The following packages will be installed: locarna Fetching README... 0%100%100%100%100%100%Done Fetching locarna.SlackBuild... 0%100%100%100%100%100%Done Fetching locarna.info... 0%100%100%100%100%100%Done Fetching slack-desc... 0%100%100%100%100%100%Done locarna-1.9.2.3/ locarna-1.9.2.3/aclocal.m4 locarna-1.9.2.3/Makefile.am locarna-1.9.2.3/Doc/ locarna-1.9.2.3/Doc/doxygen.cfg locarna-1.9.2.3/Doc/man/ locarna-1.9.2.3/Doc/man/Makefile.am locarna-1.9.2.3/Doc/man/dot2pp.1 locarna-1.9.2.3/Doc/man/aln-seqs.pl.1 locarna-1.9.2.3/Doc/man/locarnap-revisit-RNAz-hits.pl.1 locarna-1.9.2.3/Doc/man/ribosum2cc.1 locarna-1.9.2.3/Doc/man/pp2dot.1 locarna-1.9.2.3/Doc/man/locarnap-predict-and-plot.pl.1 locarna-1.9.2.3/Doc/man/gen-reliab-dot.pl.1 locarna-1.9.2.3/Doc/man/Makefile.in locarna-1.9.2.3/Doc/man/plot-bmprobs.1 locarna-1.9.2.3/Doc/man/exparna_p.1 locarna-1.9.2.3/Doc/man/locarnate.1 locarna-1.9.2.3/Doc/man/mlocarna.1 locarna-1.9.2.3/Doc/man/locarnap-revcomp.pl.1 locarna-1.9.2.3/Doc/man/alnsel.pl.1 locarna-1.9.2.3/Doc/man/sparse.1 locarna-1.9.2.3/Doc/man/reliability-profile.pl.1 locarna-1.9.2.3/Doc/man/average-dot.pl.1 locarna-1.9.2.3/Doc/man/exploc_p.1 locarna-1.9.2.3/Doc/man/locarna_deviation.1 locarna-1.9.2.3/Doc/man/mlocarna_nnames.1 locarna-1.9.2.3/Doc/man/locarnap-realign-all.pl.1 locarna-1.9.2.3/Doc/man/locarna_p.1 locarna-1.9.2.3/Doc/man/locarna-motif-scan.1 locarna-1.9.2.3/Doc/man/locarna.1 locarna-1.9.2.3/Doc/man/locarna_rnafold_pp.1 locarna-1.9.2.3/Doc/man/aln2fa.pl.1 locarna-1.9.2.3/Doc/man/locarna-mea.pl.1 locarna-1.9.2.3/Doc/man/locarnap_fit.1 locarna-1.9.2.3/Doc/Makefile.am locarna-1.9.2.3/Doc/Makefile.in locarna-1.9.2.3/Doc/doxygen.am locarna-1.9.2.3/config.h.in locarna-1.9.2.3/NEWS locarna-1.9.2.3/COPYING locarna-1.9.2.3/config/ locarna-1.9.2.3/config/depcomp locarna-1.9.2.3/config/test-driver locarna-1.9.2.3/config/compile locarna-1.9.2.3/config/missing locarna-1.9.2.3/config/config.guess locarna-1.9.2.3/config/ltmain.sh locarna-1.9.2.3/config/config.sub locarna-1.9.2.3/config/install-sh locarna-1.9.2.3/m4/ locarna-1.9.2.3/m4/lt~obsolete.m4 locarna-1.9.2.3/m4/ax_pthread.m4 locarna-1.9.2.3/m4/ax_append_flag.m4 locarna-1.9.2.3/m4/ltsugar.m4 locarna-1.9.2.3/m4/doxygen.m4 locarna-1.9.2.3/m4/ltversion.m4 locarna-1.9.2.3/m4/libtool.m4 locarna-1.9.2.3/m4/ltoptions.m4 locarna-1.9.2.3/ChangeLog locarna-1.9.2.3/Makefile.in locarna-1.9.2.3/TODO locarna-1.9.2.3/Data/ locarna-1.9.2.3/Data/Examples/ locarna-1.9.2.3/Data/Examples/SECIS_15_ref.aln locarna-1.9.2.3/Data/Examples/example-wo-anchors.fa locarna-1.9.2.3/Data/Examples/SECIS_15.fa locarna-1.9.2.3/Data/Examples/haca.snoRNA_anchor.bed locarna-1.9.2.3/Data/Examples/gcvT.fa locarna-1.9.2.3/Data/Examples/archaea.fa locarna-1.9.2.3/Data/Examples/human.fa locarna-1.9.2.3/Data/Examples/archaea-wrong.fa locarna-1.9.2.3/Data/Examples/ferritin.fa locarna-1.9.2.3/Data/Examples/mouse.fa locarna-1.9.2.3/Data/Examples/short-example.cfg locarna-1.9.2.3/Data/Examples/hammerhead_3.fa locarna-1.9.2.3/Data/Examples/example-w-constraints.fa locarna-1.9.2.3/Data/Examples/example-realign.aln locarna-1.9.2.3/Data/Examples/haca.snoRNA.fa locarna-1.9.2.3/Data/Examples/example.fa locarna-1.9.2.3/Data/Examples/archaea-aln.fa locarna-1.9.2.3/Data/Examples/archaea.aln locarna-1.9.2.3/Data/Examples/example-anchors.bed locarna-1.9.2.3/Data/Examples/example.cfg locarna-1.9.2.3/Data/Matrices/ locarna-1.9.2.3/Data/Matrices/RIBOSUM85_60 locarna-1.9.2.3/configure locarna-1.9.2.3/configure.ac locarna-1.9.2.3/README locarna-1.9.2.3/Packaging/ locarna-1.9.2.3/Packaging/debian/ locarna-1.9.2.3/Packaging/debian/control.in locarna-1.9.2.3/Packaging/rpm/ locarna-1.9.2.3/Packaging/rpm/locarna.spec.in locarna-1.9.2.3/AUTHORS locarna-1.9.2.3/INSTALL locarna-1.9.2.3/lib/ locarna-1.9.2.3/lib/Makefile.am locarna-1.9.2.3/lib/Makefile.in locarna-1.9.2.3/lib/perl/ locarna-1.9.2.3/lib/perl/Makefile.am locarna-1.9.2.3/lib/perl/MLocarna/ locarna-1.9.2.3/lib/perl/MLocarna/MatchProbs.pm locarna-1.9.2.3/lib/perl/MLocarna/Aux.pm locarna-1.9.2.3/lib/perl/MLocarna/Makefile.am locarna-1.9.2.3/lib/perl/MLocarna/unthreaded.pm locarna-1.9.2.3/lib/perl/MLocarna/Trees.pm locarna-1.9.2.3/lib/perl/MLocarna/Makefile.in locarna-1.9.2.3/lib/perl/MLocarna/threaded.pm locarna-1.9.2.3/lib/perl/MLocarna/PairwiseAligners.pm locarna-1.9.2.3/lib/perl/MLocarna/SparseMatrix.pm locarna-1.9.2.3/lib/perl/MLocarna.pm locarna-1.9.2.3/lib/perl/Makefile.in locarna-1.9.2.3/lib/LocARNA.pc.in locarna-1.9.2.3/src/ locarna-1.9.2.3/src/Makefile.am locarna-1.9.2.3/src/sparse.cc locarna-1.9.2.3/src/exparna_p.cc locarna-1.9.2.3/src/package_constants.hh.in locarna-1.9.2.3/src/locarna_p.cc locarna-1.9.2.3/src/ribosum2cc.cc locarna-1.9.2.3/src/Makefile.in locarna-1.9.2.3/src/locarna.cc locarna-1.9.2.3/src/deviation.cc locarna-1.9.2.3/src/LocARNA/ locarna-1.9.2.3/src/LocARNA/ribosum.hh locarna-1.9.2.3/src/LocARNA/sparsification_mapper.cc locarna-1.9.2.3/src/LocARNA/matrix.hh locarna-1.9.2.3/src/LocARNA/ext_rna_data.hh locarna-1.9.2.3/src/LocARNA/alignment.hh locarna-1.9.2.3/src/LocARNA/rna_data.cc locarna-1.9.2.3/src/LocARNA/global_stopwatch.hh locarna-1.9.2.3/src/LocARNA/type_wrapper.hh locarna-1.9.2.3/src/LocARNA/sequence_annotation.cc