academic/locarna: Upgrade to version 2.0.1 #13942

brobr · 2026-01-13T00:55:20Z

No description provided.

github-actions · 2026-01-13T00:56:03Z

reverse dependencies - academic/locarna

None

github-actions · 2026-01-13T00:56:21Z

✅ sbolint - academic/locarna ✅

sbolint: locarna checks out OK

willysr · 2026-01-13T12:59:28Z

@sbo-bot: build academic/locarna

sbo-bot · 2026-01-13T13:00:34Z

buildpkg i586 academic/locarna

Creating hintfile directory: /etc/repo/SBo/hintfiles
Checking whether git is clean ... yes.
Indexing SlackBuilds ... done.
git repo: /var/lib/repo/SBo/slackbuilds
branch:   HEAD
date:     Tue Jan 13 00:55:24 GMT 2026
revision: 741e48ab031ff43b2ef36aefbf96793e7a9466f7
title:    Merge 6b8e86132cca137f30592bd72d5e4fedbad7f120 into 025fc8f2d13a6c442b42df058e6e76bb3a62bc95

================================================================================
academic/locarna                                                        13:00:15
================================================================================

Calculating dependencies ... 
Dependency tree:
academic/locarna (aborted)
  academic/ViennaRNA (unsupported)
    academic/lapacke (ok)
      libraries/lapack (ok)
        libraries/blas (ok)

:-/ academic/ViennaRNA is UNSUPPORTED on i586 /-:

ERROR: Cannot build academic/locarna.
:-/ academic/locarna is UNSUPPORTED /-:
Missing dependencies:
  
Unsupported dependencies:
  academic/ViennaRNA

================================================================================
SUMMARY                                                                 13:00:16
================================================================================

Logfile:     /var/log/repo/SBo/repo_2026-01-13_13:00:14.log
Runtime:     0h 0m 2s
Unsupported: 2
  academic/ViennaRNA
  academic/locarna

Snipped Build Log

Details

 2026-01-13 13:00:16
:-/ academic/locarna is UNSUPPORTED /-:
Missing dependencies:
  
Unsupported dependencies:
  academic/ViennaRNA

sbo-bot · 2026-01-13T13:02:44Z

buildpkg x86_64 academic/locarna

Creating hintfile directory: /etc/repo/SBo/hintfiles
Checking whether git is clean ... yes.
Indexing SlackBuilds ... done.
git repo: /var/lib/repo/SBo/slackbuilds
branch:   HEAD
date:     Tue Jan 13 00:55:24 GMT 2026
revision: 741e48ab031ff43b2ef36aefbf96793e7a9466f7
title:    Merge 6b8e86132cca137f30592bd72d5e4fedbad7f120 into 025fc8f2d13a6c442b42df058e6e76bb3a62bc95

================================================================================
academic/locarna                                                        13:01:10
================================================================================

Calculating dependencies ... 
Dependency tree:
academic/locarna (update for version 2.0.1)
  academic/ViennaRNA (ok)
    academic/lapacke (ok)
      libraries/lapack (ok)
        libraries/blas (ok)

Building academic/locarna (update for version 2.0.1) ------------------ 13:01:11
Testing SlackBuild files ... done.
Downloading source files ...
Verifying source files ... done.
Installing dependencies ...
blas-3.12.0-x86_64-1_SBo: Basic Linear Algebra Subprograms ............. [ 980K]
lapack-3.12.0-x86_64-1_SBo: linear algebra routines .................... [  13M]
lapacke-3.12.0-x86_64-1_SBo: C interface to LAPACK ..................... [ 4.1M]
ViennaRNA-2.7.2-x86_64-3_SBo: C Library ................................ [  97M]
Running locarna.SlackBuild ...                                      ETA 13:02:??
env MAKEFLAGS='-j24 -l13' nice -n 5 bash ./locarna.SlackBuild
Built ok:  locarna-2.0.1-x86_64-1_SBo.txz                               13:02:13
Testing package locarna-2.0.1-x86_64-1_SBo.txz ... done.
Test installing locarna-2.0.1-x86_64-1_SBo.txz ...
locarna-2.0.1-x86_64-1_SBo: Local RNA alignment on structural basis .... [  15M]
Unmounting chroot ... done.
Backed up: locarna-1.9.2.3-x86_64-6_SBo.txz
✅ academic/locarna Updated for version 2.0.1 ✅

================================================================================
SUMMARY                                                                 13:02:14
================================================================================

Logfile:     /var/log/repo/SBo/repo_2026-01-13_13:01:10.log
Runtime:     0h 1m 5s
Updated:     1
  academic/locarna/locarna-2.0.1-x86_64-1_SBo.txz

