=> Building biology/tRNAscan-SE Started : Thursday, 12 OCT 2017 at 07:11:00 UTC Platform: 4.9-DEVELOPMENT DragonFly v4.9.0.699.g39a93-DEVELOPMENT #22: Tue Sep 19 22:06:52 PDT 2017 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.0-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.0-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 -------------------------------------------------- ===> The following configuration options are available for tRNAscan-SE-1.23_1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings -------------------------------------------------- -- 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/tRNAscan-SE XDG_CONFIG_HOME=/construction/biology/tRNAscan-SE HOME=/construction/biology/tRNAscan-SE TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc50 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- -------------------------------------------------- -- MAKE_ENV -------------------------------------------------- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/construction/biology/tRNAscan-SE XDG_CONFIG_HOME=/construction/biology/tRNAscan-SE HOME=/construction/biology/tRNAscan-SE 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 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" -------------------------------------------------- -- MAKE_ARGS -------------------------------------------------- BINDIR="/usr/local/bin" LIBDIR="/usr/local/share/tRNAscan-SE" CC="cc" CFLAGS="-pipe -O2 -fno-strict-aliasing" DESTDIR=/construction/biology/tRNAscan-SE/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib PERL_VERSION=5.24.3 PERL_VER=5.24 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/5.24 PROFILE="@comment " DOCSDIR="share/doc/tRNAscan-SE" EXAMPLESDIR="share/examples/tRNAscan-SE" DATADIR="share/tRNAscan-SE" WWWDIR="www/tRNAscan-SE" ETCDIR="etc/tRNAscan-SE" -------------------------------------------------- -- SUB_LIST -------------------------------------------------- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/tRNAscan-SE DOCSDIR=/usr/local/share/doc/tRNAscan-SE EXAMPLESDIR=/usr/local/share/examples/tRNAscan-SE WWWDIR=/usr/local/www/tRNAscan-SE ETCDIR=/usr/local/etc/tRNAscan-SE -------------------------------------------------- -- /etc/make.conf -------------------------------------------------- SYNTHPROFILE=Release-5.0 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 HAVE_COMPAT_IA32_KERN= CONFIGURE_MAX_CMD_LEN=262144 _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500000 OSVERSION=9999999 OSREL=5.0 _OSRELEASE=5.0-SYNTH -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> NOTICE: The tRNAscan-SE 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 -------------------------------------------------------------------------------- ===> tRNAscan-SE-1.23_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz Installing pkg-1.10.1... Extracting pkg-1.10.1: .......... done ===> tRNAscan-SE-1.23_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of tRNAscan-SE-1.23_1 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> NOTICE: The tRNAscan-SE 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 tRNAscan-SE-1.23_1 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> NOTICE: The tRNAscan-SE 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 tRNAscan-SE-1.23_1 for building => SHA256 Checksum OK for tRNAscan-SE-1.23.tar.Z. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> NOTICE: The tRNAscan-SE 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 tRNAscan-SE-1.23_1 for building ===> Extracting for tRNAscan-SE-1.23_1 => SHA256 Checksum OK for tRNAscan-SE-1.23.tar.Z. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for tRNAscan-SE-1.23_1 ===> Applying ports patches for tRNAscan-SE-1.23_1 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> tRNAscan-SE-1.23_1 depends on package: perl5>=5.24<5.25 - not found ===> Installing existing package /packages/All/perl5-5.24.3.txz Installing perl5-5.24.3... Extracting perl5-5.24.3: .......... done Message from perl5-5.24.3: 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. ===> tRNAscan-SE-1.23_1 depends on package: perl5>=5.24<5.25 - found ===> Returning to build of tRNAscan-SE-1.23_1 -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for tRNAscan-SE-1.23_1 -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for tRNAscan-SE-1.23_1 --- tRNAscanSE --- --- trnascan.o --- --- align.o --- --- dbviterbi.o --- --- debug.o --- --- tRNAscanSE --- /usr/local/bin/perl checkversion.pl --- trnascan.o --- cc -pipe -O2 -fno-strict-aliasing -c trnascan.c --- align.o --- cc -pipe -O2 -fno-strict-aliasing -c align.c --- dbviterbi.o --- cc -pipe -O2 -fno-strict-aliasing -c dbviterbi.c --- debug.o --- cc -pipe -O2 -fno-strict-aliasing -c debug.c --- tRNAscanSE --- sed 's#/tmp#/tmp#g' tRNAscan-SE.src | sed 's#bindir = ""#bindir =\"/usr/local/bin/"#g' | sed 's#/usr/local/lib/tRNAscanSE#/usr/local/share/tRNAscan-SE#g' | sed 's#version = ""#version = "1.23"#' | sed 's#release_date = ""#release_date = "April 2002"#' | sed 's#/usr/bin/perl#/usr/local/bin/perl#' > tRNAscan-SE sed 's#/usr/bin/perl#/usr/local/bin/perl#' instman.pl > instman sed 's#/usr/bin/perl#/usr/local/bin/perl#' sstofa.pl > sstofa --- trnascan.o --- trnascan.c:335:1: warning: return type defaults to 'int' [-Wimplicit-int] main(int argc, char **argv) ^ trnascan.c: In function 'main': trnascan.c:433:16: warning: implicit declaration of function 'getopt' [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, "csraho:v:i:")) != -1) ^ --- tRNAscanSE --- tRNAscan-SE built --- emit.o --- --- trnascan.o --- trnascan.c: At top level: trnascan.c:1418:1: warning: return type defaults to 'int' [-Wimplicit-int] myindex (char *s, char *t) ^ --- emit.o --- cc -pipe -O2 -fno-strict-aliasing -c emit.c --- fast-dbviterbi.o --- cc -pipe -O2 -fno-strict-aliasing -c fast-dbviterbi.c --- fastmodelmaker.o --- cc -pipe -O2 -fno-strict-aliasing -c fastmodelmaker.c --- konings.o --- cc -pipe -O2 -fno-strict-aliasing -c konings.c --- lengthdist.o --- cc -pipe -O2 -fno-strict-aliasing -c lengthdist.c --- maxmodelmaker.o --- cc -pipe -O2 -fno-strict-aliasing -c maxmodelmaker.c --- misc.o --- --- model.o --- --- misc.o --- cc -pipe -O2 -fno-strict-aliasing -c misc.c --- model.o --- cc -pipe -O2 -fno-strict-aliasing -c model.c --- modelmaking.o --- cc -pipe -O2 -fno-strict-aliasing -c modelmaking.c --- prior.o --- cc -pipe -O2 -fno-strict-aliasing -c prior.c --- probify.o --- cc -pipe -O2 -fno-strict-aliasing -c probify.c --- save.o --- cc -pipe -O2 -fno-strict-aliasing -c save.c --- smallviterbi.o --- cc -pipe -O2 -fno-strict-aliasing -c smallviterbi.c --- scorestack.o --- cc -pipe -O2 -fno-strict-aliasing -c scorestack.c scorestack.c: In function 'free_hitstack': scorestack.c:247:54: warning: comparison between pointer and integer while (pop_hitstack(hstack, &left, &right, &score) != NULL) ^ --- structs.o --- cc -pipe -O2 -fno-strict-aliasing -c structs.c --- trace.o --- cc -pipe -O2 -fno-strict-aliasing -c trace.c --- viterbi.o --- cc -pipe -O2 -fno-strict-aliasing -c viterbi.c --- alignio.o --- cc -pipe -O2 -fno-strict-aliasing -c alignio.c --- sqerror.o --- cc -pipe -O2 -fno-strict-aliasing -c sqerror.c --- sqio.o --- cc -pipe -O2 -fno-strict-aliasing -c sqio.c --- iupac.o --- cc -pipe -O2 -fno-strict-aliasing -c iupac.c --- msf.o --- cc -pipe -O2 -fno-strict-aliasing -c msf.c --- revcomp.o --- cc -pipe -O2 -fno-strict-aliasing -c revcomp.c --- selex.o --- cc -pipe -O2 -fno-strict-aliasing -c selex.c --- sre_ctype.o --- cc -pipe -O2 -fno-strict-aliasing -c sre_ctype.c --- sre_math.o --- cc -pipe -O2 -fno-strict-aliasing -c sre_math.c --- sre_string.o --- cc -pipe -O2 -fno-strict-aliasing -c sre_string.c --- stack.o --- cc -pipe -O2 -fno-strict-aliasing -c stack.c --- types.o --- cc -pipe -O2 -fno-strict-aliasing -c types.c --- gnuregex.o --- cc -pipe -O2 -fno-strict-aliasing -c gnuregex.c gnuregex.c: In function 're_match_2': gnuregex.c:3752:31: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] if ((int) old_regend[r] >= (int) regstart[r]) ^ gnuregex.c:3752:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] if ((int) old_regend[r] >= (int) regstart[r]) ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:3758:19: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p1 + mcnt, d, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:3905:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, NULL, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, d, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:3958:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (p + mcnt, d, -2); ^ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (sdummy, pdummy, ^ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4064:13: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (sdummy, pdummy, ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:4097:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2394:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (lowest_active_reg); \ ^ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2315:42: warning: cast to pointer from integer of different size [-Wint-to-pointer-cast] fail_stack.stack[fail_stack.avail++] = (fail_stack_elt_t) item ^ gnuregex.c:2397:5: note: in expansion of macro 'PUSH_FAILURE_ITEM' PUSH_FAILURE_ITEM (highest_active_reg); \ ^ gnuregex.c:4110:11: note: in expansion of macro 'PUSH_FAILURE_POINT' PUSH_FAILURE_POINT (0, 0, -2); ^ gnuregex.c:2482:14: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] high_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (d, p, ^ gnuregex.c:2485:13: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast] low_reg = (unsigned) POP_FAILURE_ITEM (); \ ^ gnuregex.c:4278:11: note: in expansion of macro 'POP_FAILURE_POINT' POP_FAILURE_POINT (d, p, ^ --- interleaved.o --- cc -pipe -O2 -fno-strict-aliasing -c interleaved.c --- getopt.o --- cc -pipe -O2 -fno-strict-aliasing -c getopt.c --- scan_main.o --- cc -pipe -O2 -fno-strict-aliasing -c scan_main.c scan_main.c: In function 'main': scan_main.c:100:18: warning: implicit declaration of function 'getopt' [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, OPTIONS)) != -1) ^ --- score_main.o --- cc -pipe -O2 -fno-strict-aliasing -c score_main.c score_main.c: In function 'main': score_main.c:87:18: warning: implicit declaration of function 'getopt' [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, OPTIONS)) != -1) ^ --- pavesi.o --- cc -pipe -O2 -fno-strict-aliasing -c pavesi.c --- eufind_main.o --- cc -pipe -O2 -fno-strict-aliasing -c eufind_main.c --- trnascan-1.4 --- cc -pipe -O2 -fno-strict-aliasing -DTSCANDIR=\"/usr/local/share/tRNAscan-SE\" -o trnascan-1.4 trnascan.c --- eufind_main.o --- eufind_main.c: In function 'main': eufind_main.c:106:21: warning: implicit declaration of function 'getopt' [-Wimplicit-function-declaration] while ((optchar = getopt(argc, argv, OPTIONS)) != -1) ^ eufind_main.c:168:17: warning: implicit declaration of function 'IntEncodeSeq' [-Wimplicit-function-declaration] if (errno = IntEncodeSeq(iseq,seq,sqinfo.len)) ^ eufind_main.c:175:7: warning: implicit declaration of function 'Init_tRNA' [-Wimplicit-function-declaration] Init_tRNA(prev_tRNA); /* clear previous tRNA */ ^ eufind_main.c:194:14: warning: implicit declaration of function 'GetBbox' [-Wimplicit-function-declaration] while (GetBbox(&FirstScore,&seqidx,iseq,sqinfo.len,strand, ^ eufind_main.c:204:10: warning: implicit declaration of function 'GetSecABox' [-Wimplicit-function-declaration] && (GetSecABox(tRNA,seq))){ ^ eufind_main.c:206:9: warning: implicit declaration of function 'GetBestTrxTerm' [-Wimplicit-function-declaration] if (!GetBestTrxTerm(tRNA,seq,sqinfo.len,NoTermPenalty) && ^ eufind_main.c:218:4: warning: implicit declaration of function 'GetBestABox' [-Wimplicit-function-declaration] GetBestABox(tRNA,seq,iseq,sqinfo.len,strand,ShowScores, ^ eufind_main.c:239:2: warning: implicit declaration of function 'Get_tRNA_stats' [-Wimplicit-function-declaration] Get_tRNA_stats(tRNA,seq,sqinfo.len,strand); ^ eufind_main.c:241:6: warning: implicit