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Maintainer: w...@freebsd.org Last committer: mar...@freebsd.org Ident: $FreeBSD: head/biology/embassy/Makefile 355684 2014-05-29 10:47:58Z marino $ Log URL: http://beefy1.isc.freebsd.org/bulk/10i386-default/2014-06-05_14h45m00s/logs/embassy-6.2.0_2.log Build URL: http://beefy1.isc.freebsd.org/bulk/10i386-default/2014-06-05_14h45m00s Log: ====>> Building biology/embassy build started at Fri Jun 6 01:37:56 UTC 2014 port directory: /usr/ports/biology/embassy building for: FreeBSD 10i386-default-job-23 10.0-RELEASE-p3 FreeBSD 10.0-RELEASE-p3 i386 maintained by: w...@freebsd.org Makefile ident: $FreeBSD: head/biology/embassy/Makefile 355684 2014-05-29 10:47:58Z marino $ Poudriere version: 3.1-pre Host OSVERSION: 1100013 Jail OSVERSION: 1000510 ---Begin Environment--- UNAME_m=i386 UNAME_p=i386 OSVERSION=1000510 UNAME_v=FreeBSD 10.0-RELEASE-p3 UNAME_r=10.0-RELEASE-p3 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/build/10i386-default/ref PKG_EXT=txz tpid=99553 PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNG=1 PKGNAME=embassy-6.2.0_2 PKG_DELETE=/usr/local/sbin/pkg-static delete -y -f PKG_ADD=/usr/local/sbin/pkg-static add OLDPWD=/usr/local/poudriere/data/build/10i386-default/ref/poudriere/rdeps PWD=/usr/local/poudriere/data/build/10i386-default/ref/poudriere/pool MASTERNAME=10i386-default USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes PKG_VERSION=/poudriere/pkg-static version PKG_BIN=/usr/local/sbin/pkg-static ---End Environment--- ---Begin OPTIONS List--- ===> The following configuration options are available for embassy-6.2.0_2: CBSTOOLS=on: CBS Tools DOMAINATRIX=on: Protein domain apps DOMALIGN=on: Protein domain apps DOMSEARCH=on: Protein domain apps EMNU=on: EMBOSS simple menu ESIM4=on: Align cDNA/EST to genome HMMER=on: HMM alignment and searches IPRSCAN=on: InterPro scan MEMENEW=on: Motif detection MIRA=on: Whole Genome shotgun and EST assembler MSE=on: A multiple sequence screen editor MYEMBOSS=on: Examples for developers of EMBOSS apps PHYLIPNEW=on: Phylogeny inference SIGNATURE=on: Protein domain apps STRUCTURE=on: Protein domain apps TOPO=on: Transmembrane display VIENNA=on: RNA folding ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local/emboss ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- CPPFLAGS="-I/usr/local/emboss/include -I/usr/local/include -I/usr/local/emboss/include" LDFLAGS=" -L/usr/local/emboss/lib -L/usr/local/lib -L/usr/local/emboss/lib" TMPDIR="/tmp" TMPDIR="/tmp" MAKE=gmake SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- TMPDIR="/tmp" TMPDIR="/tmp" MOTIFLIB="-L/usr/local/lib -lXm -lXp" SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local/emboss LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="-I/usr/local/emboss/include -I/usr/local/include -I/usr/local/emboss/include" LDFLAGS=" -L/usr/local/emboss/lib -L/usr/local/lib -L/usr/local/emboss/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fno-strict-aliasing" MANPREFIX="/usr/local/emboss" 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 444" BSD_INSTALL_MAN="install -o root -g wheel -m 444" --End MAKE_ENV-- --PLIST_SUB-- PLIST_DOMAINATRIX="" PLIST_EMNU="" PLIST_ESIM4="" PLIST_HMMER="" PLIST_MEMENEW="" PLIST_MSE="" PLIST_PHYLIPNEW="" PLIST_TOPO="" PLIST_DOMALIGN="" PLIST_DOMSEARCH="" PLIST_SIGNATURE="" PLIST_STRUCTURE="" PLIST_MYEMBOSS="" PLIST_VIENNA="" PLIST_MIRA="" PLIST_IPRSCAN="" PLIST_CBSTOOLS="" OSREL=10.0 PREFIX=%D LOCALBASE=/usr/local PORTDOCS="" PORTEXAMPLES="" PORTDATA="" LIB32DIR=lib DOCSDIR="share/doc/embassy" EXAMPLESDIR="share/examples/embassy" DATADIR="share/embassy" WWWDIR="www/embassy" ETCDIR="etc/embassy" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local/emboss LOCALBASE=/usr/local