locarna-1.9.2.3/src/LocARNA/options.cc locarna-1.9.2.3/src/LocARNA/sparse_vector.hh locarna-1.9.2.3/src/LocARNA/multiple_alignment.cc locarna-1.9.2.3/src/LocARNA/alphabet.hh locarna-1.9.2.3/src/LocARNA/rna_data_impl.hh locarna-1.9.2.3/src/LocARNA/infty_int.hh locarna-1.9.2.3/src/LocARNA/ribosum85_60.icc locarna-1.9.2.3/src/LocARNA/rna_structure.hh locarna-1.9.2.3/src/LocARNA/ribofit_will2014.icc locarna-1.9.2.3/src/LocARNA/anchor_constraints.cc locarna-1.9.2.3/src/LocARNA/alphabet.icc locarna-1.9.2.3/src/LocARNA/aux.hh locarna-1.9.2.3/src/LocARNA/basepairs.cc locarna-1.9.2.3/src/LocARNA/sequence.cc locarna-1.9.2.3/src/LocARNA/sparse_matrix.hh locarna-1.9.2.3/src/LocARNA/mcc_matrices.cc locarna-1.9.2.3/src/LocARNA/pfold_params.hh locarna-1.9.2.3/src/LocARNA/string1.hh locarna-1.9.2.3/src/LocARNA/sequence.hh locarna-1.9.2.3/src/LocARNA/match_probs.hh locarna-1.9.2.3/src/LocARNA/plusvector.hh locarna-1.9.2.3/src/LocARNA/rna_structure.cc locarna-1.9.2.3/src/LocARNA/stral_score.hh locarna-1.9.2.3/src/LocARNA/matrices.hh locarna-1.9.2.3/src/LocARNA/params.hh locarna-1.9.2.3/src/LocARNA/scoring.cc locarna-1.9.2.3/src/LocARNA/stopwatch.cc locarna-1.9.2.3/src/LocARNA/aligner.hh locarna-1.9.2.3/src/LocARNA/ribofit_will2014.ihh locarna-1.9.2.3/src/LocARNA/fitonoff.hh locarna-1.9.2.3/src/LocARNA/ribosum.cc locarna-1.9.2.3/src/LocARNA/basepairs.hh locarna-1.9.2.3/src/LocARNA/arc_matches.hh locarna-1.9.2.3/src/LocARNA/exact_matcher.hh locarna-1.9.2.3/src/LocARNA/base_pair_filter.hh locarna-1.9.2.3/src/LocARNA/pfold_params.cc locarna-1.9.2.3/src/LocARNA/ext_rna_data_impl.hh locarna-1.9.2.3/src/LocARNA/options.hh locarna-1.9.2.3/src/LocARNA/aux.cc locarna-1.9.2.3/src/LocARNA/aligner_n.cc locarna-1.9.2.3/src/LocARNA/trace_controller.cc locarna-1.9.2.3/src/LocARNA/aligner_restriction.hh locarna-1.9.2.3/src/LocARNA/trace_controller.hh locarna-1.9.2.3/src/LocARNA/aligner_p.hh locarna-1.9.2.3/src/LocARNA/arc_matches.cc locarna-1.9.2.3/src/LocARNA/params.cc locarna-1.9.2.3/src/LocARNA/ribofit.hh locarna-1.9.2.3/src/LocARNA/ribofit.cc locarna-1.9.2.3/src/LocARNA/alignment.cc locarna-1.9.2.3/src/LocARNA/exact_matcher.cc locarna-1.9.2.3/src/LocARNA/rna_ensemble_impl.hh locarna-1.9.2.3/src/LocARNA/discrete_distribution.hh locarna-1.9.2.3/src/LocARNA/mcc_matrices.hh locarna-1.9.2.3/src/LocARNA/confusion_matrix.hh locarna-1.9.2.3/src/LocARNA/match_probs.cc locarna-1.9.2.3/src/LocARNA/infty_int.cc locarna-1.9.2.3/src/LocARNA/scoring.hh locarna-1.9.2.3/src/LocARNA/aligner_n.hh locarna-1.9.2.3/src/LocARNA/scoring_fwd.hh locarna-1.9.2.3/src/LocARNA/aligner.cc locarna-1.9.2.3/src/LocARNA/main_helper.icc locarna-1.9.2.3/src/LocARNA/global_stopwatch.cc locarna-1.9.2.3/src/LocARNA/sparsification_mapper.hh locarna-1.9.2.3/src/LocARNA/stopwatch.hh locarna-1.9.2.3/src/LocARNA/stral_score.cc locarna-1.9.2.3/src/LocARNA/tuples.hh locarna-1.9.2.3/src/LocARNA/aligner_impl.hh locarna-1.9.2.3/src/LocARNA/rna_data.hh locarna-1.9.2.3/src/LocARNA/sequence_annotation.hh locarna-1.9.2.3/src/LocARNA/rna_ensemble.cc locarna-1.9.2.3/src/LocARNA/anchor_constraints.hh locarna-1.9.2.3/src/LocARNA/fitonoff.cc locarna-1.9.2.3/src/LocARNA/alignment_impl.hh locarna-1.9.2.3/src/LocARNA/confusion_matrix.cc locarna-1.9.2.3/src/LocARNA/rna_ensemble.hh locarna-1.9.2.3/src/LocARNA/multiple_alignment.hh locarna-1.9.2.3/src/LocARNA/aligner_p.cc locarna-1.9.2.3/src/fit.cc locarna-1.9.2.3/src/Tests/ locarna-1.9.2.3/src/Tests/mlocarna-haca-constraints.testresult locarna-1.9.2.3/src/Tests/mlocarna-threads.testresult locarna-1.9.2.3/src/Tests/locarnate.testresult locarna-1.9.2.3/src/Tests/rna_data.cc locarna-1.9.2.3/src/Tests/Makefile.am locarna-1.9.2.3/src/Tests/exparna_p.testresult locarna-1.9.2.3/src/Tests/locarna-local.testresult locarna-1.9.2.3/src/Tests/multiple_alignment.cc locarna-1.9.2.3/src/Tests/test_locarna_lib.cc locarna-1.9.2.3/src/Tests/locarna-normalized.testresult locarna-1.9.2.3/src/Tests/anchor_constraints.cc locarna-1.9.2.3/src/Tests/Makefile.in locarna-1.9.2.3/src/Tests/mlocarna-bed-anchors.testresult locarna-1.9.2.3/src/Tests/rna_structure.cc locarna-1.9.2.3/src/Tests/mlocarna-probabilistic.testresult locarna-1.9.2.3/src/Tests/catch.hpp locarna-1.9.2.3/src/Tests/test_programs locarna-1.9.2.3/src/Tests/mlocarna-realign.testresult locarna-1.9.2.3/src/Tests/trace_controller.cc locarna-1.9.2.3/src/Tests/matrices.cc locarna-1.9.2.3/src/Tests/rna_ensemble.cc locarna-1.9.2.3/src/Tests/mlocarna-archaea-alifold.testresult locarna-1.9.2.3/src/Tests/mlocarna-sparse.testresult locarna-1.9.2.3/src/Tests/ext_rna_data.cc locarna-1.9.2.3/src/locarna_rnafold_pp.cc locarna-1.9.2.3/src/Utils/ locarna-1.9.2.3/src/Utils/plot-bmprobs locarna-1.9.2.3/src/Utils/gen-reliab-dot.pl locarna-1.9.2.3/src/Utils/locarna-motif-scan locarna-1.9.2.3/src/Utils/Makefile.am locarna-1.9.2.3/src/Utils/average-dot.pl locarna-1.9.2.3/src/Utils/locarnap-predict-and-plot.pl locarna-1.9.2.3/src/Utils/mlocarna locarna-1.9.2.3/src/Utils/reliability-profile.pl locarna-1.9.2.3/src/Utils/pp2dot locarna-1.9.2.3/src/Utils/Makefile.in locarna-1.9.2.3/src/Utils/mlocarna_nnames locarna-1.9.2.3/src/Utils/locarna-mea.pl locarna-1.9.2.3/src/Utils/exploc_p locarna-1.9.2.3/src/Utils/RNAz.pm