=> Building biology/tRNAscan-SE Started : Sunday, 7 JUL 2019 at 04:54:43 UTC Platform: 5.7-DEVELOPMENT DragonFly v5.7.0.83.g49866-DEVELOPMENT #40: Sun Jun 30 03:00:04 PDT 2019 root@pkgbox64.dragonflybsd.org:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 -------------------------------------------------- -- Environment -------------------------------------------------- UNAME_r=5.4-SYNTH UNAME_m=x86_64 UNAME_p=x86_64 UNAME_v=DragonFly 5.4-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/tRNAscan-SE XDG_CONFIG_HOME=/construction/biology/tRNAscan-SE HOME=/construction/biology/tRNAscan-SE TMPDIR="/tmp" PATH=/construction/biology/tRNAscan-SE/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CCVER=gcc80 CONFIG_SITE=/xports/Templates/config.site lt_cv_sys_max_cmd_len=262144 -------------------------------------------------- -- CONFIGURE_ARGS -------------------------------------------------- --prefix=/usr/local ${_LATE_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" PATH=/construction/biology/tRNAscan-SE/.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/tRNAscan-SE/stage -------------------------------------------------- -- PLIST_SUB -------------------------------------------------- OSREL=5.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.28.2 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/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-5.4 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 _PERL5_FROM_BIN=5.28.1 _ALTCCVERSION_921dbbb2=none _OBJC_ALTCCVERSION_921dbbb2=none _SMP_CPUS=8 UID=0 ARCH=x86_64 OPSYS=DragonFly DFLYVERSION=500400 OSVERSION=9999999 OSREL=5.4 _OSRELEASE=5.4-SYNTH PYTHONBASE=/usr/local _PKG_CHECKED=1 -------------------------------------------------------------------------------- -- Phase: check-sanity -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user -------------------------------------------------------------------------------- -- Phase: pkg-depends -------------------------------------------------------------------------------- ===> tRNAscan-SE-2.0.3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.11.1.txz Installing pkg-1.11.1... Extracting pkg-1.11.1: .......... done ===> tRNAscan-SE-2.0.3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of tRNAscan-SE-2.0.3 -------------------------------------------------------------------------------- -- Phase: fetch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: fetch -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by tRNAscan-SE-2.0.3 for building -------------------------------------------------------------------------------- -- Phase: checksum -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by tRNAscan-SE-2.0.3 for building => SHA256 Checksum OK for trnascan-se-2.0.3.tar.gz. -------------------------------------------------------------------------------- -- Phase: extract-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: extract -------------------------------------------------------------------------------- ===> License GPLv3+ accepted by the user ===> Fetching all distfiles required by tRNAscan-SE-2.0.3 for building ===> Extracting for tRNAscan-SE-2.0.3 => SHA256 Checksum OK for trnascan-se-2.0.3.tar.gz. -------------------------------------------------------------------------------- -- Phase: patch-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: patch -------------------------------------------------------------------------------- ===> Patching for tRNAscan-SE-2.0.3 ===> Applying ports patches for tRNAscan-SE-2.0.3 -------------------------------------------------------------------------------- -- Phase: build-depends -------------------------------------------------------------------------------- ===> tRNAscan-SE-2.0.3 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_2.txz Installing autoconf-2.69_2... `-- Installing autoconf-wrapper-20131203... `-- Extracting autoconf-wrapper-20131203: .......... done `-- Installing indexinfo-0.3.1... `-- Extracting indexinfo-0.3.1: .... done `-- Installing m4-1.4.18_1,1... `-- Extracting m4-1.4.18_1,1: .......... done `-- Installing perl5-5.28.2... `-- Extracting perl5-5.28.2: .......... done Extracting autoconf-2.69_2: .......... done Message from perl5-5.28.2: 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-2.0.3 depends on package: autoconf>=2.69 - found ===> Returning to build of tRNAscan-SE-2.0.3 ===> tRNAscan-SE-2.0.3 depends on package: automake>=1.16.1 - not found ===> Installing existing package /packages/All/automake-1.16.1_1.txz Installing automake-1.16.1_1... Extracting automake-1.16.1_1: .......... done ===> tRNAscan-SE-2.0.3 depends on package: automake>=1.16.1 - found ===> Returning to build of tRNAscan-SE-2.0.3 ===> tRNAscan-SE-2.0.3 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: lib-depends -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- -- Phase: configure -------------------------------------------------------------------------------- ===> Configuring for tRNAscan-SE-2.0.3 configure.ac:11: installing './compile' configure: loading site script /xports/Templates/config.site checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking whether cc understands -c and -o together... yes checking for a BSD-compatible install... /usr/bin/install -c checking for perl... (cached) /usr/local/bin/perl checking for Perl version 5.0.0 or later... yes checking how to run the C preprocessor... cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for ANSI C header files... (cached) yes checking for sys/types.h... (cached) yes checking for sys/stat.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for memory.h... (cached) yes checking for strings.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for unistd.h... (cached) yes checking for size_t... (cached) yes checking for working alloca.h... no checking for alloca... yes checking for limits.h... (cached) yes checking for memory.h... (cached) yes checking for stddef.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for unistd.h... (cached) yes checking for stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for size_t... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for bzero... (cached) yes checking for memset... (cached) yes checking for re_comp... no checking for regcomp... yes checking for strcasecmp... (cached) yes checking for strchr... (cached) yes checking for strstr... (cached) yes checking for library containing sqrt... -lm checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking whether make supports the include directive... yes (GNU style) checking whether make supports nested variables... yes checking dependency style of cc... gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands -------------------------------------------------------------------------------- -- Phase: build -------------------------------------------------------------------------------- ===> Building for tRNAscan-SE-2.0.3 /usr/bin/make all-am depbase=`echo src/alignio.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/alignio.o -MD -MP -MF $depbase.Tpo -c -o src/alignio.o src/alignio.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sqerror.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/sqerror.o -MD -MP -MF $depbase.Tpo -c -o src/sqerror.o src/sqerror.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sqio.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/sqio.o -MD -MP -MF $depbase.Tpo -c -o src/sqio.o src/sqio.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/iupac.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/iupac.o -MD -MP -MF $depbase.Tpo -c -o src/iupac.o src/iupac.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/msf.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/msf.o -MD -MP -MF $depbase.Tpo -c -o src/msf.o src/msf.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/revcomp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/revcomp.o -MD -MP -MF $depbase.Tpo -c -o src/revcomp.o src/revcomp.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/selex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/selex.o -MD -MP -MF $depbase.Tpo -c -o src/selex.o src/selex.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sre_ctype.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/sre_ctype.o -MD -MP -MF $depbase.Tpo -c -o src/sre_ctype.o src/sre_ctype.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sre_math.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/sre_math.o -MD -MP -MF $depbase.Tpo -c -o src/sre_math.o src/sre_math.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/sre_string.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/sre_string.o -MD -MP -MF $depbase.Tpo -c -o src/sre_string.o src/sre_string.