------------------------------------------------------------------------------- -- Phase: setup ------------------------------------------------------------------------------- Installing /packages/All/perl5-5.32.0.txz SUCCEEDED 00:00:09 ------------------------------------------------------------------------------- -- 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 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unmaintained and dead upstream, does not build with -fno-common (llvm 11). It is scheduled to be removed on or after 2021-04-01. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: pkg-depends ------------------------------------------------------------------------------- ===> lagan-2.0_2 depends on file: /usr/local/sbin/pkg - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: fetch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- 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 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unmaintained and dead upstream, does not build with -fno-common (llvm 11). It is scheduled to be removed on or after 2021-04-01. ===> lagan-2.0_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by lagan-2.0_2 for building SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- 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 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unmaintained and dead upstream, does not build with -fno-common (llvm 11). It is scheduled to be removed on or after 2021-04-01. ===> lagan-2.0_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by lagan-2.0_2 for building => SHA256 Checksum OK for lagan20.tar.gz. SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: extract-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- 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 ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Unmaintained and dead upstream, does not build with -fno-common (llvm 11). It is scheduled to be removed on or after 2021-04-01. ===> lagan-2.0_2 depends on file: /usr/local/sbin/pkg - found ===> Fetching all distfiles required by lagan-2.0_2 for building ===> Extracting for lagan-2.0_2 => SHA256 Checksum OK for lagan20.tar.gz. Extracted Memory Use: 2.44M SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: patch ------------------------------------------------------------------------------- ===> Patching for lagan-2.0_2 ===> Applying ports patches for lagan-2.0_2 from /xports/biology/lagan/files SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: lib-depends ------------------------------------------------------------------------------- SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: configure ------------------------------------------------------------------------------- ===> Configuring for lagan-2.0_2 SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: build ------------------------------------------------------------------------------- ===> Building for lagan-2.0_2 (cd src; /usr/bin/make) cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../anchors anchors.c skiplist.c cc -pipe -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -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 -fcommon -O2 -fno-strict-aliasing -o ../utils/bin2mf utils/bin2mf.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/bin2bl utils/bin2bl.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/cextract utils/cextract.c cc -pipe -fcommon -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 -fcommon -O2 -fno-strict-aliasing -o ../utils/contigorder utils/contigorder.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/getbounds utils/getbounds.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/getlength utils/getlength.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/getoverlap utils/getoverlap.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/rc utils/rc.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/seqmerge utils/seqmerge.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/scorealign utils/scorealign.c -lm cc -pipe -fcommon -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 -fcommon -O2 -fno-strict-aliasing -o ../utils/getcontigpos utils/getcontigpos.c cc -pipe -fcommon -O2 -fno-strict-aliasing -o ../utils/fa2xfa utils/fa2xfa.c c++ -pipe -fcommon -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 -fcommon -O2 -fno-strict-aliasing -o ../utils/dotplot utils/dotplot.cpp cc -pipe -fcommon -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 -fcommon -O2 -fno-strict-aliasing -I./ -c glocal.cpp cc -Wno-deprecated -pipe -fcommon -O2 -fno-strict-aliasing -I./ -c io.cpp cc -Wno-deprecated -pipe -fcommon -O2 -fno-strict-aliasing -I./ -c rightinfluence.cpp cc -Wno-deprecated -pipe -fcommon -O2 -fno-strict-aliasing -I./ -c leftinfluence.cpp cc -Wno-deprecated -pipe -fcommon -O2 -fno-strict-aliasing -I./ -c score.cpp c++ glocal.o io.o rightinfluence.o leftinfluence.o score.o -o ../../glocal -lm SUCCEEDED 00:00:37 ------------------------------------------------------------------------------- -- Phase: run-depends ------------------------------------------------------------------------------- ===> lagan-2.0_2 depends on package: perl5>=5.32.r0<5.33 - found SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: stage ------------------------------------------------------------------------------- ===> Staging for lagan-2.0_2 ===> lagan-2.0_2 depends on package: perl5>=5.32.r0<5.33 - found ===> 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) ====> Running Q/A tests (stage-qa) Warning: You have disabled the licenses framework with DISABLE_LICENSES, unable to run checks Warning: Possible REINPLACE_CMD issues: - - REINPLACE_CMD ran, but did not modify file contents: Makefile - - REINPLACE_CMD ran, but did not modify file contents: src/translate.c - - REINPLACE_CMD ran, but did not modify file contents: src/diagmatrix.c - - REINPLACE_CMD ran, but did not modify file contents: src/global.c - - REINPLACE_CMD ran, but did not modify file contents: src/prolagan.c - - REINPLACE_CMD ran, but did not modify file contents: src/mempage.c - - REINPLACE_CMD ran, but did not modify file contents: src/mlagan.c - - REINPLACE_CMD ran, but did not modify file contents: src/sortlist.c - - REINPLACE_CMD ran, but did not modify file contents: src/thrtrie.c - - REINPLACE_CMD ran, but did not modify file contents: src/anchors.c - - REINPLACE_CMD ran, but did not modify file contents: src/skiplist.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/getlength.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/overlay.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/getoverlap.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/seqmerge.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/bin2mf.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/getcontigpos.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/contigorder.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/cextract.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/bin2bl.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/rc.c - - REINPLACE_CMD ran, but did not modify file contents: src/utils/fa2xfa.c - - REINPLACE_CMD ran, but did not modify file contents: src/filebuffer.c SUCCEEDED 00:00:04 ------------------------------------------------------------------------------- -- Phase: check-plist ------------------------------------------------------------------------------- ====> Checking for pkg-plist issues (check-plist) ===> Parsing plist ===> Checking for items in STAGEDIR missing from pkg-plist ===> Checking for items in pkg-plist which are not in STAGEDIR ===> No pkg-plist issues found (check-plist) SUCCEEDED 00:00:00 ------------------------------------------------------------------------------- -- Phase: package ------------------------------------------------------------------------------- ===> Building package for lagan-2.0_2 file sizes/checksums [41]: 0% file sizes/checksums [41]: 100% packing files [41]: 0% packing files [41]: 100% packing directories [0]: 0% packing directories [0]: 100% SUCCEEDED 00:00:01 TOTAL TIME 00:00:52