Snipped Build Log

Details

o LocARNA/aux.lo LocARNA/aux.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/basepairs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/basepairs.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/basepairs.lo LocARNA/basepairs.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/confusion_matrix.lo | sed 's|[^/]*$|.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 $depbase.Plo
depbase=`echo LocARNA/exact_matcher.lo | sed 's|[^/]*$|.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 $depbase.Plo
depbase=`echo LocARNA/global_stopwatch.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/global_stopwatch.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/global_stopwatch.lo LocARNA/global_stopwatch.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/infty_int.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/infty_int.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/infty_int.lo LocARNA/infty_int.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/edge_probs.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/edge_probs.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/edge_probs.lo LocARNA/edge_probs.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/mcc_matrices.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/mcc_matrices.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/mcc_matrices.lo LocARNA/mcc_matrices.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/multiple_alignment.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/multiple_alignment.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/multiple_alignment.lo LocARNA/multiple_alignment.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/options.lo | sed 's|[^/]*$|.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 -o LocARNA/options.lo LocARNA/options.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/ribofit.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/ribofit.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/ribofit.lo LocARNA/ribofit.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/ribosum.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/ribosum.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/ribosum.lo LocARNA/ribosum.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/rna_data.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/rna_data.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/rna_data.lo LocARNA/rna_data.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/rna_ensemble.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/rna_ensemble.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/rna_ensemble.lo LocARNA/rna_ensemble.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/rna_structure.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/rna_structure.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/rna_structure.lo LocARNA/rna_structure.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/scoring.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/scoring.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/scoring.lo LocARNA/scoring.cc &&\
mv -f $depbase.Tpo $depbase.Plo
depbase=`echo LocARNA/sequence.lo | sed 's|[^/]*$|.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 $depbase.Plo
depbase=`echo LocARNA/sequence_annotation.lo | sed 's|[^/]*$|.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_annotation.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/sequence_annotation.lo LocARNA/sequence_annotation.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++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/aligner.lo -MD -MP -MF LocARNA/.deps/aligner.Tpo -c LocARNA/aligner.cc  -fPIC -DPIC -o LocARNA/.libs/aligner.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/aligner_n.lo -MD -MP -MF LocARNA/.deps/aligner_n.Tpo -c LocARNA/aligner_n.cc  -fPIC -DPIC -o LocARNA/.libs/aligner_n.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/arc_matches.lo -MD -MP -MF LocARNA/.deps/arc_matches.Tpo -c LocARNA/arc_matches.cc  -fPIC -DPIC -o LocARNA/.libs/arc_matches.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  -fPIC -DPIC -o LocARNA/.libs/exact_matcher.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/ribosum.lo -MD -MP -MF LocARNA/.deps/ribosum.Tpo -c LocARNA/ribosum.cc  -fPIC -DPIC -o LocARNA/.libs/ribosum.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/edge_probs.lo -MD -MP -MF LocARNA/.deps/edge_probs.Tpo -c LocARNA/edge_probs.cc  -fPIC -DPIC -o LocARNA/.libs/edge_probs.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/infty_int.lo -MD -MP -MF LocARNA/.deps/infty_int.Tpo -c LocARNA/infty_int.cc  -fPIC -DPIC -o LocARNA/.libs/infty_int.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/anchor_constraints.lo -MD -MP -MF LocARNA/.deps/anchor_constraints.Tpo -c LocARNA/anchor_constraints.cc  -fPIC -DPIC -o LocARNA/.libs/anchor_constraints.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  -fPIC -DPIC -o LocARNA/.libs/aux.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/ribofit.lo -MD -MP -MF LocARNA/.deps/ribofit.Tpo -c LocARNA/ribofit.cc  -fPIC -DPIC -o LocARNA/.libs/ribofit.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/rna_data.lo -MD -MP -MF LocARNA/.deps/rna_data.Tpo -c LocARNA/rna_data.cc  -fPIC -DPIC -o LocARNA/.libs/rna_data.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/multiple_alignment.lo -MD -MP -MF LocARNA/.deps/multiple_alignment.Tpo -c LocARNA/multiple_alignment.cc  -fPIC -DPIC -o LocARNA/.libs/multiple_alignment.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/basepairs.lo -MD -MP -MF LocARNA/.deps/basepairs.Tpo -c LocARNA/basepairs.cc  -fPIC -DPIC -o LocARNA/.libs/basepairs.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/global_stopwatch.lo -MD -MP -MF LocARNA/.deps/global_stopwatch.Tpo -c LocARNA/global_stopwatch.cc  -fPIC -DPIC -o LocARNA/.libs/global_stopwatch.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/alignment.lo -MD -MP -MF LocARNA/.deps/alignment.Tpo -c LocARNA/alignment.cc  -fPIC -DPIC -o LocARNA/.libs/alignment.