=> Building biology/mummer build started at Tue Oct 4 21:03:25 PDT 2016 port directory: /usr/ports/biology/mummer 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/../02//usr/ports/biology/mummer/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=mummer-3.23_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--- ===> The following configuration options are available for mummer-3.23_1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl XDG_DATA_HOME=/wrkdirs/biology/mummer XDG_CONFIG_HOME=/wrkdirs/biology/mummer HOME=/wrkdirs/biology/mummer TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/biology/mummer XDG_CONFIG_HOME=/wrkdirs/biology/mummer HOME=/wrkdirs/biology/mummer 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/mummer" EXAMPLESDIR="share/examples/mummer" DATADIR="share/mummer" WWWDIR="www/mummer" ETCDIR="etc/mummer" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mummer DOCSDIR=/usr/local/share/doc/mummer EXAMPLESDIR=/usr/local/share/examples/mummer WWWDIR=/usr/local/www/mummer ETCDIR=/usr/local/etc/mummer --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 mummer 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 =========================================================================== =================================================== ===> mummer-3.23_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 ===> mummer-3.23_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of mummer-3.23_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The mummer 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 ===> Fetching all distfiles required by mummer-3.23_1 for building =========================================================================== =================================================== ===> NOTICE: The mummer 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 ===> Fetching all distfiles required by mummer-3.23_1 for building => SHA256 Checksum OK for MUMmer3.23.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: The mummer 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 ===> Fetching all distfiles required by mummer-3.23_1 for building ===> Extracting for mummer-3.23_1 => SHA256 Checksum OK for MUMmer3.23.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for mummer-3.23_1 ===> Applying ports patches for mummer-3.23_1 =========================================================================== =================================================== ===> mummer-3.23_1 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_1.txz Installing gmake-4.2.1_1... `-- Installing indexinfo-0.2.5... `-- Extracting indexinfo-0.2.5: .... done `-- Installing gettext-runtime-0.19.8.1... `-- Extracting gettext-runtime-0.19.8.1: .......... done Extracting gmake-4.2.1_1: .......... done ===> mummer-3.23_1 depends on executable: gmake - found ===> Returning to build of mummer-3.23_1 ===> mummer-3.23_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. ===> mummer-3.23_1 depends on package: perl5>=5.20<5.21 - found ===> Returning to build of mummer-3.23_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for mummer-3.23_1 =========================================================================== =================================================== ===> Building for mummer-3.23_1 gmake[1]: Entering directory '/wrkdirs/biology/mummer/MUMmer3.23' cd /wrkdirs/biology/mummer/MUMmer3.23/src/kurtz; gmake mummer cd /wrkdirs/biology/mummer/MUMmer3.23/src/tigr; gmake all cd /wrkdirs/biology/mummer/MUMmer3.23/scripts; gmake all gmake[2]: Entering directory '/wrkdirs/biology/mummer/MUMmer3.23/src/kurtz' cd libbasedir; gmake libbase.a gmake[2]: Entering directory '/wrkdirs/biology/mummer/MUMmer3.23/src/tigr' c++ -pipe -O2 -fno-strict-aliasing tigrinc.cc -c -o tigrinc.o gmake[2]: Entering directory '/wrkdirs/biology/mummer/MUMmer3.23/scripts' gmake[3]: Entering directory '/wrkdirs/biology/mummer/MUMmer3.23/src/kurtz/libbasedir' cc -pipe -O2 -fno-strict-aliasing -c -o cleanMUMcand.o cleanMUMcand.c cc -pipe -O2 -fno-strict-aliasing -c -o clock.o clock.c cc -pipe -O2 -fno-strict-aliasing -c -o mapfile.o mapfile.c /usr/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23?g' \ -e 's?