printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild viennarna 2>&1 The package 'viennarna' will be built without being installed. Reading build dependency for viennarna-1.8.5-205... Reading dependency for viennarna-1.8.5-205... Reading dependency for viennarna-dev-1.8.5-205... Reading build conflict for viennarna-1.8.5-205... The package 'gcc48' will be installed. Reading dependency for gcc48-4.8.3-1000... Reading runtime dependency for gcc48-4.8.3-1000... The package 'gcc48-shlibs' will be installed. Reading dependency for gcc48-shlibs-4.8.3-1000... Reading runtime dependency for gcc48-shlibs-4.8.3-1000... The package 'gcc48-compiler' will be installed. Reading dependency for gcc48-compiler-4.8.3-1000... Reading runtime dependency for gcc48-compiler-4.8.3-1000... The package 'gmp5-shlibs' will be installed. Reading dependency for gmp5-shlibs-6.0.0a-1... Reading runtime dependency for gmp5-shlibs-6.0.0a-1... The package 'libgmpxx5-shlibs' will be installed. Reading dependency for libgmpxx5-shlibs-6.0.0a-1... Reading runtime dependency for libgmpxx5-shlibs-6.0.0a-1... The package 'libmpfr4-shlibs' will be installed. Reading dependency for libmpfr4-shlibs-3.1.2-1... Reading runtime dependency for libmpfr4-shlibs-3.1.2-1... The package 'cloog-org2-shlibs' will be installed. Reading dependency for cloog-org2-shlibs-0.18.2-1... Reading runtime dependency for cloog-org2-shlibs-0.18.2-1... The package 'isl-shlibs' will be installed. Reading dependency for isl-shlibs-0.12.2-2... Reading runtime dependency for isl-shlibs-0.12.2-2... The package 'libmpc3-shlibs' will be installed. Reading dependency for libmpc3-shlibs-1.0.2-1... Reading runtime dependency for libmpc3-shlibs-1.0.2-1... The following package will be rebuilt: viennarna The following 9 additional packages will be installed: cloog-org2-shlibs gcc48 gcc48-compiler gcc48-shlibs gmp5-shlibs isl-shlibs libgmpxx5-shlibs libmpc3-shlibs libmpfr4-shlibs Do you want to continue? [Y/n] (assuming default) curl --connect-timeout 30 -f -L -A 'fink/0.37.0' -O http://distfiles.master.finkmirrors.net/distfiles/ViennaRNA-1.8.5.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 35 1276k 35 456k 0 0 526k 0 0:00:02 --:--:-- 0:00:02 526k 100 1276k 100 1276k 0 0 899k 0 0:00:01 0:00:01 --:--:-- 899k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb Selecting previously deselected package libgmpxx5-shlibs. (Reading database ... 4296 files and directories currently installed.) Unpacking libgmpxx5-shlibs (from .../libgmpxx5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Selecting previously deselected package gmp5-shlibs. Unpacking gmp5-shlibs (from .../gmp5-shlibs_6.0.0a-1_darwin-x86_64.deb) ... Setting up gmp5-shlibs (6.0.0a-1) ... Setting up libgmpxx5-shlibs (6.0.0a-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libmpfr4-shlibs_3.1.2-1_darwin-x86_64.deb Selecting previously deselected package libmpfr4-shlibs. (Reading database ... 4325 files and directories currently installed.) Unpacking libmpfr4-shlibs (from .../libmpfr4-shlibs_3.1.2-1_darwin-x86_64.deb) ... Setting up libmpfr4-shlibs (3.1.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/isl-shlibs_0.12.2-2_darwin-x86_64.deb Selecting previously deselected package isl-shlibs. (Reading database ... 4338 files and directories currently installed.) Unpacking isl-shlibs (from .../isl-shlibs_0.12.2-2_darwin-x86_64.deb) ... Setting up isl-shlibs (0.12.2-2) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libmpc3-shlibs_1.0.2-1_darwin-x86_64.deb Selecting previously deselected package libmpc3-shlibs. (Reading database ... 4339 files and directories currently installed.) Unpacking libmpc3-shlibs (from .../libmpc3-shlibs_1.0.2-1_darwin-x86_64.deb) ... Setting up libmpc3-shlibs (1.0.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/cloog-org2-shlibs_0.18.2-1_darwin-x86_64.deb Selecting previously deselected package cloog-org2-shlibs. (Reading database ... 4342 files and directories currently installed.) Unpacking cloog-org2-shlibs (from .../cloog-org2-shlibs_0.18.2-1_darwin-x86_64.deb) ... Setting up cloog-org2-shlibs (0.18.2-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/gcc48_4.8.3-1000_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc48-shlibs_4.8.3-1000_darwin-x86_64.deb /sw/fink/dists/stable/main/binary-darwin-x86_64/languages/gcc48-compiler_4.8.3-1000_darwin-x86_64.deb Selecting previously deselected package gcc48. (Reading database ... 4343 files and directories currently installed.) Unpacking gcc48 (from .../gcc48_4.8.3-1000_darwin-x86_64.deb) ... Selecting previously deselected package gcc48-shlibs. Unpacking gcc48-shlibs (from .../gcc48-shlibs_4.8.3-1000_darwin-x86_64.deb) ... Selecting previously deselected package gcc48-compiler. Unpacking gcc48-compiler (from .../gcc48-compiler_4.8.3-1000_darwin-x86_64.deb) ... Setting up gcc48-shlibs (4.8.3-1000) ... Clearing dependency_libs of .la files being installed Setting up gcc48-compiler (4.8.3-1000) ... Clearing dependency_libs of .la files being installed Setting up gcc48 (4.8.3-1000) ... * Classpath Tools: (cp-tools). GNU Classpath Tools Guide install-info(/sw/share/info/cp-tools.info): creating new section `GNU Libraries' * gcc: (gcc). The GNU Compiler Collection. install-info(/sw/share/info/gcc.info): replacing existing dir entry for `gcc' * gfortran: (gfortran). The GNU Fortran Compiler. * Cpp: (cpp). The GNU C preprocessor. install-info(/sw/share/info/cpp.info): replacing existing dir entry for `cpp' * gccinstall: (gccinstall). Installing the GNU Compiler Collection. install-info(/sw/share/info/gccinstall.info): replacing existing dir entry for `gccinstall' * libgomp: (libgomp). GNU OpenMP runtime library * Cpplib: (cppinternals). Cpplib internals. install-info(/sw/share/info/cppinternals.info): replacing existing dir entry for `cppinternals' * gccint: (gccint). Internals of the GNU Compiler Collection. install-info(/sw/share/info/gccint.info): replacing existing dir entry for `gccint' * Gcj: (gcj). Ahead-of-time compiler for the Java language Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-viennarna-1.8.5-205 /sw/build.build dpkg-deb: building package `fink-buildlock-viennarna-1.8.5-205' in `/sw/build.build/fink-buildlock-viennarna-1.8.5-205_2014.07.26-04.58.55_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-viennarna-1.8.5-205_2014.07.26-04.58.55_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-viennarna-1.8.5-205. (Reading database ... 