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/mcc_matrices.lo -MD -MP -MF LocARNA/.deps/mcc_matrices.Tpo -c LocARNA/mcc_matrices.cc  -fPIC -DPIC -o LocARNA/.libs/mcc_matrices.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/scoring.lo -MD -MP -MF LocARNA/.deps/scoring.Tpo -c LocARNA/scoring.cc  -fPIC -DPIC -o LocARNA/.libs/scoring.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/options.lo -MD -MP -MF LocARNA/.deps/options.Tpo -c LocARNA/options.cc  -fPIC -DPIC -o LocARNA/.libs/options.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sequence_annotation.lo -MD -MP -MF LocARNA/.deps/sequence_annotation.Tpo -c LocARNA/sequence_annotation.cc  -fPIC -DPIC -o LocARNA/.libs/sequence_annotation.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/rna_ensemble.lo -MD -MP -MF LocARNA/.deps/rna_ensemble.Tpo -c LocARNA/rna_ensemble.cc  -fPIC -DPIC -o LocARNA/.libs/rna_ensemble.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  -fPIC -DPIC -o LocARNA/.libs/sequence.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  -fPIC -DPIC -o LocARNA/.libs/rna_structure.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/infty_int.lo -MD -MP -MF LocARNA/.deps/infty_int.Tpo -c LocARNA/infty_int.cc -o LocARNA/infty_int.o >/dev/null 2>&1
depbase=`echo LocARNA/sparsification_mapper.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/sparsification_mapper.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/sparsification_mapper.lo LocARNA/sparsification_mapper.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/global_stopwatch.lo -MD -MP -MF LocARNA/.deps/global_stopwatch.Tpo -c LocARNA/global_stopwatch.cc -o LocARNA/global_stopwatch.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/ribofit.lo -MD -MP -MF LocARNA/.deps/ribofit.Tpo -c LocARNA/ribofit.cc -o LocARNA/ribofit.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/aux.lo -MD -MP -MF LocARNA/.deps/aux.Tpo -c LocARNA/aux.cc -o LocARNA/aux.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/confusion_matrix.lo -MD -MP -MF LocARNA/.deps/confusion_matrix.Tpo -c LocARNA/confusion_matrix.cc -o LocARNA/confusion_matrix.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/mcc_matrices.lo -MD -MP -MF LocARNA/.deps/mcc_matrices.Tpo -c LocARNA/mcc_matrices.cc -o LocARNA/mcc_matrices.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sequence.lo -MD -MP -MF LocARNA/.deps/sequence.Tpo -c LocARNA/sequence.cc -o LocARNA/sequence.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sparsification_mapper.lo -MD -MP -MF LocARNA/.deps/sparsification_mapper.Tpo -c LocARNA/sparsification_mapper.cc  -fPIC -DPIC -o LocARNA/.libs/sparsification_mapper.o
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/sequence_annotation.lo -MD -MP -MF LocARNA/.deps/sequence_annotation.Tpo -c LocARNA/sequence_annotation.cc -o LocARNA/sequence_annotation.o >/dev/null 2>&1
depbase=`echo LocARNA/stopwatch.lo | sed 's|[^/]*$|.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 $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/options.lo -MD -MP -MF LocARNA/.deps/options.Tpo -c LocARNA/options.cc -o LocARNA/options.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/rna_structure.lo -MD -MP -MF LocARNA/.deps/rna_structure.Tpo -c LocARNA/rna_structure.cc -o LocARNA/rna_structure.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/edge_probs.lo -MD -MP -MF LocARNA/.deps/edge_probs.Tpo -c LocARNA/edge_probs.cc -o LocARNA/edge_probs.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/stopwatch.lo -MD -MP -MF LocARNA/.deps/stopwatch.Tpo -c LocARNA/stopwatch.cc  -fPIC -DPIC -o LocARNA/.libs/stopwatch.o
depbase=`echo LocARNA/stral_score.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/stral_score.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/stral_score.lo LocARNA/stral_score.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/alignment.lo -MD -MP -MF LocARNA/.deps/alignment.Tpo -c LocARNA/alignment.cc -o LocARNA/alignment.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/basepairs.lo -MD -MP -MF LocARNA/.deps/basepairs.Tpo -c LocARNA/basepairs.cc -o LocARNA/basepairs.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/anchor_constraints.lo -MD -MP -MF LocARNA/.deps/anchor_constraints.Tpo -c LocARNA/anchor_constraints.cc -o LocARNA/anchor_constraints.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/scoring.lo -MD -MP -MF LocARNA/.deps/scoring.Tpo -c LocARNA/scoring.cc -o LocARNA/scoring.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/arc_matches.lo -MD -MP -MF LocARNA/.deps/arc_matches.Tpo -c LocARNA/arc_matches.cc -o LocARNA/arc_matches.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/stral_score.lo -MD -MP -MF LocARNA/.deps/stral_score.Tpo -c LocARNA/stral_score.cc  -fPIC -DPIC -o LocARNA/.libs/stral_score.o
depbase=`echo LocARNA/trace_controller.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ../libtool  --tag=CXX   --mode=compile g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/trace_controller.lo -MD -MP -MF $depbase.Tpo -c -o LocARNA/trace_controller.lo LocARNA/trace_controller.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/ribosum.lo -MD -MP -MF LocARNA/.deps/ribosum.Tpo -c LocARNA/ribosum.cc -o LocARNA/ribosum.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/rna_ensemble.lo -MD -MP -MF LocARNA/.deps/rna_ensemble.Tpo -c LocARNA/rna_ensemble.cc -o LocARNA/rna_ensemble.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/trace_controller.lo -MD -MP -MF LocARNA/.deps/trace_controller.Tpo -c LocARNA/trace_controller.cc  -fPIC -DPIC -o LocARNA/.libs/trace_controller.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
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/aligner.lo -MD -MP -MF LocARNA/.deps/aligner.Tpo -c LocARNA/aligner.cc -o LocARNA/aligner.o >/dev/null 2>&1
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
