_2... [93amd64-default-job-22] `-- Extracting gmp-5.1.3_2... done [93amd64-default-job-22] `-- Installing mpc-1.0.3... [93amd64-default-job-22] | `-- Installing mpfr-3.1.2_2... [93amd64-default-job-22] | `-- Extracting mpfr-3.1.2_2... done [93amd64-default-job-22] `-- Extracting mpc-1.0.3... done [93amd64-default-job-22] Extracting gcc-4.8.4_1... done Message for gcc-4.8.4_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/gcc48 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> 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 file: /usr/local/bin/perl5.18.4 - not found ===> Verifying install for /usr/local/bin/perl5.18.4 in /usr/ports/lang/perl5.18 ===> Installing existing package /packages/All/perl5-5.18.4_13.txz [93amd64-default-job-22] Installing perl5-5.18.4_13... [93amd64-default-job-22] Extracting perl5-5.18.4_13... done ===> 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 ===> Verifying for libpcre.so in /usr/ports/devel/pcre ===> Installing existing package /packages/All/pcre-8.35_2.txz [93amd64-default-job-22] Installing pcre-8.35_2... [93amd64-default-job-22] Extracting pcre-8.35_2... done ===> 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: error: --localstatedir=/var: unknown option; use --help to show usage ===> Script "configure" failed unexpectedly. Please report the problem to jwbacon@tds.net [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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