9831 files and directories currently installed.) Unpacking fink-buildlock-viennarna-1.8.5-205 (from .../fink-buildlock-viennarna-1.8.5-205_2014.07.26-04.58.55_darwin-x86_64.deb) ... Setting up fink-buildlock-viennarna-1.8.5-205 (2014.07.26-04.58.55) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.2kXBb env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/ViennaRNA-1.8.5.tar.gz ViennaRNA-1.8.5/ ViennaRNA-1.8.5/config.sub ViennaRNA-1.8.5/configure ViennaRNA-1.8.5/acinclude.m4 ViennaRNA-1.8.5/Progs/ ViennaRNA-1.8.5/Progs/RNAfold.c ViennaRNA-1.8.5/Progs/Makefile.am ViennaRNA-1.8.5/Progs/RNAcofold.c ViennaRNA-1.8.5/Progs/RNAdistance.c ViennaRNA-1.8.5/Progs/Makefile.in ViennaRNA-1.8.5/Progs/RNAplfold.c ViennaRNA-1.8.5/Progs/RNAplot.c ViennaRNA-1.8.5/Progs/RNApaln.c ViennaRNA-1.8.5/Progs/RNALfold.c ViennaRNA-1.8.5/Progs/RNAaliduplex.c ViennaRNA-1.8.5/Progs/RNAinverse.c ViennaRNA-1.8.5/Progs/RNAalifold.c ViennaRNA-1.8.5/Progs/RNAduplex.c ViennaRNA-1.8.5/Progs/RNApdist.c ViennaRNA-1.8.5/Progs/RNAheat.c ViennaRNA-1.8.5/Progs/RNAeval.c ViennaRNA-1.8.5/Progs/RNAup.c ViennaRNA-1.8.5/Progs/RNAsubopt.c ViennaRNA-1.8.5/aclocal.m4 ViennaRNA-1.8.5/THANKS ViennaRNA-1.8.5/H/ ViennaRNA-1.8.5/H/fold.h ViennaRNA-1.8.5/H/ProfileAln.h ViennaRNA-1.8.5/H/inverse.h ViennaRNA-1.8.5/H/part_func_up.h ViennaRNA-1.8.5/H/Makefile.am ViennaRNA-1.8.5/H/params.h ViennaRNA-1.8.5/H/Makefile.in ViennaRNA-1.8.5/H/duplex.h ViennaRNA-1.8.5/H/LPfold.h ViennaRNA-1.8.5/H/utils.h ViennaRNA-1.8.5/H/alifold.h ViennaRNA-1.8.5/H/MEA.h ViennaRNA-1.8.5/H/treedist.h ViennaRNA-1.8.5/H/Lfold.h ViennaRNA-1.8.5/H/energy_par.h ViennaRNA-1.8.5/H/fold_vars.h ViennaRNA-1.8.5/H/findpath.h ViennaRNA-1.8.5/H/edit_cost.h ViennaRNA-1.8.5/H/cofold.h ViennaRNA-1.8.5/H/profiledist.h ViennaRNA-1.8.5/H/part_func.h ViennaRNA-1.8.5/H/part_func_co.h ViennaRNA-1.8.5/H/RNAstruct.h ViennaRNA-1.8.5/H/pair_mat.h ViennaRNA-1.8.5/H/ribo.h ViennaRNA-1.8.5/H/PS_dot.h ViennaRNA-1.8.5/H/aln_util.h ViennaRNA-1.8.5/H/subopt.h ViennaRNA-1.8.5/H/energy_const.h ViennaRNA-1.8.5/H/dist_vars.h ViennaRNA-1.8.5/H/stringdist.h ViennaRNA-1.8.5/Kinfold/ ViennaRNA-1.8.5/Kinfold/configure ViennaRNA-1.8.5/Kinfold/acinclude.m4 ViennaRNA-1.8.5/Kinfold/aclocal.m4 ViennaRNA-1.8.5/Kinfold/cmdline.h ViennaRNA-1.8.5/Kinfold/Makefile.am ViennaRNA-1.8.5/Kinfold/nachbar.h ViennaRNA-1.8.5/Kinfold/NEWS ViennaRNA-1.8.5/Kinfold/INSTALL ViennaRNA-1.8.5/Kinfold/globals.c ViennaRNA-1.8.5/Kinfold/ChangeLog ViennaRNA-1.8.5/Kinfold/main.c ViennaRNA-1.8.5/Kinfold/kinfold.ggo ViennaRNA-1.8.5/Kinfold/Example/ ViennaRNA-1.8.5/Kinfold/Example/Makefile.am ViennaRNA-1.8.5/Kinfold/Example/hpin.e.log ViennaRNA-1.8.5/Kinfold/Example/hpin.log ViennaRNA-1.8.5/Kinfold/Example/Makefile.in ViennaRNA-1.8.5/Kinfold/Example/hpin.nolp.log ViennaRNA-1.8.5/Kinfold/Example/traj.nolp ViennaRNA-1.8.5/Kinfold/Example/README ViennaRNA-1.8.5/Kinfold/Example/traj.ae ViennaRNA-1.8.5/Kinfold/Example/traj ViennaRNA-1.8.5/Kinfold/Example/hpin.in ViennaRNA-1.8.5/Kinfold/Example/hpin.ae.log ViennaRNA-1.8.5/Kinfold/Example/traj.e ViennaRNA-1.8.5/Kinfold/Makefile.in ViennaRNA-1.8.5/Kinfold/cache_util.h ViennaRNA-1.8.5/Kinfold/README ViennaRNA-1.8.5/Kinfold/globals.h ViennaRNA-1.8.5/Kinfold/AUTHORS ViennaRNA-1.8.5/Kinfold/Laplace/ ViennaRNA-1.8.5/Kinfold/Laplace/extract_data.pl ViennaRNA-1.8.5/Kinfold/Laplace/README ViennaRNA-1.8.5/Kinfold/Laplace/seq1_ref.ps ViennaRNA-1.8.5/Kinfold/Laplace/laplace.sh ViennaRNA-1.8.5/Kinfold/Laplace/to_boxplot.R ViennaRNA-1.8.5/Kinfold/Laplace/seq1 ViennaRNA-1.8.5/Kinfold/cache.c ViennaRNA-1.8.5/Kinfold/config.h.in ViennaRNA-1.8.5/Kinfold/cmdline.c ViennaRNA-1.8.5/Kinfold/COPYING ViennaRNA-1.8.5/Kinfold/configure.in ViennaRNA-1.8.5/Kinfold/nachbar.c ViennaRNA-1.8.5/Kinfold/baum.c ViennaRNA-1.8.5/Kinfold/baum.h ViennaRNA-1.8.5/install-sh ViennaRNA-1.8.5/Makefile.am ViennaRNA-1.8.5/vienna13.par ViennaRNA-1.8.5/NEWS ViennaRNA-1.8.5/compile ViennaRNA-1.8.5/INSTALL ViennaRNA-1.8.5/ViennaRNA.spec.in ViennaRNA-1.8.5/Readseq/ ViennaRNA-1.8.5/Readseq/nucleic.std ViennaRNA-1.8.5/Readseq/Readseq.help ViennaRNA-1.8.5/Readseq/ureadseq.c.orig ViennaRNA-1.8.5/Readseq/alphabet.std ViennaRNA-1.8.5/Readseq/ureadasn.c ViennaRNA-1.8.5/Readseq/multi.std ViennaRNA-1.8.5/Readseq/Readme ViennaRNA-1.8.5/Readseq/upper.std ViennaRNA-1.8.5/Readseq/readseq.c.orig ViennaRNA-1.8.5/Readseq/Formats ViennaRNA-1.8.5/Readseq/readseqSIOW.make ViennaRNA-1.8.5/Readseq/macinit.r ViennaRNA-1.8.5/Readseq/Make.com ViennaRNA-1.8.5/Readseq/Stdfiles ViennaRNA-1.8.5/Readseq/translate.patch ViennaRNA-1.8.5/Readseq/ureadseq.c ViennaRNA-1.8.5/Readseq/ureadseq.h ViennaRNA-1.8.5/Readseq/readseq.c ViennaRNA-1.8.5/Readseq/macinit.c ViennaRNA-1.8.5/Readseq/ureadseq.h.orig ViennaRNA-1.8.5/Readseq/Makefile ViennaRNA-1.8.5/Readseq/add.gdemenu ViennaRNA-1.8.5/Readseq/Make.ncbi ViennaRNA-1.8.5/ChangeLog ViennaRNA-1.8.5/Makefile.in ViennaRNA-1.8.5/missing ViennaRNA-1.8.5/README ViennaRNA-1.8.5/RNAforester/ ViennaRNA-1.8.5/RNAforester/configure ViennaRNA-1.8.5/RNAforester/aclocal.m4 ViennaRNA-1.8.5/RNAforester/TODO ViennaRNA-1.8.5/RNAforester/install-sh ViennaRNA-1.8.5/RNAforester/Makefile.am ViennaRNA-1.8.5/RNAforester/NEWS ViennaRNA-1.8.5/RNAforester/INSTALL ViennaRNA-1.8.5/RNAforester/ChangeLog ViennaRNA-1.8.5/RNAforester/src/ ViennaRNA-1.8.5/RNAforester/src/fold.h ViennaRNA-1.8.5/RNAforester/src/alignment.h ViennaRNA-1.8.5/RNAforester/src/ppforestsz.h ViennaRNA-1.8.5/RNAforester/src/pointer.c ViennaRNA-1.8.5/RNAforester/src/ppforestali.h ViennaRNA-1.8.5/RNAforester/src/rna_profile_alignment.cpp ViennaRNA-1.8.5/RNAforester/src/unpairs.c ViennaRNA-1.8.5/RNAforester/src/treeedit.h ViennaRNA-1.8.5/RNAforester/src/pairs.c ViennaRNA-1.8.5/RNAforester/src/Makefile.am ViennaRNA-1.8.5/RNAforester/src/rnaforestsz.cpp ViennaRNA-1.8.5/RNAforester/src/readgraph.c ViennaRNA-1.8.5/RNAforester/src/treeedit.t.cpp ViennaRNA-1.8.5/RNAforester/src/misc.h ViennaRNA-1.8.5/RNAforester/src/rnaforester_options.h ViennaRNA-1.8.5/RNAforester/src/Makefile.in ViennaRNA-1.8.5/RNAforester/src/rna_alphabet.h ViennaRNA-1.8.5/RNAforester/src/wmatch.c ViennaRNA-1.8.5/RNAforester/src/rna_alignment.cpp ViennaRNA-1.8.5/RNAforester/src/utils.h ViennaRNA-1.8.5/RNAforester/src/ppforest.t.cpp ViennaRNA-1.8.5/RNAforester/src/Arguments.cpp ViennaRNA-1.8.5/RNAforester/src/rna_algebra.cpp ViennaRNA-1.8.5/RNAforester/src/wmatch.h ViennaRNA-1.8.5/RNAforester/src/rnafuncs.cpp ViennaRNA-1.8.5/RNAforester/src/ppforestbase.h ViennaRNA-1.8.5/RNAforester/src/types.h ViennaRNA-1.8.5/RNAforester/src/graphtypes.h ViennaRNA-1.8.5/RNAforester/src/matrix.h ViennaRNA-1.8.5/RNAforester/src/rna_algebra.h ViennaRNA-1.8.5/RNAforester/src/main.cpp ViennaRNA-1.8.5/RNAforester/src/debug.h ViennaRNA-1.8.5/RNAforester/src/fold_vars.h ViennaRNA-1.8.5/RNAforester/src/rna_alignment.h ViennaRNA-1.8.5/RNAforester/src/match.defs ViennaRNA-1.8.5/RNAforester/src/rnaforest.h ViennaRNA-1.8.5/RNAforester/src/rna_profile_alignment.h ViennaRNA-1.8.5/RNAforester/src/term.c ViennaRNA-1.8.5/RNAforester/src/rnafuncs.h ViennaRNA-1.8.5/RNAforester/src/ppforestsz.t.cpp ViennaRNA-1.8.5/RNAforester/src/part_func.h ViennaRNA-1.8.5/RNAforester/src/glib.c ViennaRNA-1.8.5/RNAforester/src/progressive_align.h ViennaRNA-1.8.5/RNAforester/src/ppforest.h ViennaRNA-1.8.5/RNAforester/src/alignment.t.cpp ViennaRNA-1.8.5/RNAforester/src/progressive_align.cpp ViennaRNA-1.8.5/RNAforester/src/rnaforest.cpp ViennaRNA-1.8.5/RNAforester/src/algebra.h ViennaRNA-1.8.5/RNAforester/src/misc.t.cpp ViennaRNA-1.8.5/RNAforester/src/rnaforester_options.cpp ViennaRNA-1.8.5/RNAforester/src/ppforestbase.cpp ViennaRNA-1.8.5/RNAforester/src/Arguments.h ViennaRNA-1.8.5/RNAforester/src/rnaforestsz.h ViennaRNA-1.8.5/RNAforester/src/rna_alphabet.cpp ViennaRNA-1.8.5/RNAforester/mkinstalldirs ViennaRNA-1.8.5/RNAforester/Makefile.in ViennaRNA-1.8.5/RNAforester/missing ViennaRNA-1.8.5/RNAforester/README ViennaRNA-1.8.5/RNAforester/depcomp ViennaRNA-1.8.5/RNAforester/AUTHORS ViennaRNA-1.8.5/RNAforester/config.guess ViennaRNA-1.8.5/RNAforester/config.h.in ViennaRNA-1.8.5/RNAforester/COPYING ViennaRNA-1.8.5/RNAforester/configure.in ViennaRNA-1.8.5/RNAforester/man/ ViennaRNA-1.8.5/RNAforester/man/Makefile.am ViennaRNA-1.8.5/RNAforester/man/Makefile.in ViennaRNA-1.8.5/RNAforester/man/RNAforester.1 ViennaRNA-1.8.5/RNAforester/g2-0.70/ ViennaRNA-1.8.5/RNAforester/g2-0.70/config.sub ViennaRNA-1.8.5/RNAforester/g2-0.70/configure ViennaRNA-1.8.5/RNAforester/g2-0.70/g2.dsw ViennaRNA-1.8.5/RNAforester/g2-0.70/g2demo.dsp ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/ ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/pointer.