locarna-1.9.2.3/src/Utils/locarnap-revisit-RNAz-hits.pl locarna-1.9.2.3/src/Utils/locarnate locarna-1.9.2.3/src/Utils/locarnap-revcomp.pl locarna-1.9.2.3/src/Utils/aln-seqs.pl locarna-1.9.2.3/src/Utils/LocARNA_RNAz.pm locarna-1.9.2.3/src/Utils/locarnap-realign-all.pl locarna-1.9.2.3/src/Utils/dot2pp locarna-1.9.2.3/src/Utils/aln2fa.pl locarna-1.9.2.3/src/Utils/alnsel.pl checking build system type... x86_64-slackware-linux-gnu checking host system type... x86_64-slackware-linux-gnu checking how to print strings... printf checking for gcc... gcc 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 gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking for a sed that does not truncate output... /usr/bin/sed checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for fgrep... /usr/bin/grep -F checking for ld used by gcc... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B checking the name lister (/usr/bin/nm 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GNU checking whether make supports nested variables... yes checking dependency style of gcc... gcc3 checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking for ld used by g++... /usr/bin/ld -m elf_x86_64 checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking for g++ option to produce PIC... -fPIC -DPIC checking if g++ PIC flag -fPIC -DPIC works... yes checking if g++ static flag -static works... yes checking if g++ supports -c -o file.o... yes checking if g++ supports -c -o file.o... (cached) yes checking whether the g++ linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes checking dynamic linker characteristics... (cached) GNU/Linux ld.so checking how to hardcode library paths into programs... immediate checking dependency style of g++... gcc3 checking how to run the C++ preprocessor... g++ -E checking for gcc... (cached) gcc checking whether we are using the GNU C compiler... (cached) yes checking whether gcc accepts -g... (cached) yes checking for gcc option to accept ISO C89... (cached) none needed checking whether gcc understands -c and -o together... (cached) yes checking how to run the C preprocessor... gcc -E checking for perl... perl checking for pod2man... pod2man checking for doxygen... /usr/bin/doxygen checking for perl... /usr/bin/perl checking for dot... /usr/bin/dot checking for strdup... yes checking for pkg-config... true checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for VRNA... yes checking for vrna_C11_features in -lRNA... yes configure: VRNA_LIBS=-fno-lto -Wl,-fno-lto -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++; VRNA_CFLAGS=-pthread -I/usr/include/ViennaRNA checking for ANSI C header files... (cached) yes checking whether to build with debug information... no checking if compiler needs -Werror to reject unknown flags... no checking for the pthreads library -lpthreads... no checking whether pthreads work without any flags... yes checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking if more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes configure: pthread: , checking whether to link statically... no checking whether to link binaries dynamically to libLocARNA... no checking whether to support large partition function... no checking for stdbool.h that conforms to C99... no checking for _Bool... no checking for an ANSI C-conforming const... yes checking for size_t... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating src/Tests/Makefile config.status: creating src/Utils/Makefile config.status: creating Doc/Makefile config.status: creating Doc/man/Makefile config.status: creating lib/Makefile config.status: creating lib/perl/Makefile config.status: creating lib/perl/MLocarna/Makefile config.status: creating LocARNA-1.6.pc config.status: creating src/package_constants.hh config.status: creating Packaging/debian/control config.status: creating Packaging/rpm/locarna.spec config.status: creating src/config.h config.status: executing libtool commands config.status: executing depfiles commands Making all in src make[1]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' depbase=`echo ribosum2cc.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT ribosum2cc.o -MD -MP -MF $depbase.Tpo -c -o ribosum2cc.o ribosum2cc.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo LocARNA/aux.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/aux.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/aux.lo LocARNA/aux.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/aux.lo -MD -MP -MF LocARNA/.deps/aux.Tpo -c LocARNA/aux.cc -fPIC -DPIC -o LocARNA/.libs/aux.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/aux.lo -MD -MP -MF LocARNA/.deps/aux.Tpo -c LocARNA/aux.cc -o LocARNA/aux.o >/dev/null 2>&1 depbase=`echo LocARNA/sequence.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sequence.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/sequence.lo LocARNA/sequence.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sequence.lo -MD -MP -MF LocARNA/.deps/sequence.Tpo -c LocARNA/sequence.cc -fPIC -DPIC -o LocARNA/.libs/sequence.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sequence.lo -MD -MP -MF LocARNA/.deps/sequence.Tpo -c LocARNA/sequence.cc -o LocARNA/sequence.o >/dev/null 2>&1 depbase=`echo LocARNA/stopwatch.