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/aligner_n.lo -MD -MP -MF LocARNA/.deps/aligner_n.Tpo -c LocARNA/aligner_n.cc -o LocARNA/aligner_n.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/stral_score.lo -MD -MP -MF LocARNA/.deps/stral_score.Tpo -c LocARNA/stral_score.cc -o LocARNA/stral_score.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/multiple_alignment.lo -MD -MP -MF LocARNA/.deps/multiple_alignment.Tpo -c LocARNA/multiple_alignment.cc -o LocARNA/multiple_alignment.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/trace_controller.lo -MD -MP -MF LocARNA/.deps/trace_controller.Tpo -c LocARNA/trace_controller.cc -o LocARNA/trace_controller.o >/dev/null 2>&1
libtool: compile:  g++ -DHAVE_CONFIG_H -I. -pthread -I/usr/include/ViennaRNA -O2 -fPIC -MT LocARNA/rna_data.lo -MD -MP -MF LocARNA/.deps/rna_data.Tpo -c LocARNA/rna_data.cc -o LocARNA/rna_data.o >/dev/null 2>&1
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
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -fPIC -version-info 1:4:0 -lquadmath  -o libLocARNA-2.0.la -rpath /usr/lib64 LocARNA/aligner.lo LocARNA/aligner_n.lo LocARNA/alignment.lo LocARNA/anchor_constraints.lo LocARNA/arc_matches.lo LocARNA/aux.lo LocARNA/basepairs.lo LocARNA/confusion_matrix.lo LocARNA/exact_matcher.lo LocARNA/global_stopwatch.lo LocARNA/infty_int.lo LocARNA/edge_probs.lo LocARNA/mcc_matrices.lo LocARNA/multiple_alignment.lo LocARNA/options.lo LocARNA/ribofit.lo LocARNA/ribosum.lo LocARNA/rna_data.lo LocARNA/rna_ensemble.lo LocARNA/rna_structure.lo LocARNA/scoring.lo LocARNA/sequence.lo LocARNA/sequence_annotation.lo LocARNA/sparsification_mapper.lo LocARNA/stopwatch.lo LocARNA/stral_score.lo LocARNA/trace_controller.lo  -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
libtool: link: g++  -fPIC -DPIC -shared -nostdlib /usr/lib64/gcc/x86_64-slackware-linux/11.2.0/../../../../lib64/crti.o /usr/lib64/gcc/x86_64-slackware-linux/11.2.0/crtbeginS.o  LocARNA/.libs/aligner.o LocARNA/.libs/aligner_n.o LocARNA/.libs/alignment.o LocARNA/.libs/anchor_constraints.o LocARNA/.libs/arc_matches.o LocARNA/.libs/aux.o LocARNA/.libs/basepairs.o LocARNA/.libs/confusion_matrix.o LocARNA/.libs/exact_matcher.o LocARNA/.libs/global_stopwatch.o LocARNA/.libs/infty_int.o LocARNA/.libs/edge_probs.o LocARNA/.libs/mcc_matrices.o LocARNA/.libs/multiple_alignment.o LocARNA/.libs/options.o LocARNA/.libs/ribofit.o LocARNA/.libs/ribosum.o LocARNA/.libs/rna_data.o LocARNA/.libs/rna_ensemble.o LocARNA/.libs/rna_structure.o LocARNA/.libs/scoring.o LocARNA/.libs/sequence.o LocARNA/.libs/sequence_annotation.o LocARNA/.libs/sparsification_mapper.o LocARNA/.libs/stopwatch.o LocARNA/.libs/stral_score.o LocARNA/.libs/trace_controller.o   -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -L/usr/lib64/gcc/x86_64-slackware-linux/11.2.0 -L/usr/lib64/gcc/x86_64-slackware-linux/11.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-slackware-linux/11.2.0/../../.. -lstdc++ -lm -lc -lgcc_s /usr/lib64/gcc/x86_64-slackware-linux/11.2.0/crtendS.o /usr/lib64/gcc/x86_64-slackware-linux/11.2.0/../../../../lib64/crtn.o  -O2   -Wl,-soname -Wl,libLocARNA-2.0.so.1 -o .libs/libLocARNA-2.0.so.1.0.4
libtool: link: (cd ".libs" && rm -f "libLocARNA-2.0.so.1" && ln -s "libLocARNA-2.0.so.1.0.4" "libLocARNA-2.0.so.1")
libtool: link: (cd ".libs" && rm -f "libLocARNA-2.0.so" && ln -s "libLocARNA-2.0.so.1.0.4" "libLocARNA-2.0.so")
libtool: link: ar cr .libs/libLocARNA-2.0.a  LocARNA/aligner.o LocARNA/aligner_n.o LocARNA/alignment.o LocARNA/anchor_constraints.o LocARNA/arc_matches.o LocARNA/aux.o LocARNA/basepairs.o LocARNA/confusion_matrix.o LocARNA/exact_matcher.o LocARNA/global_stopwatch.o LocARNA/infty_int.o LocARNA/edge_probs.o LocARNA/mcc_matrices.o LocARNA/multiple_alignment.o LocARNA/options.o LocARNA/ribofit.o LocARNA/ribosum.o LocARNA/rna_data.o LocARNA/rna_ensemble.o LocARNA/rna_structure.o LocARNA/scoring.o LocARNA/sequence.o LocARNA/sequence_annotation.o LocARNA/sparsification_mapper.o LocARNA/stopwatch.o LocARNA/stral_score.o LocARNA/trace_controller.o
libtool: link: ranlib .libs/libLocARNA-2.0.a
libtool: link: ( cd ".libs" && rm -f "libLocARNA-2.0.la" && ln -s "../libLocARNA-2.0.la" "libLocARNA-2.0.la" )
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -fPIC -static -lquadmath  -o ribosum2cc ribosum2cc.o libLocARNA-2.0.la -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
libtool: link: g++ -O2 -fPIC -o ribosum2cc ribosum2cc.o  ./.libs/libLocARNA-2.0.a -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++
./ribosum2cc Ribosum85_60 "../Data/Matrices/RIBOSUM85_60" LocARNA/ribosum85_60.icc
make  all-recursive
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
Making all in Utils
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Utils'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Utils'
Making all in .
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/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 $depbase.Po
depbase=`echo locarna_p.o | sed 's|[^/]*$|.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 $depbase.Po
depbase=`echo fit.o | sed 's|[^/]*$|.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 $depbase.Po
depbase=`echo LocARNA/fitonoff.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT LocARNA/fitonoff.o -MD -MP -MF $depbase.Tpo -c -o LocARNA/fitonoff.o LocARNA/fitonoff.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo deviation.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT deviation.o -MD -MP -MF $depbase.Tpo -c -o deviation.o deviation.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo locarna_rnafold_pp.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -DHAVE_CONFIG_H -I.   -pthread -I/usr/include/ViennaRNA   -O2 -fPIC -MT locarna_rnafold_pp.o -MD -MP -MF $depbase.Tpo -c -o locarna_rnafold_pp.o locarna_rnafold_pp.cc &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo exparna_p.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
g++ -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 $depbase.Po
depbase=`echo sparse.o | sed 's|[^/]*$|.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 -lquadmath  -o locarnap_fit fit.o LocARNA/fitonoff.o libLocARNA-2.0.la -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -fPIC -static -lquadmath  -o locarna_deviation deviation.o libLocARNA-2.0.la -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
libtool: link: g++ -O2 -fPIC -o locarnap_fit fit.o LocARNA/fitonoff.o  ./.libs/libLocARNA-2.0.a -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++
