=> Building biology/lagan build started at Tue Oct 4 21:02:53 PDT 2016 port directory: /usr/ports/biology/lagan building for: DragonFly pkgbox64.dragonflybsd.org 4.7-DEVELOPMENT DragonFly v4.7.0.78.g7d868-DEVELOPMENT #7: Mon Aug 1 22:25:32 PDT 2016 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 maintained by: ports@FreeBSD.org ident warning: no id keywords in /build/boomdata/data/.m/bleeding-edge-default/ref/../04//usr/ports/biology/lagan/Makefile Makefile ident: Poudriere version: 3.1-pre Host OSVERSION: 400700 Jail OSVERSION: 400702 !!! Jail is newer than host. (Jail: 400702, Host: 400700) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- STATUS=1 SAVED_TERM=screen MASTERMNT=/build/boomdata/data/.m/bleeding-edge-default/ref PATH=/usr/local/libexec/poudriere:/sbin:/bin:/usr/sbin:/usr/bin:/usr/pkg/bin:/usr/pkg/sbin:/usr/games:/usr/local/sbin:/usr/local/bin:/usr/pkg/xorg/bin:/usr/X11R6/bin:/root/bin:/sbin:/usr/sbin POUDRIERE_BUILD_TYPE=bulk PKGNAME=lagan-2.0_1 OLDPWD=/root/boom PWD=/build/boomdata/data/.m/bleeding-edge-default/ref/.p/pool MASTERNAME=bleeding-edge-default TERM=cons25 USER=root HOME=/root POUDRIERE_VERSION=3.1-pre LOCALBASE=/usr/local PACKAGE_BUILDING=yes ---End Environment--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/biology/lagan XDG_CONFIG_HOME=/wrkdirs/biology/lagan HOME=/wrkdirs/biology/lagan TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/lagan XDG_CONFIG_HOME=/wrkdirs/biology/lagan HOME=/wrkdirs/biology/lagan TMPDIR="/tmp" NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc50 PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" NOPROFILE=1 CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS=" -pipe -O2 -fno-strict-aliasing" 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-- OSREL=4.7 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 PROFILE="@comment " DOCSDIR="share/doc/lagan" EXAMPLESDIR="share/examples/lagan" DATADIR="share/lagan" WWWDIR="www/lagan" ETCDIR="etc/lagan" --End PLIST_SUB-- --SUB_LIST-- LAGAN_DIR="/usr/local/lagan" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/lagan DOCSDIR=/usr/local/share/doc/lagan EXAMPLESDIR=/usr/local/share/examples/lagan WWWDIR=/usr/local/www/lagan ETCDIR=/usr/local/etc/lagan --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs NO_BACKUP=yes USE_PACKAGE_DEPENDS=yes PKG_CREATE_VERBOSE=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORT_DBDIR=/options PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles MAKE_JOBS_NUMBER=5 ---End make.conf--- =================================================== ===> NOTICE: The lagan 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 ===> License GPLv2 accepted by the user =========================================================================== =================================================== ===> lagan-2.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.8.7_3.txz Installing pkg-1.8.7_3... Extracting pkg-1.8.7_3: .......... done ===> lagan-2.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of lagan-2.0_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The lagan 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by lagan-2.0_1 for building =========================================================================== =================================================== ===> NOTICE: The lagan 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by lagan-2.0_1 for building => SHA256 Checksum OK for lagan20.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The lagan 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 ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by lagan-2.0_1 for building ===> Extracting for lagan-2.0_1 => SHA256 Checksum OK for lagan20.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for lagan-2.0_1 ===> Applying ports patches for lagan-2.0_1 =========================================================================== =================================================== =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for lagan-2.0_1 =========================================================================== =================================================== ===> Building for lagan-2.0_1 (cd src; /usr/bin/make) cc -pipe -O2 -fno-strict-aliasing -o ../anchors anchors.c skiplist.c cc -pipe -O2 -fno-strict-aliasing -o ../chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG filebuffer.c: In function 'FileRead': filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? ^ cc -pipe -O2 -fno-strict-aliasing -o ../order order.c diagmatrix.c filebuffer.c order.c: In function 'doAlign': order.c:409:5: warning: implicit declaration of function 'printMFAAlign' [-Wimplicit-function-declaration] printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); ^ order.c:411:5: warning: implicit declaration of function 'printXMFAAlign' [-Wimplicit-function-declaration] printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); ^ filebuffer.c: In function 'FileRead': filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? ^ cc -pipe -O2 -fno-strict-aliasing -o ../mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG mlagan.c: In function 'main': mlagan.c:1071:5: warning: implicit declaration of function 'printXMFAAlign' [-Wimplicit-function-declaration] printXMFAAlign(outfile, final); ^ filebuffer.c: In function 'FileRead': filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? ^ cc -pipe -O2 -fno-strict-aliasing -o ../prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG prolagan.c: In function 'main': prolagan.c:1091:5: warning: implicit declaration of function 'printXMFAAlign' [-Wimplicit-function-declaration] printXMFAAlign(outfile, final); ^ filebuffer.c: In function 'FileRead': filebuffer.c:123:34: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] temp[i] = (strchr (alphabet, toupper ((char) i)) != 0) ? ^ cc -pipe -O2 -fno-strict-aliasing -o ../utils/bin2mf utils/bin2mf.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/bin2bl utils/bin2bl.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/cextract utils/cextract.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/cstat utils/cstat.c utils/cstat.c: In function 'cntlets': utils/cstat.c:51:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] if (!isspace(currchar)) { ^ utils/cstat.c:52:18: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] currchar = toupper(currchar); ^ cc -pipe -O2 -fno-strict-aliasing -o ../utils/contigorder utils/contigorder.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/getbounds utils/getbounds.