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/simple_FIG.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/descrip.mms ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/demo_f.f ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/ ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/CVS/ ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/CVS/Root ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/CVS/Repository ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/CVS/Entries ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/Root ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/Repository ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/Template ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/CVS/Entries ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/xlink.opt ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/simple_PS.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/penguin.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/g2_splines_demo.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/g2_anim.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/Makefile.in ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/g2_arc.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/demo_cpp.cpp ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/g2_test.f ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/g2_test.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/simple_gd.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/simple_X11.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/Makefile ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/simple_win32.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/handles.c ViennaRNA-1.8.5/RNAforester/g2-0.70/demo/penguin.inc ViennaRNA-1.8.5/RNAforester/g2-0.70/TODO ViennaRNA-1.8.5/RNAforester/g2-0.70/descrip.mms ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/ ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/CVS/ ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/CVS/Root ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/CVS/Repository ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/CVS/Entries ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/Root ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/Repository ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/Template ViennaRNA-1.8.5/RNAforester/g2-0.70/CVS/Entries ViennaRNA-1.8.5/RNAforester/g2-0.70/install-sh ViennaRNA-1.8.5/RNAforester/g2-0.70/INSTALL ViennaRNA-1.8.5/RNAforester/g2-0.70/CHANGES ViennaRNA-1.8.5/RNAforester/g2-0.70/doc/ ViennaRNA-1.8.5/RNAforester/g2-0.70/doc/g2_main.dox ViennaRNA-1.8.5/RNAforester/g2-0.70/doc/CVS/ ViennaRNA-1.8.5/RNAforester/g2-0.70/doc/CVS/CVS/ ViennaRNA-1.8.5/RNAforester/g2-0.70/doc/CVS/CVS/Root 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ViennaRNA-1.8.5/lib/alicircfold.inc ViennaRNA-1.8.5/lib/energy_par.c ViennaRNA-1.8.5/lib/list.h ViennaRNA-1.8.5/lib/RNAstruct.c ViennaRNA-1.8.5/lib/aln_util.c ViennaRNA-1.8.5/man/ ViennaRNA-1.8.5/man/RNApdist.1.in ViennaRNA-1.8.5/man/RNAplot.1 ViennaRNA-1.8.5/man/RNAinverse.1 ViennaRNA-1.8.5/man/RNAup.1.in ViennaRNA-1.8.5/man/Makefile.am ViennaRNA-1.8.5/man/RNAalifold.1 ViennaRNA-1.8.5/man/RNAlib.texinfo ViennaRNA-1.8.5/man/RNAcofold.1.in ViennaRNA-1.8.5/man/RNAalifold.1.in ViennaRNA-1.8.5/man/RNAdistance.1 ViennaRNA-1.8.5/man/RNAplot.1.in ViennaRNA-1.8.5/man/RNAfold.1 ViennaRNA-1.8.5/man/RNAsubopt.1 ViennaRNA-1.8.5/man/RNAplfold.1.in ViennaRNA-1.8.5/man/Makefile.in ViennaRNA-1.8.5/man/texinfo.tex ViennaRNA-1.8.5/man/RNAheat.1.in ViennaRNA-1.8.5/man/RNAdistance.1.in ViennaRNA-1.8.5/man/RNAeval.1.in ViennaRNA-1.8.5/man/RNAaliduplex.1 ViennaRNA-1.8.5/man/RNALfold.1 ViennaRNA-1.8.5/man/RNAup.1 ViennaRNA-1.8.5/man/RNAinverse.1.in ViennaRNA-1.8.5/man/RNApdist.1 ViennaRNA-1.8.5/man/RNAaliduplex.1.in ViennaRNA-1.8.5/man/RNAeval.1 ViennaRNA-1.8.5/man/RNApaln.1.in ViennaRNA-1.8.5/man/RNAcofold.1 ViennaRNA-1.8.5/man/RNAduplex.1 ViennaRNA-1.8.5/man/RNALfold.1.in ViennaRNA-1.8.5/man/RNAlib.info ViennaRNA-1.8.5/man/RNAplfold.1 ViennaRNA-1.8.5/man/RNAsubopt.1.in ViennaRNA-1.8.5/man/RNAduplex.1.in ViennaRNA-1.8.5/man/RNAheat.1 ViennaRNA-1.8.5/man/RNAfold.1.in ViennaRNA-1.8.5/man/RNApaln.1 sudo -u fink-bld [ENV] sh -c /tmp/fink.IqKZ1 /tmp/fink.RtfbU # system-wide environment settings for zsh(1) if [ -x /usr/libexec/path_helper ]; then eval `/usr/libexec/path_helper -s` fi #!/bin/zsh -efv perl -pi -e 's|Version 1.6|Version 1.8|g' README perl -pi -e 's|Version 1.6|Version 1.8|g' man/RNAlib.texinfo sudo -u fink-bld [ENV] sh -c /tmp/fink.5blip /tmp/fink.OL1hu # system-wide environment settings for zsh(1) if [ -x /usr/libexec/path_helper ]; then eval `/usr/libexec/path_helper -s` fi #!/bin/zsh -efv export ARCHFLAGS='' ./configure --prefix=/sw --mandir=/sw/share/man --infodir=/sw/share/info CC=/sw/lib/gcc4.8/bin/gcc-fsf-4.8 CXX=/sw/lib/gcc4.8/bin/g++-fsf-4.8 CFLAGS="-I/sw/include" --prefix=/sw PerlCmd=/usr/bin/perl5.16 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking build system type... i386-apple-darwin13.3.0 checking host system type... i386-apple-darwin13.3.0 checking for gcc... /sw/lib/gcc4.8/bin/gcc-fsf-4.8 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /sw/lib/gcc4.8/bin/gcc-fsf-4.8 accepts -g... yes checking for /sw/lib/gcc4.8/bin/gcc-fsf-4.8 option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of /sw/lib/gcc4.8/bin/gcc-fsf-4.8... gcc3 checking whether /sw/lib/gcc4.8/bin/gcc-fsf-4.8 accepts -fpic... yes checking for a BSD-compatible install... /usr/bin/install -c checking for ranlib... ranlib checking whether /sw/lib/gcc4.8/bin/gcc-fsf-4.8 and cc understand -c and -o together... yes checking for perl... /usr/bin/perl5.16 checking how to run the C preprocessor... /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking malloc.h usability... no checking malloc.h presence... no checking for malloc.h... no checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... yes checking for inline... inline checking for strdup... yes checking for strstr... yes checking for strchr... yes checking for erand48... yes configure: creating ./config.status config.status: creating Makefile config.status: creating ViennaRNA.spec config.status: creating Utils/Makefile config.status: creating Progs/Makefile config.status: creating lib/Makefile config.status: creating man/Makefile config.status: creating Cluster/Makefile config.status: creating H/Makefile config.status: creating Perl/Makefile config.status: creating man/RNAheat.1 config.status: creating man/RNAsubopt.1 config.status: creating man/RNAdistance.1 config.status: creating man/RNAinverse.1 config.status: creating man/RNAeval.1 config.status: creating man/RNAfold.1 config.status: creating man/RNApdist.1 config.status: creating man/RNAplot.1 config.status: creating man/RNALfold.1 config.status: creating man/RNAalifold.1 config.status: creating man/RNAduplex.1 config.status: creating man/RNAcofold.1 config.status: creating man/RNAplfold.1 config.status: creating man/RNAup.1 config.status: creating man/RNApaln.1 config.status: creating man/RNAaliduplex.1 config.status: creating config.h config.status: executing depfiles commands === configuring in RNAforester (/sw/build.build/viennarna-1.8.5-205/ViennaRNA-1.8.5/RNAforester) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/sw' '--mandir=/sw/share/man' '--infodir=/sw/share/info' 'CC=/sw/lib/gcc4.8/bin/gcc-fsf-4.8' 'CXX=/sw/lib/gcc4.8/bin/g++-fsf-4.8' 'CFLAGS=-I/sw/include' 'PerlCmd=/usr/bin/perl5.16' 'LDFLAGS=-L/sw/lib' 'CPPFLAGS=-I/sw/include' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether /sw/lib/gcc4.8/bin/g++-fsf-4.8 accepts -g... yes checking for style of include used by make... GNU checking dependency style of /sw/lib/gcc4.8/bin/g++-fsf-4.8... gcc3 checking for gcc... /sw/lib/gcc4.8/bin/gcc-fsf-4.8 checking whether we are using the GNU C compiler... yes checking whether /sw/lib/gcc4.8/bin/gcc-fsf-4.8 accepts -g... yes checking for /sw/lib/gcc4.8/bin/gcc-fsf-4.8 option to accept ISO C89... none needed checking dependency style of /sw/lib/gcc4.8/bin/gcc-fsf-4.8... gcc3 using (to be built) libRNA.a in ../lib checking for main in -lgd... no checking how to run the C++ preprocessor... /sw/lib/gcc4.8/bin/g++-fsf-4.8 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... no checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking g2.h usability... yes checking g2.h presence... yes checking for g2.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... yes configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in g2-0.70 (/sw/build.build/viennarna-1.8.5-205/ViennaRNA-1.8.5/RNAforester/g2-0.70) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/sw' '--mandir=/sw/share/man' '--infodir=/sw/share/info' 'CC=/sw/lib/gcc4.8/bin/gcc-fsf-4.8' 'CXX=/sw/lib/gcc4.8/bin/g++-fsf-4.8' 'CFLAGS=-I/sw/include' 'PerlCmd=/usr/bin/perl5.16' 'LDFLAGS=-L/sw/lib' 'CPPFLAGS=-I/sw/include' --cache-file=/dev/null --srcdir=. checking build system type... i686-apple-darwin13.3.0 checking host system type... i686-apple-darwin13.3.0 checking for gcc... /sw/lib/gcc4.8/bin/gcc-fsf-4.8 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /sw/lib/gcc4.8/bin/gcc-fsf-4.8 accepts -g... yes checking for /sw/lib/gcc4.8/bin/gcc-fsf-4.8 option to accept ISO C89... none needed checking how to run the C preprocessor... /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -E checking whether we are using the GNU C++ compiler... yes checking whether /sw/lib/gcc4.8/bin/g++-fsf-4.8 accepts -g... yes checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking for find... find checking for makedepend... makedepend checking for dlopen in -ldl... yes checking for X... libraries /usr/X11/lib, headers /usr/X11/include checking whether -R must be followed by a space... neither works checking for gethostbyname... yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for main in -lm... yes checking for main in -lX11... yes checking for main in -lgd... no checking host system type... (cached) i686-apple-darwin13.3.0 checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes configure: creating ./config.status config.status: creating Makefile config.status: creating demo/Makefile config.status: creating g2_perl/Makefile.PL Supported devices: PostScript FIG X11 Unsupported devices: Win32 GD Run 'make depend' to create dependencies. === configuring in Kinfold (/sw/build.build/viennarna-1.8.5-205/ViennaRNA-1.8.5/Kinfold) configure: running /bin/sh ./configure --disable-option-checking '--prefix=/sw' '--mandir=/sw/share/man' '--infodir=/sw/share/info' 'CC=/sw/lib/gcc4.8/bin/gcc-fsf-4.8' 'CXX=/sw/lib/gcc4.8/bin/g++-fsf-4.8' 'CFLAGS=-I/sw/include' 'PerlCmd=/usr/bin/perl5.16' 'LDFLAGS=-L/sw/lib' 'CPPFLAGS=-I/sw/include' --cache-file=/dev/null --srcdir=. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... ./../install-sh -c -d checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking if malloc debugging is wanted... no checking for gcc... /sw/lib/gcc4.8/bin/gcc-fsf-4.8 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /sw/lib/gcc4.8/bin/gcc-fsf-4.8 accepts -g... yes checking for /sw/lib/gcc4.8/bin/gcc-fsf-4.8 option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of /sw/lib/gcc4.8/bin/gcc-fsf-4.8... gcc3 checking build system type... i386-apple-darwin13.3.0 checking host system type... i386-apple-darwin13.3.0 checking for strdup... yes checking for memset... yes checking for strchr... yes checking for ViennaRNA package... headers in "../H" and library... "../lib" checking how to run the C preprocessor... /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking fold.h usability... yes checking fold.h presence... yes checking for fold.h... yes checking for exp in -lm... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible realloc... yes checking for an ANSI C-conforming const... yes configure: creating ./config.status config.status: creating Example/Makefile config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands configure: Configure successful with the following options: Perl Extension: yes Analyse{Dists,Seqs}: no Kinfold: yes RNAforester: yes Files will be installed in the following directories: Executables: /sw/bin Libraries: /sw/lib Header files: /sw/include Extra Data: ${prefix}/share Man pages: /sw/share/man make /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in lib /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-dist_vars.o -MD -MP -MF .deps/libRNA_a-dist_vars.Tpo -c -o libRNA_a-dist_vars.o `test -f 'dist_vars.c' || echo './'`dist_vars.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-fold_vars.o -MD -MP -MF .deps/libRNA_a-fold_vars.Tpo -c -o libRNA_a-fold_vars.o `test -f 'fold_vars.c' || echo './'`fold_vars.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-part_func.o -MD -MP -MF .deps/libRNA_a-part_func.Tpo -c -o libRNA_a-part_func.o `test -f 'part_func.c' || echo './'`part_func.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-read_epars.o -MD -MP -MF .deps/libRNA_a-read_epars.Tpo -c -o libRNA_a-read_epars.o `test -f 'read_epars.c' || echo './'`read_epars.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-treedist.o -MD -MP -MF .deps/libRNA_a-treedist.Tpo -c -o libRNA_a-treedist.o `test -f 'treedist.c' || echo './'`treedist.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-energy_par.o -MD -MP -MF .deps/libRNA_a-energy_par.Tpo -c -o libRNA_a-energy_par.o `test -f 'energy_par.c' || echo './'`energy_par.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-inverse.o -MD -MP -MF .deps/libRNA_a-inverse.Tpo -c -o libRNA_a-inverse.o `test -f 'inverse.c' || echo './'`inverse.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-ProfileDist.o -MD -MP -MF .deps/libRNA_a-ProfileDist.Tpo -c -o libRNA_a-ProfileDist.o `test -f 'ProfileDist.c' || echo './'`ProfileDist.c mv -f .deps/libRNA_a-dist_vars.Tpo .deps/libRNA_a-dist_vars.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-RNAstruct.o -MD -MP -MF .deps/libRNA_a-RNAstruct.Tpo -c -o libRNA_a-RNAstruct.o `test -f 'RNAstruct.c' || echo './'`RNAstruct.c mv -f .deps/libRNA_a-fold_vars.Tpo .deps/libRNA_a-fold_vars.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-utils.o -MD -MP -MF .deps/libRNA_a-utils.Tpo -c -o libRNA_a-utils.o `test -f 'utils.c' || echo './'`utils.c inverse.c: In function 'pf_cost': inverse.c:488:4: warning: passing argument 1 of 'pf_fold' discards 'const' qualifier from pointer target type [enabled by default] f = pf_fold(string, structure); ^ In file included from inverse.c:20:0: ./../H/part_func.h:6:15: note: expected 'char *' but argument is of type 'const char *' extern float pf_fold(char *sequence, char *structure); ^ mv -f .deps/libRNA_a-ProfileDist.Tpo .deps/libRNA_a-ProfileDist.