libtool: link: g++ -O2 -fPIC -o locarna_deviation deviation.o  ./.libs/libLocARNA-2.0.a -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -fPIC -static -lquadmath  -o locarna_rnafold_pp locarna_rnafold_pp.o libLocARNA-2.0.la -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
libtool: link: g++ -O2 -fPIC -o locarna_rnafold_pp locarna_rnafold_pp.o  ./.libs/libLocARNA-2.0.a -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -fPIC -static -lquadmath  -o exparna_p exparna_p.o libLocARNA-2.0.la -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
libtool: link: g++ -O2 -fPIC -o exparna_p exparna_p.o  ./.libs/libLocARNA-2.0.a -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -fPIC -static -lquadmath  -o sparse sparse.o libLocARNA-2.0.la -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
libtool: link: g++ -O2 -fPIC -o sparse sparse.o  ./.libs/libLocARNA-2.0.a -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -fPIC -static -lquadmath  -o locarna.bin locarna.o libLocARNA-2.0.la -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
libtool: link: g++ -O2 -fPIC -o locarna.bin locarna.o  ./.libs/libLocARNA-2.0.a -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++
/bin/sh ../libtool  --tag=CXX   --mode=link g++  -O2 -fPIC -static -lquadmath  -o locarna_p locarna_p.o libLocARNA-2.0.la -lquadmath   -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ 
libtool: link: g++ -O2 -fPIC -o locarna_p locarna_p.o  ./.libs/libLocARNA-2.0.a -lquadmath -lRNA -lgomp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
Making all in Tests
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/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 '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Tests'
make[4]: Nothing to be done for 'all-am'.
make[4]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Tests'
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Tests'
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
make[1]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
Making all in lib
make[1]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
Making all in perl
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
Making all in MLocarna
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl/MLocarna'
make[3]: Nothing to be done for 'all'.
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl/MLocarna'
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
make[3]: Nothing to be done for 'all-am'.
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
make[1]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
Making all in Doc
make[1]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
Making all in man
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc/man'
make[2]: Nothing to be done for 'all'.
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc/man'
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
make[2]: Nothing to be done for 'all-am'.
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
make[1]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
make[1]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1'
Making install in src
make[1]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
make  install-recursive
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
Making install in Utils
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Utils'
make[4]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Utils'
make[4]: Nothing to be done for 'install-data-am'.
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_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 locarna_mcc benchmark-plot.R '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin'
make[4]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Utils'
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Utils'
Making install in .
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
make[4]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64/pkgconfig'
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64'
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/include/LocARNA-2.0'
 /bin/sh ../libtool   --mode=install /usr/bin/ginstall -c   libLocARNA-2.0.la '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64'
 /usr/bin/ginstall -c -m 644 ../LocARNA-2.0.pc '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64/pkgconfig'
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/include/LocARNA-2.0/LocARNA'
 /usr/bin/ginstall -c -m 644  LocARNA/aligner.hh LocARNA/aligner_impl.hh LocARNA/aligner_n.hh LocARNA/aligner_p.hh LocARNA/aligner_p.icc LocARNA/aligner_params.hh LocARNA/aligner_restriction.hh LocARNA/alignment.hh LocARNA/alignment_impl.hh LocARNA/alphabet.hh LocARNA/alphabet.icc LocARNA/anchor_constraints.hh LocARNA/arc_matches.hh LocARNA/aux.hh LocARNA/base_pair_filter.hh LocARNA/basepairs.hh LocARNA/confusion_matrix.hh LocARNA/discrete_distribution.hh LocARNA/exact_matcher.hh LocARNA/ext_rna_data.hh LocARNA/ext_rna_data_impl.hh LocARNA/free_endgaps.hh LocARNA/global_stopwatch.hh LocARNA/infty_int.hh LocARNA/main_helper.icc LocARNA/edge_probs.hh LocARNA/edge_probs.icc LocARNA/matrices.hh LocARNA/matrix.hh LocARNA/mcc_matrices.hh LocARNA/multiple_alignment.hh LocARNA/named_arguments.hh LocARNA/options.hh LocARNA/pfold_params.hh LocARNA/quadmath.hh LocARNA/ribofit.hh LocARNA/ribofit_will2014.icc LocARNA/ribofit_will2014.ihh LocARNA/ribosum.hh LocARNA/ribosum85_60.icc '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/include/LocARNA-2.0/LocARNA'
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/include/LocARNA-2.0/LocARNA'
 /usr/bin/ginstall -c -m 644  LocARNA/rna_data.hh LocARNA/rna_data_impl.hh LocARNA/rna_ensemble.hh LocARNA/rna_ensemble_impl.hh LocARNA/rna_structure.hh LocARNA/scoring.hh LocARNA/scoring_fwd.hh LocARNA/sequence.hh LocARNA/sequence_annotation.hh LocARNA/sparse_matrix.hh LocARNA/sparse_vector.hh LocARNA/sparse_vector_base.hh LocARNA/sparsification_mapper.hh LocARNA/std_help_text.ihh LocARNA/stopwatch.hh LocARNA/stral_score.hh LocARNA/string1.hh LocARNA/trace_controller.hh LocARNA/tuples.hh LocARNA/zip.hh '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/include/LocARNA-2.0/LocARNA'
