=> Building biology/lagan Started : Thursday, 7 MAR 2019 at 18:22:29 UTC Platform: 5.5-DEVELOPMENT DragonFly v5.5.0.192.g15ae7f0-DEVELOPMENT #34: Tue Feb 19 09:07:07 PST 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.5-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.5-SYNTH UNAME_s=DragonFly PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SSL_NO_VERIFY_PEER=1 TERM=dumb PKG_CACHEDIR=/var/cache/pkg8 PKG_DBDIR=/var/db/pkg8 PORTSDIR=/xports LANG=C HOME=/root USER=root -------------------------------------------------- -- Options -------------------------------------------------- -------------------------------------------------- -- CONFIGURE_ENV -------------------------------------------------- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/lagan XDG_CONFIG_HOME=/construction/biology/lagan HOME=/construction/biology/lagan TMPDIR="/tmp" PATH=/construction/biology/lagan/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/lagan XDG_CONFIG_HOME=/construction/biology/lagan HOME=/construction/biology/lagan TMPDIR="/tmp" PATH=/construction/biology/lagan/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES CCVER=gcc80 PREFIX=/usr/local LOCALBASE=/usr/local 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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- DESTDIR=/construction/biology/lagan/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.5 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.1 PERL_VER=5.28 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/5.28 PROFILE="@comment " DOCSDIR="share/doc/lagan" EXAMPLESDIR="share/examples/lagan" DATADIR="share/lagan" WWWDIR="www/lagan" ETCDIR="etc/lagan" -------------------------------------------------- -- 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 -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-BE USE_PACKAGE_DEPENDS_ONLY=yes PACKAGE_BUILDING=yes BATCH=yes PKG_CREATE_VERBOSE=yes PORTSDIR=/xports DISTDIR=/distfiles WRKDIRPREFIX=/construction PORT_DBDIR=/options PACKAGES=/packages MAKE_JOBS_NUMBER_LIMIT=5 LICENSES_ACCEPTED= NONE HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _PERL5_FROM_BIN=5.26.2 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500500 OSVERSION=9999999 OSREL=5.5 _OSRELEASE=5.5-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> 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 -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> lagan-2.0_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz Installing pkg-1.10.5_5... Extracting pkg-1.10.5_5: .......... done ===> lagan-2.0_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of lagan-2.0_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> 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 -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> 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. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> 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. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for lagan-2.0_1 ===> Applying ports patches for lagan-2.0_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for lagan-2.0_1 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> 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'; did you mean 'printBinAlign'? [-Wimplicit-function-declaration] printMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); ^~~~~~~~~~~~~ printBinAlign order.c:411:5: warning: implicit declaration of function 'printXMFAAlign'; did you mean 'printTextAlign'? [-Wimplicit-function-declaration] printXMFAAlign(seq1->lets, seq2->lets, a, seq1->name, seq2->name); ^~~~~~~~~~~~~~ printTextAlign 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'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration] printXMFAAlign(outfile, final); ^~~~~~~~~~~~~~ printFASTAAlign 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'; did you mean 'printFASTAAlign'? [-Wimplicit-function-declaration] printXMFAAlign(outfile, final); ^~~~~~~~~~~~~~ printFASTAAlign 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: ISO C++ forbids converting a string constant to 'char*' [-Wwrite-strings] char *alpha = "ATCG"; ^~~~~~ utils/Glue.cpp:72:44: warning: ISO C++ forbids converting a 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); ^~~~~~~ utils/overlay.c:134:5: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=] strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ utils/overlay.c:134:45: note: length computed here strncpy(allseqs[target]->seqname, temp, strlen(temp)+1); ^~~~~~~~~~~~ (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 -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> lagan-2.0_1 depends on package: perl5>=5.28.r1<5.29 - not found ===> Installing existing package /packages/All/perl5-5.28.1.txz Installing perl5-5.28.1... Extracting perl5-5.28.1: .......... done Message from perl5-5.28.1: 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>=5.28.r1<5.29 - found ===> Returning to build of lagan-2.0_1 -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for lagan-2.0_1 ===> Generating temporary packing list install -s -m 555 /construction/biology/lagan/lagan20/anchors /construction/biology/lagan/stage/usr/local/lagan install -s -m 555 /construction/biology/lagan/lagan20/chaos /construction/biology/lagan/stage/usr/local/lagan install -s -m 555 /construction/biology/lagan/lagan20/glocal /construction/biology/lagan/stage/usr/local/lagan install -s -m 555 /construction/biology/lagan/lagan20/mlagan /construction/biology/lagan/stage/usr/local/lagan install -s -m 555 /construction/biology/lagan/lagan20/order /construction/biology/lagan/stage/usr/local/lagan install -m 555 /construction/biology/lagan/lagan20/anal_gloc.pl /construction/biology/lagan/stage/usr/local/lagan install -m 555 /construction/biology/lagan/lagan20/lagan.pl /construction/biology/lagan/stage/usr/local/lagan install -m 555 /construction/biology/lagan/lagan20/rechaos.pl /construction/biology/lagan/stage/usr/local/lagan install -m 555 /construction/biology/lagan/lagan20/slagan.pl /construction/biology/lagan/stage/usr/local/lagan install -s -m 555 /construction/biology/lagan/lagan20/utils/Glue /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/bin2bl /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/bin2mf /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/cextract /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/contigorder /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/cstat /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/dotplot /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/fa2xfa /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/getbounds /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/getcontigpos /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/getlength /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/getoverlap /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/rc /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/scorealign /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/scorecontigs /construction/biology/lagan/stage/usr/local/lagan/utils install -s -m 555 /construction/biology/lagan/lagan20/utils/seqmerge /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/cmerge2.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/draft.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/mextract.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/mf2bin.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/mpretty.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/mproject.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/mrun.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/mrunfile.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/mrunpairs.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 555 /construction/biology/lagan/lagan20/utils/mviz.pl /construction/biology/lagan/stage/usr/local/lagan/utils install -m 0644 /construction/biology/lagan/lagan20/Readmes/README.FIRST /construction/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /construction/biology/lagan/lagan20/Readmes/README.chaos /construction/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /construction/biology/lagan/lagan20/Readmes/README.lagan /construction/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /construction/biology/lagan/lagan20/Readmes/README.mlagan /construction/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /construction/biology/lagan/lagan20/Readmes/README.tools /construction/biology/lagan/stage/usr/local/lagan/Readmes install -m 0644 /construction/biology/lagan/lagan20/Readmes/README.shuffle /construction/biology/lagan/stage/usr/local/lagan/Readmes ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for lagan-2.0_1 file sizes/checksums [44]: . done packing files [44]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 7 MAR 2019 at 18:23:12 UTC Duration: 00:00:43