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-fold.o -MD -MP -MF .deps/libRNA_a-fold.Tpo -c -o libRNA_a-fold.o `test -f 'fold.c' || echo './'`fold.c mv -f .deps/libRNA_a-treedist.Tpo .deps/libRNA_a-treedist.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-naview.o -MD -MP -MF .deps/libRNA_a-naview.Tpo -c -o libRNA_a-naview.o `test -f 'naview.c' || echo './'`naview.c mv -f .deps/libRNA_a-inverse.Tpo .deps/libRNA_a-inverse.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-PS_dot.o -MD -MP -MF .deps/libRNA_a-PS_dot.Tpo -c -o libRNA_a-PS_dot.o `test -f 'PS_dot.c' || echo './'`PS_dot.c mv -f .deps/libRNA_a-read_epars.Tpo .deps/libRNA_a-read_epars.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-stringdist.o -MD -MP -MF .deps/libRNA_a-stringdist.Tpo -c -o libRNA_a-stringdist.o `test -f 'stringdist.c' || echo './'`stringdist.c mv -f .deps/libRNA_a-utils.Tpo .deps/libRNA_a-utils.Po mv -f .deps/libRNA_a-RNAstruct.Tpo .deps/libRNA_a-RNAstruct.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-params.o -MD -MP -MF .deps/libRNA_a-params.Tpo -c -o libRNA_a-params.o `test -f 'params.c' || echo './'`params.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-subopt.o -MD -MP -MF .deps/libRNA_a-subopt.Tpo -c -o libRNA_a-subopt.o `test -f 'subopt.c' || echo './'`subopt.c stringdist.c:24:0: warning: "INFINITY" redefined [enabled by default] #define INFINITY 10000 ^ In file included from stringdist.c:12:0: /sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/include-fixed/math.h:83:0: note: this is the location of the previous definition #define INFINITY HUGE_VALF ^ mv -f .deps/libRNA_a-energy_par.Tpo .deps/libRNA_a-energy_par.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-list.o -MD -MP -MF .deps/libRNA_a-list.Tpo -c -o libRNA_a-list.o `test -f 'list.c' || echo './'`list.c mv -f .deps/libRNA_a-stringdist.Tpo .deps/libRNA_a-stringdist.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-Lfold.o -MD -MP -MF .deps/libRNA_a-Lfold.Tpo -c -o libRNA_a-Lfold.o `test -f 'Lfold.c' || echo './'`Lfold.c mv -f .deps/libRNA_a-params.Tpo .deps/libRNA_a-params.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-cofold.o -MD -MP -MF .deps/libRNA_a-cofold.Tpo -c -o libRNA_a-cofold.o `test -f 'cofold.c' || echo './'`cofold.c mv -f .deps/libRNA_a-naview.Tpo .deps/libRNA_a-naview.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-part_func_co.o -MD -MP -MF .deps/libRNA_a-part_func_co.Tpo -c -o libRNA_a-part_func_co.o `test -f 'part_func_co.c' || echo './'`part_func_co.c mv -f .deps/libRNA_a-list.Tpo .deps/libRNA_a-list.Po mv -f .deps/libRNA_a-part_func.Tpo .deps/libRNA_a-part_func.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-ProfileAln.o -MD -MP -MF .deps/libRNA_a-ProfileAln.Tpo -c -o libRNA_a-ProfileAln.o `test -f 'ProfileAln.c' || echo './'`ProfileAln.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-duplex.o -MD -MP -MF .deps/libRNA_a-duplex.Tpo -c -o libRNA_a-duplex.o `test -f 'duplex.c' || echo './'`duplex.c mv -f .deps/libRNA_a-PS_dot.Tpo .deps/libRNA_a-PS_dot.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-alifold.o -MD -MP -MF .deps/libRNA_a-alifold.Tpo -c -o libRNA_a-alifold.o `test -f 'alifold.c' || echo './'`alifold.c mv -f .deps/libRNA_a-subopt.Tpo .deps/libRNA_a-subopt.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-alipfold.o -MD -MP -MF .deps/libRNA_a-alipfold.Tpo -c -o libRNA_a-alipfold.o `test -f 'alipfold.c' || echo './'`alipfold.c duplex.c: In function 'aliduplexfold': duplex.c:385:3: warning: passing argument 3 of 'alibacktrack' from incompatible pointer type [enabled by default] struc = alibacktrack(i_min, j_min, S1, S2); ^ duplex.c:37:16: note: expected 'const short int **' but argument is of type 'short int **' PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]); ^ duplex.c:385:3: warning: passing argument 4 of 'alibacktrack' from incompatible pointer type [enabled by default] struc = alibacktrack(i_min, j_min, S1, S2); ^ duplex.c:37:16: note: expected 'const short int **' but argument is of type 'short int **' PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]); ^ duplex.c: In function 'aliduplex_subopt': duplex.c:462:7: warning: passing argument 3 of 'alibacktrack' from incompatible pointer type [enabled by default] struc = alibacktrack(i,j,S1,S2); ^ duplex.c:37:16: note: expected 'const short int **' but argument is of type 'short int **' PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]); ^ duplex.c:462:7: warning: passing argument 4 of 'alibacktrack' from incompatible pointer type [enabled by default] struc = alibacktrack(i,j,S1,S2); ^ duplex.c:37:16: note: expected 'const short int **' but argument is of type 'short int **' PRIVATE char * alibacktrack(int i, int j, const short *S1[], const short *S2[]); ^ alifold.c: In function 'make_pscores': alifold.c:722:5: warning: passing argument 1 of 'get_ribosum' from incompatible pointer type [enabled by default] else dm=get_ribosum(AS,n_seq,n); ^ In file included from alifold.c:23:0: ./../H/ribo.h:1:16: note: expected 'char **' but argument is of type 'const char * const*' extern float **get_ribosum(char *Alseq[], int n_seq, int length); ^ alipfold.c: In function 'make_pscores': alipfold.c:1154:5: warning: passing argument 1 of 'get_ribosum' from incompatible pointer type [enabled by default] else dm=get_ribosum(AS,n_seq,n); ^ In file included from alipfold.c:22:0: ./../H/ribo.h:1:16: note: expected 'char **' but argument is of type 'const char * const*' extern float **get_ribosum(char *Alseq[], int n_seq, int length); ^ mv -f .deps/libRNA_a-ProfileAln.Tpo .deps/libRNA_a-ProfileAln.Po mv -f .deps/libRNA_a-fold.Tpo .deps/libRNA_a-fold.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-aln_util.o -MD -MP -MF .deps/libRNA_a-aln_util.Tpo -c -o libRNA_a-aln_util.o `test -f 'aln_util.c' || echo './'`aln_util.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-LPfold.o -MD -MP -MF .deps/libRNA_a-LPfold.Tpo -c -o libRNA_a-LPfold.o `test -f 'LPfold.c' || echo './'`LPfold.c mv -f .deps/libRNA_a-Lfold.Tpo .deps/libRNA_a-Lfold.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-part_func_up.o -MD -MP -MF .deps/libRNA_a-part_func_up.Tpo -c -o libRNA_a-part_func_up.o `test -f 'part_func_up.c' || echo './'`part_func_up.c mv -f .deps/libRNA_a-duplex.Tpo .deps/libRNA_a-duplex.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-ribo.o -MD -MP -MF .deps/libRNA_a-ribo.Tpo -c -o libRNA_a-ribo.o `test -f 'ribo.c' || echo './'`ribo.c mv -f .deps/libRNA_a-aln_util.Tpo .deps/libRNA_a-aln_util.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-findpath.o -MD -MP -MF .deps/libRNA_a-findpath.Tpo -c -o libRNA_a-findpath.o `test -f 'findpath.c' || echo './'`findpath.c mv -f .deps/libRNA_a-cofold.Tpo .deps/libRNA_a-cofold.