libtool: install: /usr/bin/ginstall -c .libs/libLocARNA-2.0.so.1.0.4 /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64/libLocARNA-2.0.so.1.0.4
libtool: install: (cd /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64 && { ln -s -f libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so.1 || { rm -f libLocARNA-2.0.so.1 && ln -s libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so.1; }; })
libtool: install: (cd /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64 && { ln -s -f libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so || { rm -f libLocARNA-2.0.so && ln -s libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so; }; })
libtool: install: /usr/bin/ginstall -c .libs/libLocARNA-2.0.lai /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64/libLocARNA-2.0.la
libtool: install: /usr/bin/ginstall -c .libs/libLocARNA-2.0.a /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64/libLocARNA-2.0.a
libtool: install: chmod 644 /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64/libLocARNA-2.0.a
libtool: install: ranlib /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib64/libLocARNA-2.0.a
libtool: warning: remember to run 'libtool --finish /usr/lib64'
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin'
  /bin/sh ../libtool   --mode=install /usr/bin/ginstall -c locarna.bin '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin/./locarna'
libtool: install: /usr/bin/ginstall -c locarna.bin /tmp/SBo/repo.fJNFLb/build_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 '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin'
libtool: install: /usr/bin/ginstall -c locarna_p /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin/locarna_p
libtool: install: /usr/bin/ginstall -c locarnap_fit /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin/locarnap_fit
libtool: install: /usr/bin/ginstall -c locarna_deviation /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin/locarna_deviation
libtool: install: /usr/bin/ginstall -c locarna_rnafold_pp /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin/locarna_rnafold_pp
libtool: install: /usr/bin/ginstall -c exparna_p /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin/exparna_p
libtool: install: /usr/bin/ginstall -c sparse /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin/sparse
libtool: install: /usr/bin/ginstall -c ribosum2cc /tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/bin/ribosum2cc
make[4]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
Making install in Tests
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Tests'
make  install-am
make[4]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Tests'
make[5]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/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 '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Tests'
make[4]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Tests'
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src/Tests'
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
make[1]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/src'
Making install in lib
make[1]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
Making install in perl
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
Making install in MLocarna
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl/MLocarna'
make[4]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl/MLocarna'
make[4]: Nothing to be done for 'install-exec-am'.
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib/perl/MLocarna'
 /usr/bin/ginstall -c SparseMatrix.pm Tree.pm MatchProbs.pm Aux.pm threaded.pm unthreaded.pm PairwiseAligners.pm NameNormalizer.pm '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib/perl/MLocarna'
make[4]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl/MLocarna'
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl/MLocarna'
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
make[4]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
make[4]: Nothing to be done for 'install-exec-am'.
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib/perl'
 /usr/bin/ginstall -c MLocarna.pm '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/lib/perl'
make[4]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib/perl'
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/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 '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
make[1]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/lib'
Making install in Doc
make[1]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
Making install in man
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc/man'
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc/man'
make[3]: Nothing to be done for 'install-exec-am'.
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_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_mcc.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 '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/man/man1'
make[3]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc/man'
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc/man'
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
make[3]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/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 '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
make[1]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1/Doc'
make[1]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1'
make[2]: Entering directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1'
make[2]: Nothing to be done for 'install-exec-am'.
 /usr/libexec/repo/mkdir -p '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/share/locarna/Matrices'
 /usr/bin/ginstall -c -m 644 Data/Matrices/RIBOSUM85_60 '/tmp/SBo/repo.fJNFLb/build_locarna/package-locarna/usr/share/locarna/Matrices'
make[2]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1'
make[1]: Leaving directory '/tmp/SBo/repo.fJNFLb/build_locarna/locarna-2.0.1'