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/stopwatch.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/stopwatch.lo LocARNA/stopwatch.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/stopwatch.lo -MD -MP -MF LocARNA/.deps/stopwatch.Tpo -c LocARNA/stopwatch.cc -fPIC -DPIC -o LocARNA/.libs/stopwatch.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/stopwatch.lo -MD -MP -MF LocARNA/.deps/stopwatch.Tpo -c LocARNA/stopwatch.cc -o LocARNA/stopwatch.o >/dev/null 2>&1 depbase=`echo LocARNA/options.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/options.lo -MD -MP -MF $depbase.Tpo -c 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LocARNA/rna_structure.lo -MD -MP -MF LocARNA/.deps/rna_structure.Tpo -c LocARNA/rna_structure.cc -fPIC -DPIC -o LocARNA/.libs/rna_structure.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/rna_structure.lo -MD -MP -MF LocARNA/.deps/rna_structure.Tpo -c LocARNA/rna_structure.cc -o LocARNA/rna_structure.o >/dev/null 2>&1 depbase=`echo LocARNA/confusion_matrix.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/confusion_matrix.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/confusion_matrix.lo LocARNA/confusion_matrix.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/confusion_matrix.lo -MD -MP -MF LocARNA/.deps/confusion_matrix.Tpo -c LocARNA/confusion_matrix.cc -fPIC -DPIC -o LocARNA/.libs/confusion_matrix.o libtool: compile: g++ 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g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sparsification_mapper.lo -MD -MP -MF LocARNA/.deps/sparsification_mapper.Tpo -c LocARNA/sparsification_mapper.cc -fPIC -DPIC -o LocARNA/.libs/sparsification_mapper.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sparsification_mapper.lo -MD -MP -MF LocARNA/.deps/sparsification_mapper.Tpo -c LocARNA/sparsification_mapper.cc -o LocARNA/sparsification_mapper.o >/dev/null 2>&1 depbase=`echo LocARNA/exact_matcher.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/exact_matcher.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/exact_matcher.lo LocARNA/exact_matcher.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/exact_matcher.lo -MD -MP -MF LocARNA/.deps/exact_matcher.Tpo -c LocARNA/exact_matcher.cc -fPIC -DPIC -o LocARNA/.libs/exact_matcher.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/exact_matcher.lo -MD -MP -MF LocARNA/.deps/exact_matcher.Tpo -c LocARNA/exact_matcher.cc -o LocARNA/exact_matcher.o >/dev/null 2>&1 depbase=`echo LocARNA/params.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /bin/sh ../libtool --tag=CXX --mode=compile g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/params.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/params.lo LocARNA/params.cc &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/params.lo -MD -MP -MF LocARNA/.deps/params.Tpo -c LocARNA/params.cc -fPIC -DPIC -o LocARNA/.libs/params.o libtool: compile: g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/params.lo -MD -MP -MF LocARNA/.deps/params.Tpo -c LocARNA/params.cc -o LocARNA/params.o >/dev/null 2>&1 /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -fPIC -version-info 2:0:0 -o libLocARNA-1.6.la -rpath /usr/lib64 LocARNA/aux.lo LocARNA/sequence.lo LocARNA/stopwatch.lo LocARNA/options.lo LocARNA/basepairs.lo LocARNA/alignment.lo LocARNA/rna_ensemble.lo LocARNA/rna_data.lo LocARNA/pfold_params.lo LocARNA/scoring.lo LocARNA/infty_int.lo LocARNA/match_probs.lo LocARNA/ribosum.lo LocARNA/ribofit.lo LocARNA/sequence_annotation.lo LocARNA/anchor_constraints.lo LocARNA/arc_matches.lo LocARNA/aligner.lo LocARNA/stral_score.lo LocARNA/aligner_p.lo LocARNA/trace_controller.lo LocARNA/multiple_alignment.lo LocARNA/rna_structure.lo LocARNA/confusion_matrix.lo LocARNA/global_stopwatch.lo LocARNA/mcc_matrices.lo LocARNA/aligner_n.lo LocARNA/sparsification_mapper.lo LocARNA/exact_matcher.lo LocARNA/params.lo -fno-lto -Wl,-fno-lto -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ libtool: link: g++ -fPIC -DPIC -shared -nostdlib 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LocARNA/ribosum.o LocARNA/ribofit.o LocARNA/sequence_annotation.o LocARNA/anchor_constraints.o LocARNA/arc_matches.o LocARNA/aligner.o LocARNA/stral_score.o LocARNA/aligner_p.o LocARNA/trace_controller.o LocARNA/multiple_alignment.o LocARNA/rna_structure.o LocARNA/confusion_matrix.o LocARNA/global_stopwatch.o LocARNA/mcc_matrices.o LocARNA/aligner_n.o LocARNA/sparsification_mapper.o LocARNA/exact_matcher.o LocARNA/params.o libtool: link: ranlib .libs/libLocARNA-1.6.a libtool: link: ( cd ".libs" && rm -f "libLocARNA-1.6.la" && ln -s "../libLocARNA-1.6.la" "libLocARNA-1.6.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -fPIC -static -o ribosum2cc ribosum2cc.o libLocARNA-1.6.la -fno-lto -Wl,-fno-lto -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ libtool: link: g++ -O2 -fPIC -o ribosum2cc ribosum2cc.o -fno-lto -Wl,-fno-lto -fopenmp ./.libs/libLocARNA-1.6.a -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ -fopenmp ./ribosum2cc Ribosum85_60 "../Data/Matrices/RIBOSUM85_60" LocARNA/ribosum85_60.icc make all-recursive make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' Making all in Utils make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Utils' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Utils' Making all in . make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' depbase=`echo locarna.