__SCRIPT_DIR?/wrkdirs/biology/mummer/MUMmer3.23/scripts?g' \ exact-tandems.csh > /wrkdirs/biology/mummer/MUMmer3.23/exact-tandems chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/exact-tandems /usr/bin/sed -e 's?__PERL_PATH?/usr/local/bin/perl?g' \ -e 's?__SCRIPT_DIR?/wrkdirs/biology/mummer/MUMmer3.23/scripts?g' \ mapview.pl > /wrkdirs/biology/mummer/MUMmer3.23/mapview chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/mapview /usr/bin/sed -e 's?__PERL_PATH?/usr/local/bin/perl?g' \ -e 's?__SCRIPT_DIR?/wrkdirs/biology/mummer/MUMmer3.23/scripts?g' \ -e 's?__BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23?g' \ mummerplot.pl > /wrkdirs/biology/mummer/MUMmer3.23/mummerplot chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/mummerplot /usr/bin/sed -e 's?__PERL_PATH?/usr/local/bin/perl?g' \ -e 's?__SCRIPT_DIR?/wrkdirs/biology/mummer/MUMmer3.23/scripts?g' \ -e 's?__AUX_BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23/aux_bin?g' \ -e 's?__BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23?g' \ nucmer.pl > /wrkdirs/biology/mummer/MUMmer3.23/nucmer chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/nucmer /usr/bin/sed -e 's?__PERL_PATH?/usr/local/bin/perl?g' \ -e 's?__SCRIPT_DIR?/wrkdirs/biology/mummer/MUMmer3.23/scripts?g' \ -e 's?__AUX_BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23/aux_bin?g' \ -e 's?__BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23?g' \ promer.pl > /wrkdirs/biology/mummer/MUMmer3.23/promer chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/promer /usr/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23?g' \ run-mummer1.csh > /wrkdirs/biology/mummer/MUMmer3.23/run-mummer1 chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/run-mummer1 /usr/bin/sed -e 's?__CSH_PATH?/bin/csh?g' \ -e 's?__BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23?g' \ run-mummer3.csh > /wrkdirs/biology/mummer/MUMmer3.23/run-mummer3 chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/run-mummer3 /usr/bin/sed -e 's?__PERL_PATH?/usr/local/bin/perl?g' \ nucmer2xfig.pl > /wrkdirs/biology/mummer/MUMmer3.23/nucmer2xfig cc -pipe -O2 -fno-strict-aliasing -c -o multiseq.o multiseq.c chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/nucmer2xfig /usr/bin/sed -e 's?__PERL_PATH?/usr/local/bin/perl?g' \ -e 's?__SCRIPT_DIR?/wrkdirs/biology/mummer/MUMmer3.23/scripts?g' \ -e 's?__BIN_DIR?/wrkdirs/biology/mummer/MUMmer3.23?g' \ dnadiff.pl > /wrkdirs/biology/mummer/MUMmer3.23/dnadiff chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/dnadiff gmake[2]: Leaving directory '/wrkdirs/biology/mummer/MUMmer3.23/scripts' cc -pipe -O2 -fno-strict-aliasing -c -o procopt.o procopt.c c++ -pipe -O2 -fno-strict-aliasing delta.cc -c -o delta.o c++ -pipe -O2 -fno-strict-aliasing sw_align.cc -c -o sw_align.o c++ -pipe -O2 -fno-strict-aliasing translate.cc -c -o translate.o cc -pipe -O2 -fno-strict-aliasing -c -o safescpy.o safescpy.c c++ -pipe -O2 -fno-strict-aliasing prenuc.cc tigrinc.o -o /wrkdirs/biology/mummer/MUMmer3.23/aux_bin/prenuc; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/aux_bin/prenuc c++ -pipe -O2 -fno-strict-aliasing prepro.cc tigrinc.o translate.o -o /wrkdirs/biology/mummer/MUMmer3.23/aux_bin/prepro; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/aux_bin/prepro cc -pipe -O2 -fno-strict-aliasing -c -o seterror.o seterror.c c++ -pipe -O2 -fno-strict-aliasing repeat-match.cc tigrinc.o -o /wrkdirs/biology/mummer/MUMmer3.23/repeat-match; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/repeat-match cc -pipe -O2 -fno-strict-aliasing -c -o space.o space.c c++ -pipe -O2 -fno-strict-aliasing annotate.cc tigrinc.o -o /wrkdirs/biology/mummer/MUMmer3.23/annotate; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/annotate c++ -pipe -O2 -fno-strict-aliasing combineMUMs.cc tigrinc.o -o /wrkdirs/biology/mummer/MUMmer3.23/combineMUMs; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/combineMUMs combineMUMs.cc:26:38: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] #define DEFAULT_ERROR_FILE_NAME "witherrors.gaps" ^ combineMUMs.cc:109:27: note: in expansion of macro 'DEFAULT_ERROR_FILE_NAME' char * Error_File_Name = DEFAULT_ERROR_FILE_NAME; ^ combineMUMs.cc:135:24: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] char * Query_Suffix = "Query"; ^ combineMUMs.cc:145:22: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] char * Ref_Suffix = "Ref"; ^ ar sruv libbase.a cleanMUMcand.o clock.o mapfile.o multiseq.o procopt.o safescpy.o seterror.o space.o /usr/libexec/binutils225/elf/ar: creating libbase.a a - cleanMUMcand.o a - clock.o a - mapfile.o a - multiseq.o a - procopt.o a - safescpy.o a - seterror.o a - space.o gmake[3]: Leaving directory '/wrkdirs/biology/mummer/MUMmer3.23/src/kurtz/libbasedir' cd streesrc; gmake libstree.a gmake[3]: Entering directory '/wrkdirs/biology/mummer/MUMmer3.23/src/kurtz/streesrc' cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o construct.o construct.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o access.o access.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o scanpref.o scanpref.c c++ -pipe -O2 -fno-strict-aliasing gaps.cc tigrinc.o -o /wrkdirs/biology/mummer/MUMmer3.23/gaps; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/gaps cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o linkloc.o linkloc.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o depthtab.o depthtab.c c++ -pipe -O2 -fno-strict-aliasing mgaps.cc tigrinc.o -o /wrkdirs/biology/mummer/MUMmer3.23/mgaps; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/mgaps mgaps.cc: In function 'int Process_Cluster(Match_t*, int, char*)': mgaps.cc:533:18: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] label = "#\n"; ^ mgaps.cc: In function 'void Process_Matches(Match_t*, int, char*)': mgaps.cc:620:17: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] label = "#\n"; ^ c++ -pipe -O2 -fno-strict-aliasing postnuc.cc tigrinc.o sw_align.o -o /wrkdirs/biology/mummer/MUMmer3.23/aux_bin/postnuc; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/aux_bin/postnuc cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o ex2leav.o ex2leav.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o dfs.o dfs.c c++ -pipe -O2 -fno-strict-aliasing postpro.cc tigrinc.o sw_align.o translate.o -o /wrkdirs/biology/mummer/MUMmer3.23/aux_bin/postpro; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/aux_bin/postpro cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o overmax.o overmax.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o oversucc.o oversucc.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o addleafcount.o addleafcount.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -DSTREEHUGE -c -o iterator.o iterator.c ar sruv libstree.a construct.o access.o scanpref.o linkloc.o depthtab.o ex2leav.o dfs.o overmax.o oversucc.o addleafcount.o iterator.o /usr/libexec/binutils225/elf/ar: creating libstree.a a - construct.o a - access.o a - scanpref.o a - linkloc.o a - depthtab.o a - ex2leav.o a - dfs.o a - overmax.o a - oversucc.o a - addleafcount.o a - iterator.o gmake[3]: Leaving directory '/wrkdirs/biology/mummer/MUMmer3.23/src/kurtz/streesrc' cd mm3src; gmake mummer gmake[3]: Entering directory '/wrkdirs/biology/mummer/MUMmer3.23/src/kurtz/mm3src' cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -I../streesrc -c -o maxmat3.o maxmat3.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -I../streesrc -c -o maxmatopt.o maxmatopt.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -I../streesrc -c -o maxmatinp.o maxmatinp.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -I../streesrc -c -o findmumcand.o findmumcand.