Date: Sun, 14 Apr 2019 19:43:21 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-powerpc64-default][biology/wise] Failed for wise-2.4.1_1 in build Message-ID: <201904141943.x3EJhL9a033664@pylon.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: ports@FreeBSD.org Last committer: tijl@FreeBSD.org Ident: $FreeBSD: head/biology/wise/Makefile 428152 2016-12-08 19:52:19Z tijl $ Log URL: http://pylon.nyi.freebsd.org/data/head-powerpc64-default/p498785_s346161/logs/wise-2.4.1_1.log Build URL: http://pylon.nyi.freebsd.org/build.html?mastername=head-powerpc64-default&build=p498785_s346161 Log: =>> Building biology/wise build started at Sun Apr 14 19:40:43 UTC 2019 port directory: /usr/ports/biology/wise package name: wise-2.4.1_1 building for: FreeBSD head-powerpc64-default-job-22 13.0-CURRENT FreeBSD 13.0-CURRENT 1300018 powerpc maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: head/biology/wise/Makefile 428152 2016-12-08 19:52:19Z tijl $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300012 Jail OSVERSION: 1300018 Job Id: 22 !!! Jail is newer than host. (Jail: 1300018, Host: 1300012) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300018 UNAME_v=FreeBSD 13.0-CURRENT 1300018 UNAME_r=13.0-CURRENT 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=3.2.8-3-g02cc9753 MASTERMNT=/usr/local/poudriere/data/.m/head-powerpc64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-powerpc64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-powerpc64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-powerpc64-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= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for wise-2.4.1_1: DOCS=on: Build and/or install documentation EXAMPLES=on: Build and/or install examples ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/wise/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/wise/work HOME=/wrkdirs/usr/ports/biology/wise/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/wise/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 LANG=en_US.UTF-8 LC_ALL=en_US.UTF-8 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -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-- PORTDOCS="" PORTEXAMPLES="" GTK2_VERSION="2.10.0" GTK3_VERSION="3.0.0" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/wise" EXAMPLESDIR="share/examples/wise" DATADIR="share/wise" WWWDIR="www/wise" ETCDIR="etc/wise" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/wise DOCSDIR=/usr/local/share/doc/wise EXAMPLESDIR=/usr/local/share/examples/wise WWWDIR=/usr/local/www/wise ETCDIR=/usr/local/etc/wise --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 # 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_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=Using built-in specs. Target: powerpc64-undermydesk-freebsd Configured with: FreeBSD/powerpc64 system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-Qy" "-melf64ppc_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtsavres.o" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_921dbbb2_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_921dbbb2_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_921dbbb2_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_921dbbb2_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_921dbbb2_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_921dbbb2=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300018 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--- --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: The wise 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 =========================================================================== =======================<phase: pkg-depends >============================ ===> wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-powerpc64-default-job-22] Installing pkg-1.10.5_5... [head-powerpc64-default-job-22] Extracting pkg-1.10.5_5: .......... done ===> wise-2.4.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of wise-2.4.1_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> NOTICE: The wise 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 <snip> cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ shadowseqindex.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsphandler.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspscaninterface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsp2hitscan.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsplookupscan.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsplookupthreaded.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspthreadeddb.c hspthreadeddb.dy: In function 'Wise2_threadeddb_scan_worker': hspthreadeddb.dy:154: warning: cast from pointer to integer of different size cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hspscanruntime.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ hsptwohitscan.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ proteinindexcons.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ dnaindexcons.