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT locarna.o -MD -MP -MF $depbase.Tpo -c -o locarna.o locarna.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -fPIC -static -o locarna.bin locarna.o libLocARNA-1.6.la -fno-lto -Wl,-fno-lto -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ libtool: link: g++ -O2 -fPIC -o locarna.bin locarna.o -fno-lto -Wl,-fno-lto -fopenmp ./.libs/libLocARNA-1.6.a -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ -fopenmp depbase=`echo locarna_p.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT locarna_p.o -MD -MP -MF $depbase.Tpo -c -o locarna_p.o locarna_p.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -fPIC -static -o locarna_p locarna_p.o libLocARNA-1.6.la -fno-lto -Wl,-fno-lto -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ libtool: link: g++ -O2 -fPIC -o locarna_p locarna_p.o -fno-lto -Wl,-fno-lto -fopenmp ./.libs/libLocARNA-1.6.a -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ -fopenmp depbase=`echo fit.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT fit.o -MD -MP -MF $depbase.Tpo -c -o fit.o fit.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo LocARNA/fitonoff.o | sed 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-DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT exparna_p.o -MD -MP -MF $depbase.Tpo -c -o exparna_p.o exparna_p.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -fPIC -static -o exparna_p exparna_p.o libLocARNA-1.6.la -fno-lto -Wl,-fno-lto -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ libtool: link: g++ -O2 -fPIC -o exparna_p exparna_p.o -fno-lto -Wl,-fno-lto -fopenmp ./.libs/libLocARNA-1.6.a -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ -fopenmp depbase=`echo sparse.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT sparse.o -MD -MP -MF $depbase.Tpo -c -o sparse.o sparse.cc &&\ mv -f $depbase.Tpo $depbase.Po /bin/sh ../libtool --tag=CXX --mode=link g++ -O2 -fPIC -static -o sparse sparse.o libLocARNA-1.6.la -fno-lto -Wl,-fno-lto -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ libtool: link: g++ -O2 -fPIC -o sparse sparse.o -fno-lto -Wl,-fno-lto -fopenmp ./.libs/libLocARNA-1.6.a -lRNA -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ -fopenmp make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' Making all in Tests make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' cp ../../Data/Examples/archaea.aln archaea.aln cp ../../Data/Examples/archaea-aln.fa archaea-aln.fa cp ../../Data/Examples/archaea-wrong.fa archaea-wrong.fa make all-am make[4]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make[4]: Nothing to be done for 'all-am'. make[4]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' Making all in lib make[1]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' Making all in perl make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' Making all in MLocarna make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl/MLocarna' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl/MLocarna' make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' make[3]: Nothing to be done for 'all-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' make[1]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' Making all in Doc make[1]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' Making all in man make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc/man' make[2]: Nothing to be done for 'all'. make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc/man' make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' make[2]: Nothing to be done for 'all-am'. make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' make[1]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' make[1]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3' make[1]: Nothing to be done for 'all-am'. make[1]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3' Making install in src make[1]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' make install-recursive make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' Making install in Utils make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Utils' make[4]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Utils' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/bin' /usr/bin/ginstall -c mlocarna locarnate locarna-motif-scan plot-bmprobs gen-reliab-dot.pl reliability-profile.pl aln2fa.pl alnsel.pl locarnap-realign-all.pl locarnap-revisit-RNAz-hits.pl locarnap-predict-and-plot.pl locarnap-revcomp.pl RNAz.pm LocARNA_RNAz.pm dot2pp pp2dot mlocarna_nnames locarna-mea.pl average-dot.pl aln-seqs.pl exploc_p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/bin' make[4]: Nothing to be done for 'install-data-am'. make[4]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Utils' make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Utils' Making