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -fpic -I/sw/include -MT libRNA_a-MEA.o -MD -MP -MF .deps/libRNA_a-MEA.Tpo -c -o libRNA_a-MEA.o `test -f 'MEA.c' || echo './'`MEA.c mv -f .deps/libRNA_a-part_func_co.Tpo .deps/libRNA_a-part_func_co.Po mv -f .deps/libRNA_a-findpath.Tpo .deps/libRNA_a-findpath.Po mv -f .deps/libRNA_a-alifold.Tpo .deps/libRNA_a-alifold.Po mv -f .deps/libRNA_a-ribo.Tpo .deps/libRNA_a-ribo.Po mv -f .deps/libRNA_a-LPfold.Tpo .deps/libRNA_a-LPfold.Po mv -f .deps/libRNA_a-alipfold.Tpo .deps/libRNA_a-alipfold.Po mv -f .deps/libRNA_a-part_func_up.Tpo .deps/libRNA_a-part_func_up.Po mv -f .deps/libRNA_a-MEA.Tpo .deps/libRNA_a-MEA.Po rm -f libRNA.a ar cru libRNA.a libRNA_a-dist_vars.o libRNA_a-fold_vars.o libRNA_a-part_func.o libRNA_a-read_epars.o libRNA_a-treedist.o libRNA_a-energy_par.o libRNA_a-inverse.o libRNA_a-ProfileDist.o libRNA_a-RNAstruct.o libRNA_a-utils.o libRNA_a-fold.o libRNA_a-naview.o libRNA_a-PS_dot.o libRNA_a-stringdist.o libRNA_a-params.o libRNA_a-subopt.o libRNA_a-list.o libRNA_a-Lfold.o libRNA_a-cofold.o libRNA_a-part_func_co.o libRNA_a-ProfileAln.o libRNA_a-duplex.o libRNA_a-alifold.o libRNA_a-alipfold.o libRNA_a-aln_util.o libRNA_a-LPfold.o libRNA_a-part_func_up.o libRNA_a-ribo.o libRNA_a-findpath.o libRNA_a-MEA.o ranlib libRNA.a Making all in Progs /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAfold.o -MD -MP -MF .deps/RNAfold.Tpo -c -o RNAfold.o RNAfold.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAeval.o -MD -MP -MF .deps/RNAeval.Tpo -c -o RNAeval.o RNAeval.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAheat.o -MD -MP -MF .deps/RNAheat.Tpo -c -o RNAheat.o RNAheat.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNApdist.o -MD -MP -MF .deps/RNApdist.Tpo -c -o RNApdist.o RNApdist.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAdistance.o -MD -MP -MF .deps/RNAdistance.Tpo -c -o RNAdistance.o RNAdistance.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAinverse.o -MD -MP -MF .deps/RNAinverse.Tpo -c -o RNAinverse.o RNAinverse.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAplot.o -MD -MP -MF .deps/RNAplot.Tpo -c -o RNAplot.o RNAplot.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAsubopt.o -MD -MP -MF .deps/RNAsubopt.Tpo -c -o RNAsubopt.o RNAsubopt.c RNAinverse.c:31:0: warning: "INFINITY" redefined [enabled by default] #define INFINITY 100000 ^ In file included from RNAinverse.c:9:0: /sw/lib/gcc4.8/lib/gcc/x86_64-apple-darwin13.3.0/4.8.3/include-fixed/math.h:83:0: note: this is the location of the previous definition #define INFINITY HUGE_VALF ^ mv -f .deps/RNAplot.Tpo .deps/RNAplot.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNALfold.o -MD -MP -MF .deps/RNALfold.Tpo -c -o RNALfold.o RNALfold.c mv -f .deps/RNAeval.Tpo .deps/RNAeval.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAcofold.o -MD -MP -MF .deps/RNAcofold.Tpo -c -o RNAcofold.o RNAcofold.c mv -f .deps/RNApdist.Tpo .deps/RNApdist.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNApaln.o -MD -MP -MF .deps/RNApaln.Tpo -c -o RNApaln.o RNApaln.c mv -f .deps/RNAheat.Tpo .deps/RNAheat.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAduplex.o -MD -MP -MF .deps/RNAduplex.Tpo -c -o RNAduplex.o RNAduplex.c mv -f .deps/RNAsubopt.Tpo .deps/RNAsubopt.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAalifold.o -MD -MP -MF .deps/RNAalifold.Tpo -c -o RNAalifold.o RNAalifold.c mv -f .deps/RNAfold.Tpo .deps/RNAfold.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAplfold.o -MD -MP -MF .deps/RNAplfold.Tpo -c -o RNAplfold.o RNAplfold.c mv -f .deps/RNAinverse.Tpo .deps/RNAinverse.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAup.o -MD -MP -MF .deps/RNAup.Tpo -c -o RNAup.o RNAup.c mv -f .deps/RNAdistance.Tpo .deps/RNAdistance.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT RNAaliduplex.o -MD -MP -MF .deps/RNAaliduplex.Tpo -c -o RNAaliduplex.o RNAaliduplex.c mv -f .deps/RNALfold.Tpo .deps/RNALfold.Po RNAaliduplex.c: In function 'main': RNAaliduplex.c:128:5: warning: passing argument 1 of 'aliduplex_subopt' from incompatible pointer type [enabled by default] subopt = aliduplex_subopt(AS1, AS2, delta, 5); ^ In file included from RNAaliduplex.c:14:0: ./../H/duplex.h:14:17: note: expected 'const char **' but argument is of type 'char **' extern duplexT *aliduplex_subopt(const char *s1[], const char *s2[], int delta, int w); ^ RNAaliduplex.c:128:5: warning: passing argument 2 of 'aliduplex_subopt' from incompatible pointer type [enabled by default] subopt = aliduplex_subopt(AS1, AS2, delta, 5); ^ In file included from RNAaliduplex.c:14:0: ./../H/duplex.h:14:17: note: expected 'const char **' but argument is of type 'char **' extern duplexT *aliduplex_subopt(const char *s1[], const char *s2[], int delta, int w); ^ RNAaliduplex.c:135:5: warning: passing argument 1 of 'aliduplexfold' from incompatible pointer type [enabled by default] mfe = aliduplexfold(AS1, AS2); ^ RNAaliduplex.c:22:16: note: expected 'const char **' but argument is of type 'char **' extern duplexT aliduplexfold(const char *s1[], const char *s2[]); ^ RNAaliduplex.c:135:5: warning: passing argument 2 of 'aliduplexfold' from incompatible pointer type [enabled by default] mfe = aliduplexfold(AS1, AS2); ^ RNAaliduplex.c:22:16: note: expected 'const char **' but argument is of type 'char **' extern duplexT aliduplexfold(const char *s1[], const char *s2[]); ^ /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAfold RNAfold.o ../lib/libRNA.a -lm mv -f .deps/RNAduplex.Tpo .deps/RNAduplex.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAeval RNAeval.o ../lib/libRNA.a -lm mv -f .deps/RNApaln.Tpo .deps/RNApaln.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAheat RNAheat.o ../lib/libRNA.a -lm mv -f .deps/RNAaliduplex.Tpo .deps/RNAaliduplex.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNApdist RNApdist.o ../lib/libRNA.a -lm mv -f .deps/RNAplfold.Tpo .deps/RNAplfold.Po mv -f .deps/RNAcofold.Tpo .deps/RNAcofold.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAdistance RNAdistance.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAinverse RNAinverse.o ../lib/libRNA.a -lm mv -f .deps/RNAalifold.Tpo .deps/RNAalifold.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAplot RNAplot.o ../lib/libRNA.a -lm mv -f .deps/RNAup.Tpo .deps/RNAup.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAsubopt RNAsubopt.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNALfold RNALfold.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAcofold RNAcofold.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAplfold RNAplfold.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAup RNAup.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAalifold RNAalifold.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAduplex RNAduplex.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNApaln RNApaln.o ../lib/libRNA.a -lm /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o RNAaliduplex RNAaliduplex.o ../lib/libRNA.a -lm Making all in man restore=: && backupdir=".am$$" && \ am__cwd=`pwd` && CDPATH="${ZSH_VERSION+.}:" && cd . && \ rm -rf $backupdir && mkdir $backupdir && \ if (/bin/sh /sw/build.build/viennarna-1.8.5-205/ViennaRNA-1.8.5/missing --run makeinfo --version) >/dev/null 2>&1; then \ for f in RNAlib.info RNAlib.info-[0-9] RNAlib.info-[0-9][0-9] RNAlib.i[0-9] RNAlib.i[0-9][0-9]; do \ if test -f $f; then mv $f $backupdir; restore=mv; else :; fi; \ done; \ else :; fi && \ cd "$am__cwd"; \ if /bin/sh /sw/build.build/viennarna-1.8.5-205/ViennaRNA-1.8.5/missing --run makeinfo -I . \ -o RNAlib.info RNAlib.texinfo; \ then \ rc=0; \ CDPATH="${ZSH_VERSION+.}:" && cd .; \ else \ rc=$?; \ CDPATH="${ZSH_VERSION+.}:" && cd . && \ $restore $backupdir/* `echo "./RNAlib.info" | sed 's|[^/]*$||'`; \ fi; \ rm -rf $backupdir; exit $rc Making all in Utils /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT b2ct.o -MD -MP -MF .deps/b2ct.Tpo -c -o b2ct.o b2ct.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I./../H -I/sw/include -I/sw/include -MT popt.o -MD -MP -MF .deps/popt.Tpo -c -o popt.o popt.c if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' b2mt.