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -I../streesrc -c -o findmaxmat.o findmaxmat.c cc -pipe -O2 -fno-strict-aliasing -I../libbasedir -I../streesrc -c -o procmaxmat.o procmaxmat.c cc maxmat3.o maxmatopt.o maxmatinp.o findmumcand.o findmaxmat.o procmaxmat.o ../streesrc/libstree.a ../libbasedir/libbase.a \ -o /wrkdirs/biology/mummer/MUMmer3.23/mummer; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/mummer gmake[3]: Leaving directory '/wrkdirs/biology/mummer/MUMmer3.23/src/kurtz/mm3src' gmake[2]: Leaving directory '/wrkdirs/biology/mummer/MUMmer3.23/src/kurtz' c++ -pipe -O2 -fno-strict-aliasing delta-filter.cc tigrinc.o delta.o -o /wrkdirs/biology/mummer/MUMmer3.23/delta-filter; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/delta-filter c++ -pipe -O2 -fno-strict-aliasing show-aligns.cc tigrinc.o translate.o delta.o -o /wrkdirs/biology/mummer/MUMmer3.23/show-aligns; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/show-aligns c++ -pipe -O2 -fno-strict-aliasing show-coords.cc tigrinc.o delta.o -o /wrkdirs/biology/mummer/MUMmer3.23/show-coords; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/show-coords c++ -pipe -O2 -fno-strict-aliasing show-tiling.cc tigrinc.o delta.o -o /wrkdirs/biology/mummer/MUMmer3.23/show-tiling; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/show-tiling show-coords.cc: In function 'void printBtab(std::vector)': show-coords.cc:799:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] type = "NUCMER"; ^ show-coords.cc:801:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] type = "PROMER"; ^ show-coords.cc:803:10: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] type = "NULL"; ^ c++ -pipe -O2 -fno-strict-aliasing show-snps.cc tigrinc.o translate.o delta.o -o /wrkdirs/biology/mummer/MUMmer3.23/show-snps; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/show-snps c++ -pipe -O2 -fno-strict-aliasing show-diff.cc tigrinc.o delta.o -o /wrkdirs/biology/mummer/MUMmer3.23/show-diff; chmod 755 /wrkdirs/biology/mummer/MUMmer3.23/show-diff gmake[2]: Leaving directory '/wrkdirs/biology/mummer/MUMmer3.23/src/tigr' gmake[1]: Leaving directory '/wrkdirs/biology/mummer/MUMmer3.23' =========================================================================== =================================================== ===> mummer-3.23_1 depends on package: perl5>=5.20<5.21 - found =========================================================================== =================================================== ===> Staging for mummer-3.23_1 ===> Generating temporary packing list install -s -m 555 /wrkdirs/biology/mummer/MUMmer3.23/annotate /wrkdirs/biology/mummer/MUMmer3.23/combineMUMs /wrkdirs/biology/mummer/MUMmer3.23/delta-filter /wrkdirs/biology/mummer/MUMmer3.23/gaps /wrkdirs/biology/mummer/MUMmer3.23/mgaps /wrkdirs/biology/mummer/MUMmer3.23/mummer /wrkdirs/biology/mummer/MUMmer3.23/repeat-match /wrkdirs/biology/mummer/MUMmer3.23/show-aligns /wrkdirs/biology/mummer/MUMmer3.23/show-coords /wrkdirs/biology/mummer/MUMmer3.23/show-diff /wrkdirs/biology/mummer/MUMmer3.23/show-snps /wrkdirs/biology/mummer/MUMmer3.23/show-tiling /wrkdirs/biology/mummer/stage/usr/local/bin install -m 555 /wrkdirs/biology/mummer/MUMmer3.23/dnadiff /wrkdirs/biology/mummer/MUMmer3.23/exact-tandems /wrkdirs/biology/mummer/MUMmer3.23/mapview /wrkdirs/biology/mummer/MUMmer3.23/mummerplot /wrkdirs/biology/mummer/MUMmer3.23/nucmer /wrkdirs/biology/mummer/MUMmer3.23/nucmer2xfig /wrkdirs/biology/mummer/MUMmer3.23/promer /wrkdirs/biology/mummer/MUMmer3.23/run-mummer1 /wrkdirs/biology/mummer/MUMmer3.23/run-mummer3 /wrkdirs/biology/mummer/stage/usr/local/bin install -m 0644 /wrkdirs/biology/mummer/MUMmer3.23/COPYRIGHT /wrkdirs/biology/mummer/MUMmer3.23/INSTALL /wrkdirs/biology/mummer/MUMmer3.23/LICENSE /wrkdirs/biology/mummer/MUMmer3.23/README /wrkdirs/biology/mummer/stage/usr/local/share/doc/mummer ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for mummer-3.23_1 file sizes/checksums [25]: . done packing files [25]: . done packing directories [0]: . done =========================================================================== => Cleaning up wrkdir ===> Cleaning for mummer-3.23_1 build of biology/mummer ended at Tue Oct 4 21:03:55 PDT 2016 build time: 00:00:30