install in . make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' make[4]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64' /bin/sh ../libtool --mode=install /usr/bin/ginstall -c libLocARNA-1.6.la '/usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64' libtool: install: /usr/bin/ginstall -c .libs/libLocARNA-1.6.so.2.0.0 /usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64/libLocARNA-1.6.so.2.0.0 libtool: install: (cd /usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64 && { ln -s -f libLocARNA-1.6.so.2.0.0 libLocARNA-1.6.so.2 || { rm -f libLocARNA-1.6.so.2 && ln -s libLocARNA-1.6.so.2.0.0 libLocARNA-1.6.so.2; }; }) libtool: install: (cd /usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64 && { ln -s -f libLocARNA-1.6.so.2.0.0 libLocARNA-1.6.so || { rm -f libLocARNA-1.6.so && ln -s libLocARNA-1.6.so.2.0.0 libLocARNA-1.6.so; }; }) libtool: install: /usr/bin/ginstall -c .libs/libLocARNA-1.6.lai /usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64/libLocARNA-1.6.la libtool: install: /usr/bin/ginstall -c .libs/libLocARNA-1.6.a /usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64/libLocARNA-1.6.a libtool: install: chmod 644 /usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64/libLocARNA-1.6.a libtool: install: ranlib /usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64/libLocARNA-1.6.a libtool: install: warning: remember to run `libtool --finish /usr/lib64' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/bin' /bin/sh ../libtool --mode=install /usr/bin/ginstall -c locarna.bin '/usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/./locarna' libtool: install: /usr/bin/ginstall -c locarna.bin /usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/./locarna /bin/sh ../libtool --mode=install /usr/bin/ginstall -c locarna_p locarnap_fit locarna_deviation locarna_rnafold_pp exparna_p sparse ribosum2cc '/usr/src/slapt-src/academic/locarna/package-locarna/usr/bin' libtool: install: /usr/bin/ginstall -c locarna_p /usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/locarna_p libtool: install: /usr/bin/ginstall -c locarnap_fit /usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/locarnap_fit libtool: install: /usr/bin/ginstall -c locarna_deviation /usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/locarna_deviation libtool: install: /usr/bin/ginstall -c locarna_rnafold_pp /usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/locarna_rnafold_pp libtool: install: /usr/bin/ginstall -c exparna_p /usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/exparna_p libtool: install: /usr/bin/ginstall -c sparse /usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/sparse libtool: install: /usr/bin/ginstall -c ribosum2cc /usr/src/slapt-src/academic/locarna/package-locarna/usr/bin/ribosum2cc /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/include/LocARNA-1.6' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/include/LocARNA-1.6/LocARNA' /usr/bin/ginstall -c -m 644 LocARNA/aux.hh LocARNA/plusvector.hh LocARNA/stopwatch.hh LocARNA/options.hh LocARNA/matrix.hh LocARNA/matrices.hh LocARNA/sparse_matrix.hh LocARNA/sparse_vector.hh LocARNA/sequence.hh LocARNA/basepairs.hh LocARNA/alignment.hh LocARNA/alignment_impl.hh LocARNA/rna_ensemble.hh LocARNA/rna_ensemble_impl.hh LocARNA/rna_data.hh LocARNA/ext_rna_data.hh LocARNA/rna_data_impl.hh LocARNA/ext_rna_data_impl.hh LocARNA/params.hh LocARNA/pfold_params.hh LocARNA/scoring.hh LocARNA/scoring_fwd.hh LocARNA/infty_int.hh LocARNA/match_probs.hh LocARNA/alphabet.hh LocARNA/alphabet.icc LocARNA/ribosum.hh LocARNA/ribofit.hh LocARNA/ribofit_will2014.ihh LocARNA/ribofit_will2014.icc LocARNA/sequence_annotation.hh LocARNA/anchor_constraints.hh LocARNA/arc_matches.hh LocARNA/aligner_restriction.hh LocARNA/aligner.hh LocARNA/aligner_impl.hh LocARNA/aligner_p.hh LocARNA/stral_score.hh LocARNA/trace_controller.hh LocARNA/multiple_alignment.hh '/usr/src/slapt-src/academic/locarna/package-locarna/usr/include/LocARNA-1.6/LocARNA' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/include/LocARNA-1.6/LocARNA' /usr/bin/ginstall -c -m 644 LocARNA/rna_structure.hh LocARNA/confusion_matrix.hh LocARNA/base_pair_filter.hh LocARNA/discrete_distribution.hh LocARNA/string1.hh LocARNA/type_wrapper.hh LocARNA/global_stopwatch.hh LocARNA/tuples.hh LocARNA/mcc_matrices.hh LocARNA/aligner_n.hh LocARNA/sparsification_mapper.hh LocARNA/exact_matcher.hh LocARNA/main_helper.icc LocARNA/ribosum85_60.icc '/usr/src/slapt-src/academic/locarna/package-locarna/usr/include/LocARNA-1.6/LocARNA' /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64/pkgconfig' /usr/bin/ginstall -c -m 644 ../LocARNA-1.6.pc '/usr/src/slapt-src/academic/locarna/package-locarna/usr/lib64/pkgconfig' make[4]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' Making install in Tests make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make install-am make[4]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make[5]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make[5]: Nothing to be done for 'install-exec-am'. make[5]: Nothing to be done for 