DATADIR=/usr/local/emboss/share/embassy DOCSDIR=/usr/local/emboss/share/doc/embassy EXAMPLESDIR=/usr/local/emboss/share/examples/embassy WWWDIR=/usr/local/emboss/www/embassy ETCDIR=/usr/local/emboss/etc/embassy --End SUB_LIST-- ---Begin make.conf--- ARCH=i386 MACHINE=i386 MACHINE_ARCH=i386 USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles #### /usr/local/etc/poudriere.d/make.conf #### WITH_PKGNG=yes # clean-restricted via poudriere.conf NO_RESTRICTED #NO_RESTRICTED=yes DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ===> Cleaning for embassy-6.2.0_2 =======================<phase: check-sanity >============================ =========================================================================== =======================<phase: pkg-depends >============================ ===> embassy-6.2.0_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-1.2.7_2.txz Installing pkg-1.2.7_2... done If you are upgrading from the old package format, first run: # pkg2ng ===> Returning to build of embassy-6.2.0_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> Fetching all distfiles required by embassy-6.2.0_2 for building =========================================================================== =======================<phase: checksum >============================ ===> Fetching all distfiles required by embassy-6.2.0_2 for building => SHA256 Checksum OK for emboss/DOMAINATRIX-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/EMNU-1.05.tar.gz. => SHA256 Checksum OK for emboss/ESIM4-1.0.0.tar.gz. => SHA256 Checksum OK for emboss/HMMER-2.3.2.tar.gz. => SHA256 Checksum OK for emboss/MEMENEW-4.0.0.tar.gz. => SHA256 Checksum OK for emboss/MSE-3.0.0.tar.gz. => SHA256 Checksum OK for emboss/PHYLIPNEW-3.69.tar.gz. => SHA256 Checksum OK for emboss/TOPO-2.0.0.tar.gz. => SHA256 Checksum OK for emboss/DOMALIGN-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/DOMSEARCH-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/SIGNATURE-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/STRUCTURE-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/MYEMBOSS-6.2.0.tar.gz. => SHA256 Checksum OK for emboss/VIENNA-1.7.2.tar.gz. => SHA256 Checksum OK for emboss/MIRA-2.8.2.tar.gz. => SHA256 Checksum OK for emboss/IPRSCAN-4.3.1.tar.gz. => SHA256 Checksum OK for emboss/CBSTOOLS-1.0.0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> Fetching all distfiles required by embassy-6.2.0_2 for building ===> Extracting for embassy-6.2.0_2 ===> Fetching all distfiles required by embassy-6.2.0_2 for building => SHA256 Checksum OK for emboss/DOMAINATRIX-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/EMNU-1.05.tar.gz. => SHA256 Checksum OK for emboss/ESIM4-1.0.0.tar.gz. => SHA256 Checksum OK for emboss/HMMER-2.3.2.tar.gz. => SHA256 Checksum OK for emboss/MEMENEW-4.0.0.tar.gz. => SHA256 Checksum OK for emboss/MSE-3.0.0.tar.gz. => SHA256 Checksum OK for emboss/PHYLIPNEW-3.69.tar.gz. => SHA256 Checksum OK for emboss/TOPO-2.0.0.tar.gz. => SHA256 Checksum OK for emboss/DOMALIGN-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/DOMSEARCH-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/SIGNATURE-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/STRUCTURE-0.1.0.tar.gz. => SHA256 Checksum OK for emboss/MYEMBOSS-6.2.0.tar.gz. => SHA256 Checksum OK for emboss/VIENNA-1.7.2.tar.gz. => SHA256 Checksum OK for emboss/MIRA-2.8.2.tar.gz. => SHA256 Checksum OK for emboss/IPRSCAN-4.3.1.tar.gz. => SHA256 Checksum OK for emboss/CBSTOOLS-1.0.0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for embassy-6.2.0_2 <snip> checking for vfork.h... (cached) no checking for fork... (cached) yes checking for vfork... (cached) yes checking for working fork... yes checking for working vfork... (cached) yes checking for