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' ct2b.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' dpzoom.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' mountain.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' relplot.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' rotate_ss.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' cmount.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' colorrna.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' coloraln.pl ; \ fi if test -n "/usr/bin/perl5.16"; then \ /usr/bin/perl5.16 -npi -e 's|^#!\S+|#!/usr/bin/perl5.16|' refold.pl ; \ fi mv -f .deps/popt.Tpo .deps/popt.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o popt popt.o -L../lib -lRNA -lm mv -f .deps/b2ct.Tpo .deps/b2ct.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L/sw/lib -o b2ct b2ct.o -L../lib -lRNA -lm Making all in H make[2]: Nothing to be done for `all'. Making all in Perl /usr/bin/perl5.16 Makefile.PL Writing Makefile.perl for RNA Writing MYMETA.yml and MYMETA.json /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.perl cc -c -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -I/usr/local/include -Os -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" "-I/System/Library/Perl/5.16/darwin-thread-multi-2level/CORE" RNA_wrap.c Running Mkbootstrap for RNA () chmod 644 RNA.bs cp RNA.bs blib/arch/auto/RNA/RNA.bs chmod 644 blib/arch/auto/RNA/RNA.bs cp RNA.pm blib/lib/RNA.pm In file included from RNA_wrap.c:1547: ./../H/part_func_co.h:26:16: warning: declaration of 'struct plist' will not be visible outside of this function [-Wvisibility] struct plist *prAB, ^ 1 warning generated. rm -f blib/arch/auto/RNA/RNA.bundle LD_RUN_PATH="/usr/lib" cc -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup -L/usr/local/lib -fstack-protector RNA_wrap.o -o blib/arch/auto/RNA/RNA.bundle ../lib/libRNA.a \ -lm \ ld: warning: directory not found for option '-L/usr/local/lib' chmod 755 blib/arch/auto/RNA/RNA.bundle Manifying blib/man3/RNA.3pm Making all in RNAforester /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in g2-0.70 /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I./src -I/sw/include -I/usr/X11/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o ar -cr libg2.a ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o test ! -n "ranlib" || ranlib libg2.a test -d ./include || mkdir ./include cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./include/ Making all in src /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT Arguments.o -MD -MP -MF .deps/Arguments.Tpo -c -o Arguments.o Arguments.cpp /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -I/sw/include -MT glib.o -MD -MP -MF .deps/glib.Tpo -c -o glib.o glib.c /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT ppforestbase.o -MD -MP -MF .deps/ppforestbase.Tpo -c -o ppforestbase.o ppforestbase.cpp /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT progressive_align.o -MD -MP -MF .deps/progressive_align.Tpo -c -o progressive_align.o progressive_align.cpp /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT rna_profile_alignment.o -MD -MP -MF .deps/rna_profile_alignment.Tpo -c -o rna_profile_alignment.o rna_profile_alignment.cpp /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT rna_alignment.o -MD -MP -MF .deps/rna_alignment.Tpo -c -o rna_alignment.o rna_alignment.cpp /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT rna_algebra.o -MD -MP -MF .deps/rna_algebra.Tpo -c -o rna_algebra.o rna_algebra.cpp mv -f .deps/glib.Tpo .deps/glib.Po /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT rna_alphabet.o -MD -MP -MF .deps/rna_alphabet.Tpo -c -o rna_alphabet.o rna_alphabet.cpp mv -f .deps/rna_alphabet.Tpo .deps/rna_alphabet.Po /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT rnaforest.o -MD -MP -MF .deps/rnaforest.Tpo -c -o rnaforest.o rnaforest.cpp In file included from rnaforest.h:22:0, from rna_alignment.h:24, from rna_alignment.cpp:22: rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default] }; ^ In file included from rna_profile_alignment.cpp:37:0: rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default] }; ^ In file included from rnaforest.h:22:0, from rna_alignment.h:24, from main.cpp:50: rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default] }; ^ progressive_align.cpp: In function 'node_entry* makePairsGraph(const RNAProfileAliMapType&, const DoubleScoreProfileAlgebraType*, const Matrix*, double)': progressive_align.cpp:341:30: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings] WriteGraph (graph,"test.out"); ^ mv -f .deps/ppforestbase.Tpo .deps/ppforestbase.Po /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT rnaforestsz.o -MD -MP -MF .deps/rnaforestsz.Tpo -c -o rnaforestsz.o rnaforestsz.cpp In file included from rnaforest.h:22:0, from rnaforest.cpp:24: rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default] }; ^ mv -f .deps/rna_algebra.Tpo .deps/rna_algebra.Po /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT rnafuncs.o -MD -MP -MF .deps/rnafuncs.Tpo -c -o rnafuncs.o rnafuncs.cpp mv -f .deps/rna_alignment.Tpo .deps/rna_alignment.Po /sw/lib/gcc4.8/bin/g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -g -O2 -MT rnaforester_options.o -MD -MP -MF .deps/rnaforester_options.Tpo -c -o rnaforester_options.o rnaforester_options.cpp mv -f .deps/rnaforest.Tpo .deps/rnaforest.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I.. -I/sw/include -I../g2-0.70/include/ -I/sw/include -MT wmatch.o -MD -MP -MF .deps/wmatch.Tpo -c -o wmatch.o wmatch.c mv -f .deps/wmatch.Tpo .deps/wmatch.Po In file included from rnaforestsz.cpp:15:0: rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default] }; ^ In file included from rnafuncs.cpp:23:0: rnafuncs.h:42:3: warning: 'typedef' was ignored in this declaration [enabled by default] }; ^ mv -f .deps/rnaforestsz.Tpo .deps/rnaforestsz.Po mv -f .deps/Arguments.Tpo .deps/Arguments.Po mv -f .deps/rnafuncs.Tpo .deps/rnafuncs.Po mv -f .deps/progressive_align.Tpo .deps/progressive_align.Po mv -f .deps/rna_profile_alignment.Tpo .deps/rna_profile_alignment.Po mv -f .deps/main.Tpo .deps/main.Po mv -f .deps/rnaforester_options.Tpo .deps/rnaforester_options.Po /sw/lib/gcc4.8/bin/g++-fsf-4.8 -g -O2 -L../g2-0.70 -L../../lib -L/sw/lib -o RNAforester Arguments.o glib.o main.o ppforestbase.o progressive_align.o rna_profile_alignment.o rna_alignment.o rna_algebra.o rna_alphabet.o rnaforest.o rnaforestsz.o rnafuncs.o rnaforester_options.o wmatch.o -lg2 -lRNA Making all in man make[4]: Nothing to be done for `all'. make[4]: Nothing to be done for `all-am'. Making all in Kinfold /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in Example make[4]: Nothing to be done for `all'. /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -I../H -I/sw/include -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -I../H -I/sw/include -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -I../H -I/sw/include -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -I../H -I/sw/include -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -I../H -I/sw/include -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -I../H -I/sw/include -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c mv -f .deps/cache.Tpo .deps/cache.Po mv -f .deps/main.Tpo .deps/main.Po mv -f .deps/nachbar.Tpo .deps/nachbar.Po mv -f .deps/globals.Tpo .deps/globals.Po mv -f .deps/baum.Tpo .deps/baum.Po mv -f .deps/cmdline.Tpo .deps/cmdline.Po /sw/lib/gcc4.8/bin/gcc-fsf-4.8 -I/sw/include -L../lib -L/sw/lib -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -lRNA -lm make[2]: Nothing to be done for `all-am'. /bin/rm -rf /sw/build.build/root-viennarna-1.8.5-205 /bin/mkdir -p /sw/build.build/root-viennarna-1.8.5-205/sw /bin/mkdir -p /sw/build.build/root-viennarna-1.8.5-205/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-viennarna-1.8.5-205 sudo -u fink-bld [ENV] sh -c /tmp/fink.3CtBK /tmp/fink.S7IKh # system-wide environment settings for zsh(1) if [ -x /usr/libexec/path_helper ]; then eval `/usr/libexec/path_helper -s` fi #!