'install-data-am'. make[5]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make[4]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src/Tests' make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' make[1]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/src' Making install in lib make[1]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' Making install in perl make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' Making install in MLocarna make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl/MLocarna' make[4]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl/MLocarna' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/lib/perl/MLocarna' /usr/bin/ginstall -c SparseMatrix.pm Trees.pm MatchProbs.pm Aux.pm threaded.pm unthreaded.pm PairwiseAligners.pm '/usr/src/slapt-src/academic/locarna/package-locarna/usr/lib/perl/MLocarna' make[4]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl/MLocarna' make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl/MLocarna' make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' make[4]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' make[4]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/lib/perl' /usr/bin/ginstall -c MLocarna.pm '/usr/src/slapt-src/academic/locarna/package-locarna/usr/lib/perl' make[4]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib/perl' make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' make[1]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/lib' Making install in Doc make[1]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' Making install in man make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc/man' make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc/man' make[3]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/man/man1' /usr/bin/ginstall -c -m 644 exparna_p.1 locarna_deviation.1 locarna_p.1 locarnap_fit.1 locarna_rnafold_pp.1 ribosum2cc.1 sparse.1 locarna.1 aln2fa.pl.1 alnsel.pl.1 aln-seqs.pl.1 average-dot.pl.1 dot2pp.1 exploc_p.1 gen-reliab-dot.pl.1 locarna-mea.pl.1 locarna-motif-scan.1 locarnap-predict-and-plot.pl.1 locarnap-realign-all.pl.1 locarnap-revcomp.pl.1 locarnap-revisit-RNAz-hits.pl.1 locarnate.1 mlocarna.1 mlocarna_nnames.1 plot-bmprobs.1 pp2dot.1 reliability-profile.pl.1 '/usr/src/slapt-src/academic/locarna/package-locarna/usr/man/man1' make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc/man' make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc/man' make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' make[3]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' make[3]: Nothing to be done for 'install-exec-am'. make[3]: Nothing to be done for 'install-data-am'. make[3]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' make[1]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3/Doc' make[1]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3' make[2]: Entering directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3' make[2]: Nothing to be done for 'install-exec-am'. /usr/bin/mkdir -p '/usr/src/slapt-src/academic/locarna/package-locarna/usr/share/locarna/Matrices' /usr/bin/ginstall -c -m 644 Data/Matrices/RIBOSUM85_60 '/usr/src/slapt-src/academic/locarna/package-locarna/usr/share/locarna/Matrices' make[2]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3' make[1]: Leaving directory '/usr/src/slapt-src/academic/locarna/locarna-1.9.2.3' Slackware package maker, version 3.14159265. Searching for symbolic links: usr/lib64/libLocARNA-1.6.so libLocARNA-1.6.so.2.0.0 usr/lib64/libLocARNA-1.6.so.2 libLocARNA-1.6.so.2.0.0 Making symbolic link creation script: ( cd usr/lib64 ; rm -rf libLocARNA-1.6.so ) ( cd usr/lib64 ; ln -sf libLocARNA-1.6.so.2.0.0 libLocARNA-1.6.so ) ( cd usr/lib64 ; rm -rf libLocARNA-1.6.so.2 ) ( cd usr/lib64 ; ln -sf libLocARNA-1.6.so.2.0.0 libLocARNA-1.6.so.2 ) It is recommended that you make these lines your new installation script. Would you like to make this stuff the install script for this package and remove the symbolic links ([y]es, [n]o)? y Removing symbolic links: removed './usr/lib64/libLocARNA-1.6.so.2' removed './usr/lib64/libLocARNA-1.6.so' Creating your new ./install/doinst.sh... This next step is optional - you can set the directories in your package to some sane permissions. If any of the directories in your package have special permissions, then DO NOT reset them here! Would you like to reset all directory permissions to 755 (drwxr-xr-x) and directory ownerships to root.root ([y]es, [n]o)? n Creating Slackware package: /usr/src/slapt-src/academic/locarna/locarna-1.9.2.3-x86_64-2salix15.0.txz ./ install/ install/doinst.sh install/slack-desc usr/ usr/bin/ usr/bin/LocARNA_RNAz.pm usr/bin/RNAz.pm usr/bin/aln-seqs.pl usr/bin/aln2fa.pl usr/bin/alnsel.pl usr/bin/average-dot.pl usr/bin/dot2pp usr/bin/exparna_p usr/bin/exploc_p usr/bin/gen-reliab-dot.pl usr/bin/locarna usr/bin/locarna-mea.pl usr/bin/locarna-motif-scan usr/bin/locarna_deviation usr/bin/locarna_p usr/bin/locarna_rnafold_pp usr/bin/locarnap-predict-and-plot.pl usr/bin/locarnap-realign-all.pl usr/bin/locarnap-revcomp.pl usr/bin/locarnap-revisit-RNAz-hits.pl usr/bin/locarnap_fit usr/bin/locarnate usr/bin/mlocarna usr/bin/mlocarna_nnames usr/bin/plot-bmprobs usr/bin/pp2dot