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/stack.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/stack.o -MD -MP -MF $depbase.Tpo -c -o src/stack.o src/stack.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/types.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/types.o -MD -MP -MF $depbase.Tpo -c -o src/types.o src/types.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/gnuregex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/gnuregex.o -MD -MP -MF $depbase.Tpo -c -o src/gnuregex.o src/gnuregex.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/interleaved.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/interleaved.o -MD -MP -MF $depbase.Tpo -c -o src/interleaved.o src/interleaved.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/getopt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/getopt.o -MD -MP -MF $depbase.Tpo -c -o src/getopt.o src/getopt.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/eufind_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/eufind_main.o -MD -MP -MF $depbase.Tpo -c -o src/eufind_main.o src/eufind_main.c && mv -f $depbase.Tpo $depbase.Po src/eufind_main.c: In function 'main': src/eufind_main.c:106:21: warning: implicit declaration of function 'getopt'; did you mean 'Getopt'? [-Wimplicit-function-declaration] while ((optchar = getopt(argc, argv, OPTIONS)) != -1) ^~~~~~ Getopt src/eufind_main.c:168:17: warning: implicit declaration of function 'IntEncodeSeq' [-Wimplicit-function-declaration] if (errno = IntEncodeSeq(iseq,seq,sqinfo.len)) ^~~~~~~~~~~~ src/eufind_main.c:175:7: warning: implicit declaration of function 'Init_tRNA' [-Wimplicit-function-declaration] Init_tRNA(prev_tRNA); /* clear previous tRNA */ ^~~~~~~~~ src/eufind_main.c:194:14: warning: implicit declaration of function 'GetBbox' [-Wimplicit-function-declaration] while (GetBbox(&FirstScore,&seqidx,iseq,sqinfo.len,strand, ^~~~~~~ src/eufind_main.c:204:10: warning: implicit declaration of function 'GetSecABox' [-Wimplicit-function-declaration] && (GetSecABox(tRNA,seq))){ ^~~~~~~~~~ src/eufind_main.c:206:9: warning: implicit declaration of function 'GetBestTrxTerm' [-Wimplicit-function-declaration] if (!GetBestTrxTerm(tRNA,seq,sqinfo.len,NoTermPenalty) && ^~~~~~~~~~~~~~ src/eufind_main.c:218:4: warning: implicit declaration of function 'GetBestABox' [-Wimplicit-function-declaration] GetBestABox(tRNA,seq,iseq,sqinfo.len,strand,ShowScores, ^~~~~~~~~~~ src/eufind_main.c:239:2: warning: implicit declaration of function 'Get_tRNA_stats' [-Wimplicit-function-declaration] Get_tRNA_stats(tRNA,seq,sqinfo.len,strand); ^~~~~~~~~~~~~~ src/eufind_main.c:241:6: warning: implicit declaration of function 'tRNAOverlap' [-Wimplicit-function-declaration] if (tRNAOverlap(tRNA,prev_tRNA,strand)) { ^~~~~~~~~~~ src/eufind_main.c:258:6: warning: implicit declaration of function 'Save_tRNA' [-Wimplicit-function-declaration] Save_tRNA(prev_tRNA,&sqinfo,seq,strand,ShowScores,sqoffset); ^~~~~~~~~ depbase=`echo src/pavesi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/pavesi.o -MD -MP -MF $depbase.Tpo -c -o src/pavesi.o src/pavesi.c && mv -f $depbase.Tpo $depbase.Po cc -pipe -O2 -fno-strict-aliasing -o bin/eufindtRNA src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/eufind_main.o src/pavesi.o -lm cc -DHAVE_CONFIG_H -I. -DTSCANDIR=\"/usr/local/share\/tRNAscan-SE\/models\" -pipe -O2 -fno-strict-aliasing -MT src/bin_trnascan_1_4-trnascan.o -MD -MP -MF src/.deps/bin_trnascan_1_4-trnascan.Tpo -c -o src/bin_trnascan_1_4-trnascan.o `test -f 'src/trnascan.c' || echo './'`src/trnascan.c src/trnascan.c:335:1: warning: return type defaults to 'int' [-Wimplicit-int] main(int argc, char **argv) ^~~~ src/trnascan.c: In function 'main': src/trnascan.c:433:16: warning: implicit declaration of function 'getopt'; did you mean 'cgetset'? [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, "csraho:v:i:")) != -1) ^~~~~~ cgetset src/trnascan.c: At top level: src/trnascan.c:1421:1: warning: return type defaults to 'int' [-Wimplicit-int] myindex (char *s, char *t) ^~~~~~~ mv -f src/.deps/bin_trnascan_1_4-trnascan.Tpo src/.deps/bin_trnascan_1_4-trnascan.Po cc -DTSCANDIR=\"/usr/local/share\/tRNAscan-SE\/models\" -pipe -O2 -fno-strict-aliasing -o bin/trnascan-1.4 src/bin_trnascan_1_4-trnascan.o -lm depbase=`echo src/align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/align.o -MD -MP -MF $depbase.Tpo -c -o src/align.o src/align.