vprintf... (cached) yes checking for _doprnt... no checking for strdup... (cached) yes checking for strstr... yes checking for strchr... yes checking for erand48... yes checking for memmove... (cached) yes checking X11/Xlib.h usability... yes checking X11/Xlib.h presence... yes checking for X11/Xlib.h... yes checking for gethostbyname in -lc... yes checking for socket in -lc... yes checking for main in -lm... yes checking for main in -liconv... no checking if docroot is given... no checking if gcc profiling is selected... no checking if java include directory given... no checking if java OS include directory given... no checking if png driver is wanted... yes checking for inflateEnd in -lz... no No png driver will be made due to librarys missing/old. checking if any authorisation type is given... no checking if Linux x86_64... no checking for large file support... done checking for purify... no checking for cygwin... no checking if any threading type is given... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating emboss_acd/Makefile config.status: creating emboss_doc/Makefile config.status: creating emboss_doc/html/Makefile config.status: creating emboss_doc/text/Makefile config.status: executing depfiles commands config.status: executing libtool commands configure: loading site script /usr/ports/Templates/config.site checking for a BSD-compatible install... (cached) /usr/bin/install checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether gmake sets $(MAKE)... yes checking build system type... i386-unknown-freebsd10.0 checking host system type... i386-unknown-freebsd10.0 checking for style of include used by gmake... GNU checking for gcc... no checking for cc... cc 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 cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking dependency style of cc... gcc3 checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm -B) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking for /usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm -B output from cc object... ok checking how to run the C preprocessor... cc -E checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd10.0 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for gawk... (cached) /usr/bin/awk checking whether we are using the GNU C compiler... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to accept ISO C89... (cached) none needed checking dependency style of cc... (cached) gcc3 checking how to run the C preprocessor... cc -E checking whether byte ordering is bigendian... no checking for a BSD-compatible install... /usr/bin/install checking whether ln -s works... yes checking whether gmake sets $(MAKE)... (cached) yes checking for X... libraries /usr/local/lib, headers /usr/local/include checking whether -R must be followed by a space... neither works checking for gethostbyname... (cached) yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for dirent.h that defines DIR... yes checking for library containing opendir... none required checking for ANSI C header files... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for pid_t... (cached) yes checking for size_t... (cached) yes checking whether struct tm is in sys/time.h or time.h... time.h checking whether getpgrp requires zero arguments... (cached) yes checking for strftime... (cached) yes checking for vfork.h... (cached) no checking for fork... (cached) yes checking for vfork... (cached) yes checking for working fork... yes checking for working vfork... (cached) yes checking for vprintf... (cached) yes checking for _doprnt... no checking for strdup... (cached) yes checking for strstr... yes checking for strchr... yes checking for erand48... yes checking for memmove... (cached) yes checking X11/Xlib.h