declaration of function 'tRNAOverlap' [-Wimplicit-function-declaration] if (tRNAOverlap(tRNA,prev_tRNA,strand)) { ^ eufind_main.c:258:6: warning: implicit declaration of function 'Save_tRNA' [-Wimplicit-function-declaration] Save_tRNA(prev_tRNA,&sqinfo,seq,strand,ShowScores,sqoffset); ^ --- trnascan-1.4 --- trnascan.c:335:1: warning: return type defaults to 'int' [-Wimplicit-int] main(int argc, char **argv) ^ trnascan.c: In function 'main': trnascan.c:433:16: warning: implicit declaration of function 'getopt' [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, "csraho:v:i:")) != -1) ^ trnascan.c: At top level: trnascan.c:1418:1: warning: return type defaults to 'int' [-Wimplicit-int] myindex (char *s, char *t) ^ --- covels-SE --- --- coves-SE --- --- eufindtRNA --- --- covels-SE --- cc -pipe -O2 -fno-strict-aliasing -DRELEASE="2.4.4" -DRELEASEDATE="April 2002" -o covels-SE scan_main.o align.o dbviterbi.o debug.o emit.o fast-dbviterbi.o fastmodelmaker.o konings.o lengthdist.o maxmodelmaker.o misc.o model.o modelmaking.o prior.o probify.o save.o smallviterbi.o scorestack.o structs.o trace.o viterbi.o alignio.o sqerror.o sqio.o iupac.o msf.o revcomp.o selex.o sre_ctype.o sre_math.o sre_string.o stack.o types.o gnuregex.o interleaved.o getopt.o -lm --- coves-SE --- cc -pipe -O2 -fno-strict-aliasing -DRELEASE="2.4.4" -DRELEASEDATE="April 2002" -o coves-SE score_main.o align.o dbviterbi.o debug.o emit.o fast-dbviterbi.o fastmodelmaker.o konings.o lengthdist.o maxmodelmaker.o misc.o model.o modelmaking.o prior.o probify.o save.o smallviterbi.o scorestack.o structs.o trace.o viterbi.o alignio.o sqerror.o sqio.o iupac.o msf.o revcomp.o selex.o sre_ctype.o sre_math.o sre_string.o stack.o types.o gnuregex.o interleaved.o getopt.o -lm --- eufindtRNA --- cc -pipe -O2 -fno-strict-aliasing -o eufindtRNA eufind_main.o pavesi.o alignio.o sqerror.o sqio.o iupac.o msf.o revcomp.o selex.o sre_ctype.o sre_math.o sre_string.o stack.o types.o gnuregex.o interleaved.o getopt.o -lm -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> tRNAscan-SE-1.23_1 depends on package: perl5>=5.24<5.25 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for tRNAscan-SE-1.23_1 ===> Generating temporary packing list install -s -m 555 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/covels-SE /construction/biology/tRNAscan-SE/stage/usr/local/bin install -s -m 555 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/coves-SE /construction/biology/tRNAscan-SE/stage/usr/local/bin install -s -m 555 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/eufindtRNA /construction/biology/tRNAscan-SE/stage/usr/local/bin install -s -m 555 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/trnascan-1.4 /construction/biology/tRNAscan-SE/stage/usr/local/bin install -m 555 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/tRNAscan-SE /construction/biology/tRNAscan-SE/stage/usr/local/bin install -m 444 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/tRNAscan-SE.man /construction/biology/tRNAscan-SE/stage/usr/local/man/man1/tRNAscan-SE.1 install -m 0644 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/TPCsignal /construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE install -m 0644 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/Dsignal /construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE install -m 0644 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/*.cm /construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE install -m 0644 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/gcode.* /construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE install -m 0644 /construction/biology/tRNAscan-SE/tRNAscan-SE-1.23/Manual.ps /construction/biology/tRNAscan-SE/stage/usr/local/share/doc/tRNAscan-SE ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for tRNAscan-SE-1.23_1 file sizes/checksums [25]: . done packing files [25]: . done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Thursday, 12 OCT 2017 at 07:11:16 UTC Duration: 00:00:15