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/dbviterbi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/dbviterbi.o -MD -MP -MF $depbase.Tpo -c -o src/dbviterbi.o src/dbviterbi.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/debug.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/debug.o -MD -MP -MF $depbase.Tpo -c -o src/debug.o src/debug.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/emit.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/emit.o -MD -MP -MF $depbase.Tpo -c -o src/emit.o src/emit.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/fast-dbviterbi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/fast-dbviterbi.o -MD -MP -MF $depbase.Tpo -c -o src/fast-dbviterbi.o src/fast-dbviterbi.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/fastmodelmaker.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/fastmodelmaker.o -MD -MP -MF $depbase.Tpo -c -o src/fastmodelmaker.o src/fastmodelmaker.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/konings.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/konings.o -MD -MP -MF $depbase.Tpo -c -o src/konings.o src/konings.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/lengthdist.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/lengthdist.o -MD -MP -MF $depbase.Tpo -c -o src/lengthdist.o src/lengthdist.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/maxmodelmaker.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/maxmodelmaker.o -MD -MP -MF $depbase.Tpo -c -o src/maxmodelmaker.o src/maxmodelmaker.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/misc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/misc.o -MD -MP -MF $depbase.Tpo -c -o src/misc.o src/misc.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/model.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/model.o -MD -MP -MF $depbase.Tpo -c -o src/model.o src/model.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/modelmaking.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/modelmaking.o -MD -MP -MF $depbase.Tpo -c -o src/modelmaking.o src/modelmaking.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/prior.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/prior.o -MD -MP -MF $depbase.Tpo -c -o src/prior.o src/prior.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/probify.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/probify.o -MD -MP -MF $depbase.Tpo -c -o src/probify.o src/probify.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/save.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/save.o -MD -MP -MF $depbase.Tpo -c -o src/save.o src/save.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/smallviterbi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/smallviterbi.o -MD -MP -MF $depbase.Tpo -c -o src/smallviterbi.o src/smallviterbi.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/scorestack.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/scorestack.o -MD -MP -MF $depbase.Tpo -c -o src/scorestack.o src/scorestack.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/structs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/structs.o -MD -MP -MF $depbase.Tpo -c -o src/structs.o src/structs.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/trace.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/trace.o -MD -MP -MF $depbase.Tpo -c -o src/trace.o src/trace.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/viterbi.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/viterbi.o -MD -MP -MF $depbase.Tpo -c -o src/viterbi.o src/viterbi.c && mv -f $depbase.Tpo $depbase.Po depbase=`echo src/scan_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/scan_main.o -MD -MP -MF $depbase.Tpo -c -o src/scan_main.o src/scan_main.c && mv -f $depbase.Tpo $depbase.Po src/scan_main.c: In function 'main': src/scan_main.c:100:18: warning: implicit declaration of function 'getopt'; did you mean 'Getopt'? [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, OPTIONS)) != -1) ^~~~~~ Getopt cc -pipe -O2 -fno-strict-aliasing -o bin/covels-SE src/align.o src/dbviterbi.o src/debug.o src/emit.o src/fast-dbviterbi.o src/fastmodelmaker.o src/konings.o src/lengthdist.o src/maxmodelmaker.o src/misc.o