usr/bin/reliability-profile.pl usr/bin/ribosum2cc usr/bin/sparse usr/doc/ usr/doc/locarna-1.9.2.3/ usr/doc/locarna-1.9.2.3/AUTHORS usr/doc/locarna-1.9.2.3/COPYING usr/doc/locarna-1.9.2.3/ChangeLog usr/doc/locarna-1.9.2.3/INSTALL usr/doc/locarna-1.9.2.3/README usr/doc/locarna-1.9.2.3/locarna.SlackBuild usr/include/ usr/include/LocARNA-1.6/ usr/include/LocARNA-1.6/LocARNA/ usr/include/LocARNA-1.6/LocARNA/aligner.hh usr/include/LocARNA-1.6/LocARNA/aligner_impl.hh usr/include/LocARNA-1.6/LocARNA/aligner_n.hh usr/include/LocARNA-1.6/LocARNA/aligner_p.hh usr/include/LocARNA-1.6/LocARNA/aligner_restriction.hh usr/include/LocARNA-1.6/LocARNA/alignment.hh usr/include/LocARNA-1.6/LocARNA/alignment_impl.hh usr/include/LocARNA-1.6/LocARNA/alphabet.hh usr/include/LocARNA-1.6/LocARNA/alphabet.icc usr/include/LocARNA-1.6/LocARNA/anchor_constraints.hh usr/include/LocARNA-1.6/LocARNA/arc_matches.hh usr/include/LocARNA-1.6/LocARNA/aux.hh usr/include/LocARNA-1.6/LocARNA/base_pair_filter.hh usr/include/LocARNA-1.6/LocARNA/basepairs.hh usr/include/LocARNA-1.6/LocARNA/confusion_matrix.hh usr/include/LocARNA-1.6/LocARNA/discrete_distribution.hh usr/include/LocARNA-1.6/LocARNA/exact_matcher.hh usr/include/LocARNA-1.6/LocARNA/ext_rna_data.hh usr/include/LocARNA-1.6/LocARNA/ext_rna_data_impl.hh usr/include/LocARNA-1.6/LocARNA/global_stopwatch.hh usr/include/LocARNA-1.6/LocARNA/infty_int.hh usr/include/LocARNA-1.6/LocARNA/main_helper.icc usr/include/LocARNA-1.6/LocARNA/match_probs.hh usr/include/LocARNA-1.6/LocARNA/matrices.hh usr/include/LocARNA-1.6/LocARNA/matrix.hh usr/include/LocARNA-1.6/LocARNA/mcc_matrices.hh usr/include/LocARNA-1.6/LocARNA/multiple_alignment.hh usr/include/LocARNA-1.6/LocARNA/options.hh usr/include/LocARNA-1.6/LocARNA/params.hh usr/include/LocARNA-1.6/LocARNA/pfold_params.hh usr/include/LocARNA-1.6/LocARNA/plusvector.hh usr/include/LocARNA-1.6/LocARNA/ribofit.hh usr/include/LocARNA-1.6/LocARNA/ribofit_will2014.icc usr/include/LocARNA-1.6/LocARNA/ribofit_will2014.ihh usr/include/LocARNA-1.6/LocARNA/ribosum.hh usr/include/LocARNA-1.6/LocARNA/ribosum85_60.icc usr/include/LocARNA-1.6/LocARNA/rna_data.hh usr/include/LocARNA-1.6/LocARNA/rna_data_impl.hh usr/include/LocARNA-1.6/LocARNA/rna_ensemble.hh usr/include/LocARNA-1.6/LocARNA/rna_ensemble_impl.hh usr/include/LocARNA-1.6/LocARNA/rna_structure.hh usr/include/LocARNA-1.6/LocARNA/scoring.hh usr/include/LocARNA-1.6/LocARNA/scoring_fwd.hh usr/include/LocARNA-1.6/LocARNA/sequence.hh usr/include/LocARNA-1.6/LocARNA/sequence_annotation.hh usr/include/LocARNA-1.6/LocARNA/sparse_matrix.hh usr/include/LocARNA-1.6/LocARNA/sparse_vector.hh usr/include/LocARNA-1.6/LocARNA/sparsification_mapper.hh usr/include/LocARNA-1.6/LocARNA/stopwatch.hh usr/include/LocARNA-1.6/LocARNA/stral_score.hh usr/include/LocARNA-1.6/LocARNA/string1.hh usr/include/LocARNA-1.6/LocARNA/trace_controller.hh usr/include/LocARNA-1.6/LocARNA/tuples.hh usr/include/LocARNA-1.6/LocARNA/type_wrapper.hh usr/lib/ usr/lib64/ usr/lib64/libLocARNA-1.6.a usr/lib64/libLocARNA-1.6.so.2.0.0 usr/lib64/perl5/ usr/lib64/perl5/vendor_perl/ usr/lib64/perl5/vendor_perl/MLocarna/ usr/lib64/perl5/vendor_perl/MLocarna.pm usr/lib64/perl5/vendor_perl/MLocarna/Aux.pm usr/lib64/perl5/vendor_perl/MLocarna/MatchProbs.pm usr/lib64/perl5/vendor_perl/MLocarna/PairwiseAligners.pm usr/lib64/perl5/vendor_perl/MLocarna/SparseMatrix.pm usr/lib64/perl5/vendor_perl/MLocarna/Trees.pm usr/lib64/perl5/vendor_perl/MLocarna/threaded.pm usr/lib64/perl5/vendor_perl/MLocarna/unthreaded.pm usr/lib64/pkgconfig/ usr/lib64/pkgconfig/LocARNA-1.6.pc usr/man/ usr/man/man1/ usr/man/man1/aln-seqs.pl.1.gz usr/man/man1/aln2fa.pl.1.gz usr/man/man1/alnsel.pl.1.gz usr/man/man1/average-dot.pl.1.gz usr/man/man1/dot2pp.1.gz usr/man/man1/exparna_p.1.gz usr/man/man1/exploc_p.1.gz usr/man/man1/gen-reliab-dot.pl.1.gz usr/man/man1/locarna-mea.pl.1.gz usr/man/man1/locarna-motif-scan.1.gz usr/man/man1/locarna.1.gz usr/man/man1/locarna_deviation.1.gz usr/man/man1/locarna_p.1.gz usr/man/man1/locarna_rnafold_pp.1.gz usr/man/man1/locarnap-predict-and-plot.pl.1.gz usr/man/man1/locarnap-realign-all.pl.1.gz usr/man/man1/locarnap-revcomp.pl.1.gz usr/man/man1/locarnap-revisit-RNAz-hits.pl.1.gz usr/man/man1/locarnap_fit.1.gz usr/man/man1/locarnate.1.gz usr/man/man1/mlocarna.1.gz usr/man/man1/mlocarna_nnames.1.gz usr/man/man1/plot-bmprobs.1.gz usr/man/man1/pp2dot.1.gz usr/man/man1/reliability-profile.pl.1.gz usr/man/man1/ribosum2cc.1.gz usr/man/man1/sparse.1.gz usr/share/ usr/share/locarna/ usr/share/locarna/Matrices/ usr/share/locarna/Matrices/RIBOSUM85_60 Slackware package /usr/src/slapt-src/academic/locarna/locarna-1.9.2.3-x86_64-2salix15.0.txz created. Installing package locarna-1.9.2.3-x86_64-2salix15.0... | locarna (Local RNA alignment on structural basis) | | LocARNA is a collection of alignment tools for the structural | analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously | aligns and predicts common structures for your RNAs. In this way, | LocARNA performs Sankoff-like alignment and is in particular suited | for analyzing sets of related RNAs without known common structure. | | Home:https://www.bioinf.uni-freiburg.de/Software/LocARNA/ | | | |