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ staticseq.c ar ru libdyna_glib.a subseqhash.o intallocator.o proteinstreamedindex.o shadowseq.o shadowseqindex.o hsphandler.o hspscaninterface.o hsp2hitscan.o hsplookupscan.o hsplookupthreaded.o hspthreadeddb.o hspscanruntime.o hsptwohitscan.o proteinindexcons.o dnaindexcons.o staticseq.o ar: warning: creating libdyna_glib.a if test -x /bin/ranlib; then /bin/ranlib libdyna_glib.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libdyna_glib.a; else exit 0; fi (cd external ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) (cd mott; make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include " all) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c mott_api.c -o mott_api.o mott_api.c: In function 'GetHistogram': mott_api.c:179: warning: incompatible implicit declaration of built-in function 'calloc' mott_api.c: In function 'RobinsonResidueFrequencies2': mott_api.c:230: warning: incompatible implicit declaration of built-in function 'calloc' cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -c gaplib.c -o gaplib.o cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../../dynlibsrc -I../../base wise2_mott_bridge.c ar ru libmott.a mott_api.o gaplib.o wise2_mott_bridge.o ar: warning: creating libmott.a if test -x /bin/ranlib; then /bin/ranlib libmott.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libmott.a; else exit 0; fi (cd socket ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" libwisesocket.a ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ functionserver.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ functionclient.c functionclient.dy: In function 'Wise2_new_FunctionProxyCoordinator': functionclient.dy:193: warning: passing argument 2 of 'connect' from incompatible pointer type cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ anonobj.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ transferinterface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ directsocketwrite.c ar ru libwisesocket.a functionserver.o functionclient.o anonobj.o transferinterface.o directsocketwrite.o ar: warning: creating libwisesocket.a if test -x /bin/ranlib; then /bin/ranlib libwisesocket.a; else exit 0; fi if test -x /usr/bin/ranlib; then /usr/bin/ranlib libwisesocket.a; else exit 0; fi (cd dnaindex ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_index_interface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_direct.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_hash.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_count.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_glib_index.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models singleseqspace.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models dnamapping.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models largeseqreader.c largeseqreader.dy: In function 'Wise2_read_large_dna_Sequence': largeseqreader.dy:44: warning: comparison is always false due to limited range of data type largeseqreader.dy:54: warning: comparison is always true due to limited range of data type largeseqreader.dy:63: warning: comparison is always true due to limited range of data type largeseqreader.dy:74: warning: comparison is always true due to limited range of data type cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_untangler.c kmer_assembly_untangler.dy: In function 'Wise2_show_KmerAssemblyPath': kmer_assembly_untangler.dy:52: warning: cast from pointer to integer of different size kmer_assembly_untangler.dy: In function 'Wise2_old_attempt_forward_untangle_KmerAssembly': kmer_assembly_untangler.dy:568: warning: passing argument 4 of 'Wise2_lift_backward_tangled_tail' from incompatible pointer type cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_contig.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models kmer_assembly_error.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_interface.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_fasta.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_sanger_project.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models assembly_stream_cons.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../dynlibsrc/ -I../models compressed_protein_index.c compressed_protein_index.dy: In function 'Wise2_add_direct_number_CompressedProteinIndex': compressed_protein_index.dy:223: warning: return makes integer from pointer without a cast (cd network ; /usr/bin/make CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing -c `pkg-config glib-2.0 --cflags`" all ) cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex wise_proteinindex_server.c cc -O2 -pipe -fno-strict-aliasing -c -I/usr/local/include/glib-2.0 -I/usr/local/lib/glib-2.0/include -I/usr/local/include -I../base/ -I../socket -I../dynlibsrc -I../dnaindex net_hspscan.c cc -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config glib-2.0 --libs` -pthread wise_proteinindex_server.o:(.text+0x2a0): undefined reference to `Wise2_show_help_SeqLookupLoadPara' wise_proteinindex_server.o:(.text+0x2ac): undefined reference to `Wise2_show_standard_options' wise_proteinindex_server.o:(.text+0x374): undefined reference to `Wise2_new_SeqLookupLoadPara_from_argv' wise_proteinindex_server.o:(.text+0x38c): undefined reference to `Wise2_strip_out_boolean_argument' wise_proteinindex_server.o:(.text+0x3a4): undefined reference to `Wise2_strip_out_boolean_argument' wise_proteinindex_server.o:(.text+0x3bc): undefined reference to `Wise2_strip_out_boolean_argument' wise_proteinindex_server.o:(.text+0x3d4): undefined reference to `Wise2_strip_out_boolean_argument' wise_proteinindex_server.o:(.text+0x3f0): undefined reference to `Wise2_strip_out_integer_argument' wise_proteinindex_server.o:(.text+0x404): undefined reference to `Wise2_strip_out_boolean_argument' wise_proteinindex_server.o:(.text+0x41c): undefined reference to `Wise2_strip_out_boolean_argument' wise_proteinindex_server.o:(.text+0x438): undefined reference to `Wise2_strip_out_integer_argument' wise_proteinindex_server.o:(.text+0x450): undefined reference to `Wise2_strip_out_integer_argument' wise_proteinindex_server.o:(.text+0x468): undefined reference to `Wise2_strip_out_integer_argument' wise_proteinindex_server.o:(.text+0x47c): undefined reference to `Wise2_strip_out_boolean_argument' wise_proteinindex_server.o:(.text+0x494): undefined reference to `Wise2_strip_out_boolean_argument' wise_proteinindex_server.o:(.text+0x4b0): undefined reference to `Wise2_strip_out_integer_argument' wise_proteinindex_server.o:(.text+0x4c4): undefined reference to `Wise2_strip_out_assigned_argument' wise_proteinindex_server.o:(.text+0x4e0): undefined reference to `Wise2_strip_out_integer_argument' wise_proteinindex_server.o:(.text+0x4f8): undefined reference to `Wise2_strip_out_standard_options' wise_proteinindex_server.o:(.text+0x514): undefined reference to `Wise2_new_FunctionServer' wise_proteinindex_server.o:(.text+0x524): undefined reference to `Wise2_single_fasta_SequenceDB' wise_proteinindex_server.o:(.text+0x534): undefined reference to `Wise2_read_Blast_file_CompMat' wise_proteinindex_server.o:(.text+0x568): undefined reference to `Wise2_new_ArraySeq_SeqLookupInterface' wise_proteinindex_server.o:(.text+0x580): undefined reference to `Wise2_load_SequenceDB_SeqLookupLoadPara' wise_proteinindex_server.o:(.text+0x5b0): undefined reference to `Wise2_info' wise_proteinindex_server.o:(.text+0x5c8): undefined reference to `Wise2_dump_ProteinStreamedIndex' wise_proteinindex_server.o:(.text+0x5d4): undefined reference to `Wise2_info' wise_proteinindex_server.o:(.text+0x618): undefined reference to `Wise2_new_one_off_HSPScanInterface' wise_proteinindex_server.o:(.text+0x62c): undefined reference to `Wise2_new_HSPThreadedDatabase' wise_proteinindex_server.o:(.text+0x64c): undefined reference to `Wise2_load_HSPThreadedDatabase' wise_proteinindex_server.o:(.text+0x658): undefined reference to `Wise2_new_HSPScanInterface_from_HSPThreadedDatabase' wise_proteinindex_server.o:(.text+0x670): undefined reference to `Wise2_add_FunctionServer' wise_proteinindex_server.o:(.text+0x6d4): undefined reference to `Wise2_info' wise_proteinindex_server.o:(.text+0x6e4): undefined reference to `Wise2_info' wise_proteinindex_server.o:(.text+0x6f4): undefined reference to `Wise2_main_loop_forking_FunctionServer' wise_proteinindex_server.o:(.text+0x75c): undefined reference to `Wise2_new_twohit_one_off_HSPScanInterface' wise_proteinindex_server.o:(.text+0x778): undefined reference to `Wise2_new_ordered_HSPScanInterface' wise_proteinindex_server.o:(.text+0x788): undefined reference to `Wise2_new_ProteinStreamedIndex_SeqLookupInterface' wise_proteinindex_server.o:(.text+0x7a8): undefined reference to `Wise2_load_SequenceDB_SeqLookupLoadPara' wise_proteinindex_server.o:(.text+0x7bc): undefined reference to `Wise2_new_ghash_SeqLookupInterface' wise_proteinindex_server.o:(.text+0x7e0): undefined reference to `Wise2_new_threaded_HSPScanInterface' wise_proteinindex_server.o:(.text+0x81c): undefined reference to `Wise2_new_runtime_HSPScanInterface' wise_proteinindex_server.o:(.text+0x830): undefined reference to `Wise2_print_array_occuypancy_ArraySeq' net_hspscan.o:(.text+0xc): undefined reference to `Wise2_free_LinearHSPmanager' net_hspscan.o:(.text+0x3c): undefined reference to `Wise2_free_Sequence' net_hspscan.o:(.text+0xdc): undefined reference to `Wise2_hard_link_Sequence' net_hspscan.o:(.text+0xe8): undefined reference to `Wise2_AnonymousObject_alloc' net_hspscan.o:(.text+0x194): undefined reference to `Wise2_TransferedObjectMarshaller_alloc' net_hspscan.o:(.text+0x1e4): undefined reference to `Wise2_TransferedObjectMarshaller_alloc' net_hspscan.o:(.text+0x234): undefined reference to `Wise2_TransferedObjectMarshaller_alloc' net_hspscan.o:(.text+0x288): undefined reference to `Wise2_TransferedFunctionCall_alloc_std' net_hspscan.o:(.text+0x298): undefined reference to `Wise2_stringalloc' net_hspscan.o:(.text+0x2b8): undefined reference to `Wise2_add_TransferedFunctionCall' net_hspscan.o:(.text+0x2cc): undefined reference to `Wise2_add_TransferedFunctionCall' net_hspscan.o:(.text+0x310): undefined reference to `Wise2_FunctionImplementation_alloc' net_hspscan.o:(.text+0x368): undefined reference to `Wise2_new_FunctionProxyCoordinator' net_hspscan.o:(.text+0x378): undefined reference to `Wise2_new_FunctionProxy' net_hspscan.o:(.text+0x388): undefined reference to `Wise2_add_FunctionProxyCoordinator' net_hspscan.o:(.text+0x3c0): undefined reference to `Wise2_free_FunctionProxyCoordinator' net_hspscan.o:(.text+0x414): undefined reference to `Wise2_AnonymousObjectList_alloc_len' net_hspscan.o:(.text+0x420): undefined reference to `Wise2_AnonymousObject_alloc' net_hspscan.o:(.text+0x430): undefined reference to `Wise2_hard_link_Sequence' net_hspscan.o:(.text+0x44c): undefined reference to `Wise2_add_AnonymousObjectList' net_hspscan.o:(.text+0x454): undefined reference to `Wise2_AnonymousObject_alloc' net_hspscan.o:(.text+0x464): undefined reference to `Wise2_hard_link_HSPScanInterfacePara' net_hspscan.o:(.text+0x480): undefined reference to `Wise2_add_AnonymousObjectList' net_hspscan.o:(.text+0x494): undefined reference to `Wise2_dispatch_FunctionProxy' net_hspscan.o:(.text+0x4a4): undefined reference to `Wise2_free_AnonymousObjectList' net_hspscan.o:(.text+0x4bc): undefined reference to `Wise2_free_AnonymousObject' net_hspscan.o:(.text+0x518): undefined reference to `Wise2_HSPScanInterface_alloc' net_hspscan.o:(.got+0x40): undefined reference to `Wise2_untyped_LinearHSPmanager_to_Stream' net_hspscan.o:(.got+0x48): undefined reference to `Wise2_untyped_LinearHSPmanager_from_Stream' net_hspscan.o:(.got+0x50): undefined reference to `Wise2_untyped_write_Sequence_to_Stream' net_hspscan.o:(.got+0x58): undefined reference to `Wise2_untyped_read_Sequence_from_Stream' net_hspscan.o:(.got+0x70): undefined reference to `Wise2_untyped_HSPScanInterfacePara_to_Stream' net_hspscan.o:(.got+0x78): undefined reference to `Wise2_untyped_read_HSPScanInterfacePara_from_Stream' net_hspscan.o:(.got+0x88): undefined reference to `Wise2_untyped_HSPScanInterfacePara_free' ./dnaindex/compressed_protein_index.o:(.text+0xd4): undefined reference to `Wise2_warn' ./dnaindex/compressed_protein_index.o:(.text+0x12c): undefined reference to `Wise2_warn' ./dnaindex/compressed_protein_index.o:(.text+0x268): undefined reference to `Wise2_ckfree' ./dnaindex/compressed_protein_index.o:(.text+0x294): undefined reference to `Wise2_warn' ./dnaindex/compressed_protein_index.o:(.text+0x314): undefined reference to `Wise2_ckalloc' ./dnaindex/compressed_protein_index.o:(.text+0x370): undefined reference to `Wise2_warn' ./dnaindex/compressed_protein_index.o:(.text+0x39c): undefined reference to `Wise2_ckalloc' ./dnaindex/compressed_protein_index.o:(.text+0x3f4): undefined reference to `Wise2_warn' ./dnaindex/compressed_protein_index.o:(.text+0x4a8): undefined reference to `Wise2_ckfree' ./dnaindex/compressed_protein_index.o:(.text+0x4d4): undefined reference to `Wise2_warn' ./dnaindex/compressed_protein_index.o:(.text+0x7e0): undefined reference to `Wise2_seq_number_aa_5mer' ./dnaindex/compressed_protein_index.o:(.text+0x910): undefined reference to `Wise2_fatal' ./dnaindex/compressed_protein_index.o:(.text+0x948): undefined reference to `Wise2_fatal' ./dnaindex/compressed_protein_index.o:(.text+0x9f0): undefined reference to `Wise2_SeqLookupClientInterface_alloc' ./dnaindex/compressed_protein_index.o:(.text+0xa7c): undefined reference to `Wise2_SeqLookupInterface_alloc_std' ./dnaindex/compressed_protein_index.o:(.text+0xbac): undefined reference to `Wise2_SeqLookupResultInterface_alloc' ./dnaindex/singleseqspace.o:(.text+0x304): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0x35c): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0x3e8): undefined reference to `Wise2_ckfree' ./dnaindex/singleseqspace.o:(.text+0x414): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0x538): undefined reference to `Wise2_ckfree' ./dnaindex/singleseqspace.o:(.text+0x544): undefined reference to `Wise2_ckfree' ./dnaindex/singleseqspace.o:(.text+0x570): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0x690): undefined reference to `Wise2_ckalloc' ./dnaindex/singleseqspace.o:(.text+0x700): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0x72c): undefined reference to `Wise2_ckalloc' ./dnaindex/singleseqspace.o:(.text+0x784): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0x7c8): undefined reference to `Wise2_ckcalloc' ./dnaindex/singleseqspace.o:(.text+0x80c): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0x8b4): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0x8e0): undefined reference to `Wise2_ckrealloc' ./dnaindex/singleseqspace.o:(.text+0x918): undefined reference to `Wise2_warn' ./dnaindex/singleseqspace.o:(.text+0xd18): undefined reference to `Wise2_fatal' ./dnaindex/kmer_direct.o:(.text+0x2e8): undefined reference to `Wise2_warn' *** Error code 1 Stop. make[2]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src/network *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/wise/work/wise2.4.1/src *** Error code 1 Stop. make: stopped in /usr/ports/biology/wise
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