src/model.o src/modelmaking.o src/prior.o src/probify.o src/save.o src/smallviterbi.o src/scorestack.o src/structs.o src/trace.o src/viterbi.o src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/scan_main.o -lm depbase=`echo src/score_main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; cc -DHAVE_CONFIG_H -I. -pipe -O2 -fno-strict-aliasing -MT src/score_main.o -MD -MP -MF $depbase.Tpo -c -o src/score_main.o src/score_main.c && mv -f $depbase.Tpo $depbase.Po src/score_main.c: In function 'main': src/score_main.c:87:18: warning: implicit declaration of function 'getopt'; did you mean 'Getopt'? [-Wimplicit-function-declaration] while ((optc = getopt(argc, argv, OPTIONS)) != -1) ^~~~~~ Getopt cc -pipe -O2 -fno-strict-aliasing -o bin/coves-SE src/align.o src/dbviterbi.o src/debug.o src/emit.o src/fast-dbviterbi.o src/fastmodelmaker.o src/konings.o src/lengthdist.o src/maxmodelmaker.o src/misc.o src/model.o src/modelmaking.o src/prior.o src/probify.o src/save.o src/smallviterbi.o src/scorestack.o src/structs.o src/trace.o src/viterbi.o src/alignio.o src/sqerror.o src/sqio.o src/iupac.o src/msf.o src/revcomp.o src/selex.o src/sre_ctype.o src/sre_math.o src/sre_string.o src/stack.o src/types.o src/gnuregex.o src/interleaved.o src/getopt.o src/score_main.o -lm sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./src/sstofa.in > bin/sstofa chmod +x bin/sstofa sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./src/fasta2gsi.in > bin/fasta2gsi chmod +x bin/fasta2gsi sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./EukHighConfidenceFilter.in > bin/EukHighConfidenceFilter chmod +x bin/EukHighConfidenceFilter sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./tRNAscan-SE.src > tRNAscan-SE chmod +x tRNAscan-SE sed -e 's,\@bindir\@,/usr/local/bin,g' -e 's,\@libdir\@,/usr/local/share,g' -e 's,\@sysconfdir\@,/usr/local/etc,g' -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,\@INFERNAL\@,,g' < ./tRNAscan-SE.conf.src > tRNAscan-SE.conf chmod +x tRNAscan-SE.conf -------------------------------------------------------------------------------- -- Phase: run-depends -------------------------------------------------------------------------------- ===> tRNAscan-SE-2.0.3 depends on executable: cmsearch - not found ===> Installing existing package /packages/All/infernal-1.1.2.txz Installing infernal-1.1.2... Extracting infernal-1.1.2: .......... done ===> tRNAscan-SE-2.0.3 depends on executable: cmsearch - found ===> Returning to build of tRNAscan-SE-2.0.3 ===> tRNAscan-SE-2.0.3 depends on package: perl5>=5.28.r1<5.29 - found -------------------------------------------------------------------------------- -- Phase: stage -------------------------------------------------------------------------------- ===> Staging for tRNAscan-SE-2.0.3 ===> Generating temporary packing list /bin/mkdir -p '/construction/biology/tRNAscan-SE/stage/usr/local/bin' install -s -m 555 bin/eufindtRNA bin/trnascan-1.4 bin/covels-SE bin/coves-SE '/construction/biology/tRNAscan-SE/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/tRNAscan-SE/stage/usr/local/bin' install -m 555 bin/sstofa bin/fasta2gsi bin/EukHighConfidenceFilter tRNAscan-SE '/construction/biology/tRNAscan-SE/stage/usr/local/bin' /bin/mkdir -p '/construction/biology/tRNAscan-SE/stage/usr/local/etc' install -m 0644 tRNAscan-SE.conf '/construction/biology/tRNAscan-SE/stage/usr/local/etc' /bin/mkdir -p '/construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE/gcode' install -m 0644 lib/gcode/gcode.cilnuc lib/gcode/gcode.echdmito lib/gcode/gcode.invmito lib/gcode/gcode.othmito lib/gcode/gcode.vertmito lib/gcode/gcode.ystmito '/construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE/gcode' /bin/mkdir -p '/construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE/models' install -m 0644 lib/models/Cren-eury-BHB-noncan.cm lib/models/Dsignal lib/models/ESELC.cm lib/models/PSELC.cm lib/models/TPCsignal lib/models/TRNA2-arch.cm lib/models/TRNA2-archns.cm lib/models/TRNA2-bact.cm lib/models/TRNA2-bactns.cm lib/models/TRNA2-euk.cm lib/models/TRNA2-eukns.cm lib/models/TRNA2.cm lib/models/TRNA2ns.cm lib/models/TRNAinf-1415-ns.cm lib/models/TRNAinf-1415.cm lib/models/TRNAinf-arch-3h.cm lib/models/TRNAinf-arch-5h.cm lib/models/TRNAinf-arch-SeC.cm lib/models/TRNAinf-arch-iso lib/models/TRNAinf-arch-iso.i1f