Slackware package maker, version 3.14159265.

Searching for symbolic links:
usr/lib64/libLocARNA-2.0.so	libLocARNA-2.0.so.1.0.4
usr/lib64/libLocARNA-2.0.so.1	libLocARNA-2.0.so.1.0.4

Making symbolic link creation script:
( cd usr/lib64 ; rm -rf libLocARNA-2.0.so )
( cd usr/lib64 ; ln -sf libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so )
( cd usr/lib64 ; rm -rf libLocARNA-2.0.so.1 )
( cd usr/lib64 ; ln -sf libLocARNA-2.0.so.1.0.4 libLocARNA-2.0.so.1 )

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-2.0.so.1'
removed './usr/lib64/libLocARNA-2.0.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:  /tmp/SBo/repo.fJNFLb/output_locarna/locarna-2.0.1-x86_64-1_SBo.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/benchmark-plot.R
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_mcc
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-2.0.1/
usr/doc/locarna-2.0.1/AUTHORS
usr/doc/locarna-2.0.1/COPYING
usr/doc/locarna-2.0.1/ChangeLog.md
usr/doc/locarna-2.0.1/NEWS
usr/doc/locarna-2.0.1/README
usr/doc/locarna-2.0.1/TODO
usr/doc/locarna-2.0.1/locarna.SlackBuild
usr/include/
usr/include/LocARNA-2.0/
usr/include/LocARNA-2.0/LocARNA/
usr/include/LocARNA-2.0/LocARNA/aligner.hh
usr/include/LocARNA-2.0/LocARNA/aligner_impl.hh
usr/include/LocARNA-2.0/LocARNA/aligner_n.hh
usr/include/LocARNA-2.0/LocARNA/aligner_p.hh
usr/include/LocARNA-2.0/LocARNA/aligner_p.icc
usr/include/LocARNA-2.0/LocARNA/aligner_params.hh
usr/include/LocARNA-2.0/LocARNA/aligner_restriction.hh
usr/include/LocARNA-2.0/LocARNA/alignment.hh
usr/include/LocARNA-2.0/LocARNA/alignment_impl.hh
usr/include/LocARNA-2.0/LocARNA/alphabet.hh
usr/include/LocARNA-2.0/LocARNA/alphabet.icc
usr/include/LocARNA-2.0/LocARNA/anchor_constraints.hh
usr/include/LocARNA-2.0/LocARNA/arc_matches.hh
usr/include/LocARNA-2.0/LocARNA/aux.hh
usr/include/LocARNA-2.0/LocARNA/base_pair_filter.hh
usr/include/LocARNA-2.0/LocARNA/basepairs.hh
usr/include/LocARNA-2.0/LocARNA/confusion_matrix.hh
usr/include/LocARNA-2.0/LocARNA/discrete_distribution.hh
usr/include/LocARNA-2.0/LocARNA/edge_probs.hh
usr/include/LocARNA-2.0/LocARNA/edge_probs.icc
usr/include/LocARNA-2.0/LocARNA/exact_matcher.hh
usr/include/LocARNA-2.0/LocARNA/ext_rna_data.hh
usr/include/LocARNA-2.0/LocARNA/ext_rna_data_impl.hh
usr/include/LocARNA-2.0/LocARNA/free_endgaps.hh
usr/include/LocARNA-2.0/LocARNA/global_stopwatch.hh
usr/include/LocARNA-2.0/LocARNA/infty_int.hh
usr/include/LocARNA-2.0/LocARNA/main_helper.icc
usr/include/LocARNA-2.0/LocARNA/matrices.hh
usr/include/LocARNA-2.0/LocARNA/matrix.hh
usr/include/LocARNA-2.0/LocARNA/mcc_matrices.hh
usr/include/LocARNA-2.0/LocARNA/multiple_alignment.hh
usr/include/LocARNA-2.0/LocARNA/named_arguments.hh
usr/include/LocARNA-2.0/LocARNA/options.hh
usr/include/LocARNA-2.0/LocARNA/pfold_params.hh
usr/include/LocARNA-2.0/LocARNA/quadmath.hh
usr/include/LocARNA-2.0/LocARNA/ribofit.hh
usr/include/LocARNA-2.0/LocARNA/ribofit_will2014.icc
usr/include/LocARNA-2.0/LocARNA/ribofit_will2014.ihh
usr/include/LocARNA-2.0/LocARNA/ribosum.hh
usr/include/LocARNA-2.0/LocARNA/ribosum85_60.icc
usr/include/LocARNA-2.0/LocARNA/rna_data.hh
usr/include/LocARNA-2.0/LocARNA/rna_data_impl.hh
usr/include/LocARNA-2.0/LocARNA/rna_ensemble.hh
usr/include/LocARNA-2.0/LocARNA/rna_ensemble_impl.hh
usr/include/LocARNA-2.0/LocARNA/rna_structure.hh
usr/include/LocARNA-2.0/LocARNA/scoring.hh
usr/include/LocARNA-2.0/LocARNA/scoring_fwd.hh
usr/include/LocARNA-2.0/LocARNA/sequence.hh
usr/include/LocARNA-2.0/LocARNA/sequence_annotation.hh
usr/include/LocARNA-2.0/LocARNA/sparse_matrix.hh
usr/include/LocARNA-2.0/LocARNA/sparse_vector.hh
usr/include/LocARNA-2.0/LocARNA/sparse_vector_base.hh
usr/include/LocARNA-2.0/LocARNA/sparsification_mapper.hh
usr/include/LocARNA-2.0/LocARNA/std_help_text.ihh
usr/include/LocARNA-2.0/LocARNA/stopwatch.hh
usr/include/LocARNA-2.0/LocARNA/stral_score.hh
usr/include/LocARNA-2.0/LocARNA/string1.hh
usr/include/LocARNA-2.0/LocARNA/trace_controller.hh
usr/include/LocARNA-2.0/LocARNA/tuples.hh
usr/include/LocARNA-2.0/LocARNA/zip.hh
usr/lib/
usr/lib64/
usr/lib64/libLocARNA-2.0.a
usr/lib64/libLocARNA-2.0.so.1.0.4
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/NameNormalizer.pm
usr/lib64/perl5/vendor_perl/MLocarna/PairwiseAligners.pm
usr/lib64/perl5/vendor_perl/MLocarna/SparseMatrix.pm
usr/lib64/perl5/vendor_perl/MLocarna/Tree.pm
usr/lib64/perl5/vendor_perl/MLocarna/threaded.pm
usr/lib64/perl5/vendor_perl/MLocarna/unthreaded.pm
usr/lib64/pkgconfig/
usr/lib64/pkgconfig/LocARNA-2.0.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_mcc.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
WARNING:  zero length file usr/doc/locarna-2.0.1/NEWS