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/getlength utils/getlength.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/getoverlap utils/getoverlap.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/rc utils/rc.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/seqmerge utils/seqmerge.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/scorealign utils/scorealign.c -lm cc -pipe -O2 -fno-strict-aliasing -o ../utils/scorecontigs utils/scorecontigs.c -lm utils/scorecontigs.c: In function 'cntlets': utils/scorecontigs.c:63:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] if (!isspace(currchar)) { ^ utils/scorecontigs.c:64:18: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] currchar = toupper(currchar); ^ utils/scorecontigs.c:65:27: warning: implicit declaration of function 'isalpha' [-Wimplicit-function-declaration] if (!lettersonly || isalpha (currchar)){ ^ cc -pipe -O2 -fno-strict-aliasing -o ../utils/getcontigpos utils/getcontigpos.c cc -pipe -O2 -fno-strict-aliasing -o ../utils/fa2xfa utils/fa2xfa.c c++ -pipe -O2 -fno-strict-aliasing -o ../utils/Glue utils/Glue.cpp utils/Glue.cpp: In function 'void calculateScoreMatrix(int)': utils/Glue.cpp:64:17: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] char *alpha = "ATCG"; ^ utils/Glue.cpp:72:44: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] readScoreMatrix (NUCLEOTIDE_MATRIX_FILE); ^ c++ -pipe -O2 -fno-strict-aliasing -o ../utils/dotplot utils/dotplot.cpp cc -pipe -O2 -fno-strict-aliasing -o ../utils/overlay utils/overlay.c utils/overlay.c: In function 'read_align': utils/overlay.c:119:10: warning: implicit declaration of function 'isspace' [-Wimplicit-function-declaration] if (!isspace(currchar)) { ^ utils/overlay.c:120:19: warning: implicit declaration of function 'toupper' [-Wimplicit-function-declaration] checkchar = toupper(currchar); ^ (cd glocal; /usr/bin/make) cc -Wno-deprecated -pipe -O2 -fno-strict-aliasing -I./ -c glocal.cpp cc -Wno-deprecated -pipe -O2 -fno-strict-aliasing -I./ -c io.cpp cc -Wno-deprecated -pipe -O2 -fno-strict-aliasing -I./ -c rightinfluence.cpp cc -Wno-deprecated -pipe -O2 -fno-strict-aliasing -I./ -c leftinfluence.cpp cc -Wno-deprecated -pipe -O2 -fno-strict-aliasing -I./ -c score.cpp c++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm =========================================================================== =================================================== ===> lagan-2.0_1 depends on package: perl5>=5.20<5.21 - not found ===> Installing existing package /packages/All/perl5-5.20.3_15.txz Installing perl5-5.20.3_15... 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. ===> lagan-2.0_1 depends on package: perl5>=5.20<5.21 - found ===> Returning to build of lagan-2.0_1 =========================================================================== =================================================== ===> Staging for lagan-2.0_1 ===> Generating temporary packing list install -s -m 555 /wrkdirs/biology/lagan/lagan20/anchors /wrkdirs/biology/lagan/stage/usr/local/lagan install -s -m 555 /wrkdirs/biology/lagan/lagan20/chaos /wrkdirs/biology/lagan/stage/usr/local/lagan install -s -m 555 /wrkdirs/biology/lagan/lagan20/glocal /wrkdirs/biology/lagan/stage/usr/local/lagan install -s -m 555 /wrkdirs/biology/lagan/lagan20/mlagan /wrkdirs/biology/lagan/stage/usr/local/lagan install -s -m 555 /wrkdirs/biology/lagan/lagan20/order /wrkdirs/biology/lagan/stage/usr/local/lagan install -m 555 /wrkdirs/biology/lagan/lagan20/anal_gloc.pl /wrkdirs/biology/lagan/stage/usr/local/lagan install -m 555 /wrkdirs/biology/lagan/lagan20/lagan.pl /wrkdirs/biology/lagan/stage/usr/local/lagan install -m 555 /wrkdirs/biology/lagan/lagan20/rechaos.pl /wrkdirs/biology/lagan/stage/usr/local/lagan install -m 555 /wrkdirs/biology/lagan/lagan20/slagan.pl /wrkdirs/biology/lagan/stage/usr/local/lagan install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/Glue /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/bin2bl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/bin2mf /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/cextract /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/contigorder /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/cstat /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/dotplot /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/fa2xfa /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/getbounds /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/getcontigpos /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/getlength /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/getoverlap /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/rc /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/scorealign /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/scorecontigs /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /wrkdirs/biology/lagan/lagan20/utils/seqmerge /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/cmerge2.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/draft.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/mextract.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/mf2bin.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/mpretty.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/mproject.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/mrun.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/mrunfile.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/mrunpairs.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 555 /wrkdirs/biology/lagan/lagan20/utils/mviz.pl /wrkdirs/biology/lagan/stage/usr/local/lagan/utils install -m 0644 /wrkdirs/biology/lagan/lagan20/Readmes/README.FIRST /wrkdirs/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /wrkdirs/biology/lagan/lagan20/Readmes/README.chaos /wrkdirs/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /wrkdirs/biology/lagan/lagan20/Readmes/README.lagan /wrkdirs/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /wrkdirs/biology/lagan/lagan20/Readmes/README.mlagan /wrkdirs/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /wrkdirs/biology/lagan/lagan20/Readmes/README.tools /wrkdirs/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /wrkdirs/biology/lagan/lagan20/Readmes/README.shuffle /wrkdirs/biology/lagan/stage/usr/local/lagan/Readmes ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for lagan-2.0_1 file sizes/checksums [44]: . done packing files [44]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for lagan-2.0_1 build of biology/lagan ended at Tue Oct 4 21:03:35 PDT 2016 build time: 00:00:42