lib/models/TRNAinf-arch-iso.i1i lib/models/TRNAinf-arch-iso.i1m lib/models/TRNAinf-arch-iso.i1p lib/models/TRNAinf-arch-ns.cm lib/models/TRNAinf-arch.cm lib/models/TRNAinf-bact-SeC.cm lib/models/TRNAinf-bact-iso lib/models/TRNAinf-bact-iso.i1f lib/models/TRNAinf-bact-iso.i1i lib/models/TRNAinf-bact-iso.i1m lib/models/TRNAinf-bact-iso.i1p lib/models/TRNAinf-bact-ns.cm lib/models/TRNAinf-bact.cm lib/models/TRNAinf-euk-SeC.cm lib/models/TRNAinf-euk-iso lib/models/TRNAinf-euk-iso.i1f lib/models/TRNAinf-euk-iso.i1i lib/models/TRNAinf-euk-iso.i1m lib/models/TRNAinf-euk-iso.i1p lib/models/TRNAinf-euk-ns.cm '/construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE/models' install -m 0644 lib/models/TRNAinf-euk.cm lib/models/TRNAinf-mito-mammal lib/models/TRNAinf-mito-mammal-Ala.cm lib/models/TRNAinf-mito-mammal-Arg.cm lib/models/TRNAinf-mito-mammal-Asn.cm lib/models/TRNAinf-mito-mammal-Asp.cm lib/models/TRNAinf-mito-mammal-Cys.cm lib/models/TRNAinf-mito-mammal-Gln.cm lib/models/TRNAinf-mito-mammal-Glu.cm lib/models/TRNAinf-mito-mammal-Gly.cm lib/models/TRNAinf-mito-mammal-His.cm lib/models/TRNAinf-mito-mammal-Ile.cm lib/models/TRNAinf-mito-mammal-LeuTAA.cm lib/models/TRNAinf-mito-mammal-LeuTAG.cm lib/models/TRNAinf-mito-mammal-Lys.cm lib/models/TRNAinf-mito-mammal-Met.cm lib/models/TRNAinf-mito-mammal-Phe.cm lib/models/TRNAinf-mito-mammal-Pro.cm lib/models/TRNAinf-mito-mammal-SerGCT.cm lib/models/TRNAinf-mito-mammal-SerTGA.cm lib/models/TRNAinf-mito-mammal-Thr.cm lib/models/TRNAinf-mito-mammal-Trp.cm lib/models/TRNAinf-mito-mammal-Tyr.cm lib/models/TRNAinf-mito-mammal-Val.cm lib/models/TRNAinf-mito-mammal.i1f lib/models/TRNAinf-mito-mammal.i1i lib/models/TRNAinf-mito-mammal.i1m lib/models/TRNAinf-mito-mammal.i1p lib/models/TRNAinf-mito-vert lib/models/TRNAinf-mito-vert-Ala.cm lib/models/TRNAinf-mito-vert-Arg.cm lib/models/TRNAinf-mito-vert-Asn.cm lib/models/TRNAinf-mito-vert-Asp.cm lib/models/TRNAinf-mito-vert-Cys.cm lib/models/TRNAinf-mito-vert-Gln.cm lib/models/TRNAinf-mito-vert-Glu.cm lib/models/TRNAinf-mito-vert-Gly.cm lib/models/TRNAinf-mito-vert-His.cm lib/models/TRNAinf-mito-vert-Ile.cm lib/models/TRNAinf-mito-vert-LeuTAA.cm '/construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE/models' install -m 0644 lib/models/TRNAinf-mito-vert-LeuTAG.cm lib/models/TRNAinf-mito-vert-Lys.cm lib/models/TRNAinf-mito-vert-Met.cm lib/models/TRNAinf-mito-vert-Phe.cm lib/models/TRNAinf-mito-vert-Pro.cm lib/models/TRNAinf-mito-vert-SerGCT.cm lib/models/TRNAinf-mito-vert-SerTGA.cm lib/models/TRNAinf-mito-vert-Thr.cm lib/models/TRNAinf-mito-vert-Trp.cm lib/models/TRNAinf-mito-vert-Tyr.cm lib/models/TRNAinf-mito-vert-Val.cm lib/models/TRNAinf-mito-vert.i1f lib/models/TRNAinf-mito-vert.i1i lib/models/TRNAinf-mito-vert.i1m lib/models/TRNAinf-mito-vert.i1p lib/models/TRNAinf-ns.cm lib/models/TRNAinf.cm lib/models/Thaum-BHB-noncan.cm '/construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE/models' /bin/mkdir -p '/construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE/tRNAscanSE' install -m 0644 lib/tRNAscanSE/ArrayCMscanResults.pm lib/tRNAscanSE/ArraytRNA.pm lib/tRNAscanSE/CM.pm lib/tRNAscanSE/CMscanResultFile.pm lib/tRNAscanSE/Configuration.pm lib/tRNAscanSE/Eufind.pm lib/tRNAscanSE/FpScanResultFile.pm lib/tRNAscanSE/GeneticCode.pm lib/tRNAscanSE/IntResultFile.pm lib/tRNAscanSE/LogFile.pm lib/tRNAscanSE/MultiResultFile.pm lib/tRNAscanSE/Options.pm lib/tRNAscanSE/ResultFileReader.pm lib/tRNAscanSE/SS.pm lib/tRNAscanSE/ScanResult.pm lib/tRNAscanSE/Sequence.pm lib/tRNAscanSE/SprinzlAlign.pm lib/tRNAscanSE/SprinzlAlignResults.pm lib/tRNAscanSE/SprinzlPos.pm lib/tRNAscanSE/Stats.pm lib/tRNAscanSE/Tscan.pm lib/tRNAscanSE/Utils.pm lib/tRNAscanSE/tRNA.pm '/construction/biology/tRNAscan-SE/stage/usr/local/share/tRNAscan-SE/tRNAscanSE' ====> Compressing man pages (compress-man) -------------------------------------------------------------------------------- -- Phase: package -------------------------------------------------------------------------------- ===> Building package for tRNAscan-SE-2.0.3 file sizes/checksums [139]: .. done packing files [139]: .. done packing directories [0]: . done -------------------------------------------------- -- Termination -------------------------------------------------- Finished: Sunday, 7 JUL 2019 at 04:55:42 UTC Duration: 00:00:59