Slackware package /tmp/SBo/repo.fJNFLb/output_locarna/locarna-2.0.1-x86_64-1_SBo.txz created.

Built ok:  locarna-2.0.1-x86_64-1_SBo.txz                               13:02:13
Testing package locarna-2.0.1-x86_64-1_SBo.txz ... 
Test installing locarna-2.0.1-x86_64-1_SBo.txz ...
locarna-2.0.1-x86_64-1_SBo: Local RNA alignment on structural basis .... [  15M]
Unmounting chroot ... 
Backed up: locarna-1.9.2.3-x86_64-6_SBo.txz
:-) academic/locarna Updated for version 2.0.1 (-:

sbo-bot · 2026-01-13T13:02:45Z

sbopkglint x86_64 academic/locarna

Installing dependency: blas
blas-3.12.0-x86_64-1_SBo: Basic Linear Algebra Subprograms ............. [ 980K]

Installing dependency: lapack
lapack-3.12.0-x86_64-1_SBo: linear algebra routines .................... [  13M]

Installing dependency: lapacke
lapacke-3.12.0-x86_64-1_SBo: C interface to LAPACK ..................... [ 4.1M]

Installing dependency: ViennaRNA
ViennaRNA-2.7.2-x86_64-3_SBo: C Library ................................ [  97M]

Using tests from /usr/share/sbo-maintainer-tools/sbopkglint.d
Exploding /var/lib/repo/SBo/packages/15.0/x86_64/academic/locarna/locarna-2.0.1-x86_64-1_SBo.txz to /tmp/SBo/sbopkglint.Kb4p4P ...OK
Running pre-doinst test...OK
Installing /var/lib/repo/SBo/packages/15.0/x86_64/academic/locarna/locarna-2.0.1-x86_64-1_SBo.txz to /tmp/SBo/sbopkglint.Kb4p4P ...OK
Running test: 05-basic-sanity...
___ note: package contains empty dirs, are these necessary?
drwxr-xr-x 2 root root 6 Jan 13 13:02 ./usr/lib
OK
Running test: 10-docs...
--- empty files/dirs in doc dir:
-rw-r--r-- 1 root root 0 Oct  4  2022 usr/doc/locarna-2.0.1/NEWS
FAILED
Running test: 15-noarch...OK
Running test: 20-arch...
___ note: 64-bit x86_64 package contains /usr/lib; this may or may not be a problem.
OK
Running test: 25-lafiles...OK
Running test: 30-manpages...OK
Running test: 35-desktop...OK
Running test: 40-newconfig...OK
Running test: 45-doinst...OK
Running test: 50-icons...OK
Running test: 60-usr_info...OK
Running test: 65-python...OK
Running test: 70-tmp_path...OK
Running test: 75-static_libs...___ note: usr/lib64 has both libLocARNA-2.0.so and libLocARNA-2.0.a; unless it's needed by a dependee, consider removing libLocARNA-2.0.a

OK
Running test: 85-perl...OK
Running test: 90-terminfo...OK
⛔️ !!! locarna-2.0.1-x86_64-1_SBo.txz: 1 failures ⛔️

willysr · 2026-01-13T14:08:52Z

merged

academic/locarna/Upgrade to version 2.0.1

6b8e861

willysr changed the title ~~academic/locarna/Upgrade to version 2.0.1~~ academic/locarna: Upgrade to version 2.0.1 Jan 13, 2026

willysr closed this Jan 13, 2026

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academic/locarna: Upgrade to version 2.0.1 #13942

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reverse dependencies - academic/locarna

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✅ sbolint - academic/locarna ✅

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buildpkg i586 academic/locarna

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buildpkg x86_64 academic/locarna

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sbopkglint x86_64 academic/locarna

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