usability... yes checking X11/Xlib.h presence... yes checking for X11/Xlib.h... yes checking for gethostbyname in -lc... yes checking for socket in -lc... yes checking for main in -lm... yes checking for main in -liconv... no checking if docroot is given... no checking if gcc profiling is selected... no checking if java include directory given... no checking if java OS include directory given... no checking if png driver is wanted... yes checking for inflateEnd in -lz... no No png driver will be made due to librarys missing/old. checking if any authorisation type is given... no checking if Linux x86_64... no checking for large file support... done checking for purify... no checking for cygwin... no checking if any threading type is given... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating emboss_acd/Makefile config.status: creating emboss_doc/Makefile config.status: creating emboss_doc/html/Makefile config.status: creating emboss_doc/text/Makefile config.status: executing depfiles commands config.status: executing libtool commands =========================================================================== =======================<phase: build >============================ ===> Building for embassy-6.2.0_2 gmake[2]: Entering directory `/wrkdirs/usr/ports/biology/embassy/work/embassy-6.2.0/EMBASSY/DOMAINATRIX-0.1.0' Making all in src gmake[3]: Entering directory `/wrkdirs/usr/ports/biology/embassy/work/embassy-6.2.0/EMBASSY/DOMAINATRIX-0.1.0/src' cc -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE=\"DOMAINATRIX\" -DVERSION=\"0.1.0\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DHAVE_DIRENT_H=1 -DSTDC_HEADERS=1 -DHAVE_UNISTD_H=1 -DGETPGRP_VOID=1 -DHAVE_STRFTIME=1 -DHAVE_FORK=1 -DHAVE_VFORK=1 -DHAVE_WORKING_VFORK=1 -DHAVE_WORKING_FORK=1 -DHAVE_VPRINTF=1 -DHAVE_STRDUP=1 -DHAVE_STRSTR=1 -DHAVE_STRCHR=1 -DHAVE_ERAND48=1 -DHAVE_MEMMOVE=1 -DPLD_xwin=1 -DHAVE_LIBM=1 -I. -I/usr/local/emboss/include -I/usr/local/emboss/include/eplplot -DAJ_FreeBSDLF -I/usr/local/emboss/include -I/usr/local/include -I/usr/local/emboss/include -DLENDIAN -DNO_AUTH -O2 -I/usr/local/include -MT cathparse.o -MD -MP -MF .deps/cathparse.Tpo -c -o cathparse.o cathparse.c mv -f .deps/cathparse.Tpo .deps/cathparse.Po /bin/sh ../libtool --tag=CC --mode=link cc -O2 -I/usr/local/include -L/usr/local/emboss/lib -L/usr/local/lib -L/usr/local/emboss/lib -o cathparse cathparse.o -L/usr/local/emboss/lib -lnucleus -lacd -lajaxdb -lensembl -lajaxg -lajax -leexpat -lepcre -lezlib -leplplot -L/usr/local/lib -lX11 -liconv -lm libtool: link: cc -O2 -I/usr/local/include -o cathparse cathparse.o -L/usr/local/emboss/lib -L/usr/local/lib /usr/local/emboss/lib/libnucleus.so /usr/local/emboss/lib/libacd.so /usr/local/emboss/lib/libajaxdb.so /usr/local/emboss/lib/libensembl.so /usr/local/emboss/lib/libajaxg.so /usr/local/emboss/lib/libajax.so /usr/local/emboss/lib/libeexpat.so /usr/local/emboss/lib/libepcre.so /usr/local/emboss/lib/libezlib.so /usr/local/emboss/lib/libeplplot.so /usr/local/lib/libX11.so -liconv -lm -Wl,-rpath -Wl,/usr/local/emboss/lib -Wl,-rpath -Wl,/usr/local/lib -Wl,-rpath -Wl,/usr/local/emboss/lib -Wl,-rpath -Wl,/usr/local/lib /usr/bin/ld: cannot find -liconv cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[3]: *** [cathparse] Error 1 gmake[3]: Leaving directory `/wrkdirs/usr/ports/biology/embassy/work/embassy-6.2.0/EMBASSY/DOMAINATRIX-0.1.0/src' gmake[2]: *** [all-recursive] Error 1 gmake[2]: Leaving directory `/wrkdirs/usr/ports/biology/embassy/work/embassy-6.2.0/EMBASSY/DOMAINATRIX-0.1.0' *** Error code 2 Stop. make[1]: stopped in /usr/ports/biology/embassy *** Error code 1 Stop. make: stopped in /usr/ports/biology/embassy ===> Cleaning for embassy-6.2.0_2 _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