/bin/zsh -efv perl -pi.bak -e 's|/usr/local|/sw/share|g' Perl/Makefile.perl perl -pi.bak -e 's;/usr/share/man;/sw/share/man;g' Perl/Makefile.perl mkdir -p /sw/build.build/root-viennarna-1.8.5-205/sw/share/man/man3/ mkdir -p /sw/build.build/root-viennarna-1.8.5-205/sw/lib mkdir -p /sw/build.build/root-viennarna-1.8.5-205/sw/include/ViennaRNA perl -pi.bak -e 's|/sw/|/sw/build.build/root-viennarna-1.8.5-205/sw/|g' RNAforester/g2-0.70/Makefile make -j1 install DESTDIR=/sw/build.build/root-viennarna-1.8.5-205 INSTALLPRIVLIB=/sw/lib/perl5/5.16.2/ INSTALLARCHLIB=/sw/lib/perl5/5.16.2/darwin-thread-multi-2level/ INSTALLSITELIB=/sw/lib/perl5/5.16.2/ INSTALLSITEARCH=/sw/lib/perl5/5.16.2/darwin-thread-multi-2level INSTALLSCRIPT=/sw/share/viennarna/scripts Making install in lib test -z "/sw/lib" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/lib" /usr/bin/install -c -m 644 libRNA.a '/sw/build.build/root-viennarna-1.8.5-205/sw/lib' ( cd '/sw/build.build/root-viennarna-1.8.5-205/sw/lib' && ranlib libRNA.a ) make[2]: Nothing to be done for `install-data-am'. Making install in Progs test -z "/sw/bin" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/bin" /usr/bin/install -c RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex '/sw/build.build/root-viennarna-1.8.5-205/sw/bin' make[2]: Nothing to be done for `install-data-am'. Making install in man make[2]: Nothing to be done for `install-exec-am'. test -z "/sw/share/info" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/share/info" /usr/bin/install -c -m 644 ./RNAlib.info '/sw/build.build/root-viennarna-1.8.5-205/sw/share/info' install-info --info-dir='/sw/build.build/root-viennarna-1.8.5-205/sw/share/info' '/sw/build.build/root-viennarna-1.8.5-205/sw/share/info/RNAlib.info' install-info: warning: no info dir entry in `/sw/build.build/root-viennarna-1.8.5-205/sw/share/info/RNAlib.info' test -z "/sw/share/man/man1" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/share/man/man1" /usr/bin/install -c -m 644 RNAheat.1 RNAsubopt.1 RNAdistance.1 RNAinverse.1 RNAcofold.1 RNAeval.1 RNAfold.1 RNApdist.1 RNAplot.1 RNAalifold.1 RNALfold.1 RNAduplex.1 RNAplfold.1 RNAup.1 RNApaln.1 RNAaliduplex.1 '/sw/build.build/root-viennarna-1.8.5-205/sw/share/man/man1' Making install in Utils make[2]: Nothing to be done for `install-exec-am'. test -z "/sw/share/ViennaRNA/bin" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/share/ViennaRNA/bin" /usr/bin/install -c b2ct popt '/sw/build.build/root-viennarna-1.8.5-205/sw/share/ViennaRNA/bin' test -z "/sw/share/ViennaRNA/bin" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/share/ViennaRNA/bin" /usr/bin/install -c b2mt.pl ct2b.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl colorrna.pl coloraln.pl refold.pl Fold '/sw/build.build/root-viennarna-1.8.5-205/sw/share/ViennaRNA/bin' Making install in H make[2]: Nothing to be done for `install-exec-am'. test -z "/sw/include/ViennaRNA" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/include/ViennaRNA" /usr/bin/install -c -m 644 energy_par.h pair_mat.h RNAstruct.h dist_vars.h fold.h part_func.h stringdist.h edit_cost.h fold_vars.h profiledist.h treedist.h energy_const.h inverse.h PS_dot.h utils.h params.h subopt.h cofold.h duplex.h alifold.h aln_util.h part_func_co.h ProfileAln.h LPfold.h Lfold.h part_func_up.h ribo.h findpath.h MEA.h '/sw/build.build/root-viennarna-1.8.5-205/sw/include/ViennaRNA' Making install in Perl /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.perl Skip blib/lib/RNA.pm (unchanged) cc -c -g -pipe -fno-common -DPERL_DARWIN -fno-strict-aliasing -fstack-protector -I/sw/share/include -Os -DVERSION=\"0.2\" -DXS_VERSION=\"0.2\" "-I/System/Library/Perl/5.16/darwin-thread-multi-2level/CORE" RNA_wrap.c In file included from RNA_wrap.c:1547: ./../H/part_func_co.h:26:16: warning: declaration of 'struct plist' will not be visible outside of this function [-Wvisibility] struct plist *prAB, ^ 1 warning generated. Running Mkbootstrap for RNA () chmod 644 RNA.bs rm -f blib/arch/auto/RNA/RNA.bundle LD_RUN_PATH="/usr/lib" cc -mmacosx-version-min=10.9 -bundle -undefined dynamic_lookup -L/sw/share/lib -fstack-protector RNA_wrap.o -o blib/arch/auto/RNA/RNA.bundle ../lib/libRNA.a \ -lm \ ld: warning: directory not found for option '-L/sw/share/lib' chmod 755 blib/arch/auto/RNA/RNA.bundle cp RNA.bs blib/arch/auto/RNA/RNA.bs chmod 644 blib/arch/auto/RNA/RNA.bs /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.perl /Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.perl install Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Installing /sw/build.build/root-viennarna-1.8.5-205/sw/lib/perl5/5.16.2/darwin-thread-multi-2level/auto/RNA/RNA.bs Installing /sw/build.build/root-viennarna-1.8.5-205/sw/lib/perl5/5.16.2/darwin-thread-multi-2level/auto/RNA/RNA.bundle Installing /sw/build.build/root-viennarna-1.8.5-205/sw/lib/perl5/5.16.2/darwin-thread-multi-2level/RNA.pm Installing /sw/build.build/root-viennarna-1.8.5-205/sw/share/share/man/man3/RNA.3pm Appending installation info to /sw/build.build/root-viennarna-1.8.5-205/sw/lib/perl5/5.16.2/darwin-thread-multi-2level//perllocal.pod make[2]: Nothing to be done for `install-data-am'. Making install in RNAforester Making install in g2-0.70 test -d /sw/build.build/root-viennarna-1.8.5-205/sw/lib || mkdir -p /sw/build.build/root-viennarna-1.8.5-205/sw/lib test -d /sw/build.build/root-viennarna-1.8.5-205/sw/include || mkdir -p /sw/build.build/root-viennarna-1.8.5-205/sw/include /usr/bin/install -c -m 644 libg2.a /sw/build.build/root-viennarna-1.8.5-205/sw/lib for IFILE in ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ; do \ /usr/bin/install -c -m 644 $IFILE /sw/build.build/root-viennarna-1.8.5-205/sw/include; \ done Making install in src test -z "/sw/bin" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/bin" /usr/bin/install -c RNAforester '/sw/build.build/root-viennarna-1.8.5-205/sw/bin' make[3]: Nothing to be done for `install-data-am'. Making install in man make[3]: Nothing to be done for `install-exec-am'. test -z "/sw/share/man/man1" || .././install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/share/man/man1" /usr/bin/install -c -m 644 RNAforester.1 '/sw/build.build/root-viennarna-1.8.5-205/sw/share/man/man1' make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. Making install in Kinfold Making install in Example make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. test -z "/sw/bin" || ./../install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/bin" /usr/bin/install -c Kinfold '/sw/build.build/root-viennarna-1.8.5-205/sw/bin' make[3]: Nothing to be done for `install-data-am'. make[2]: Nothing to be done for `install-exec-am'. test -z "/sw/share/ViennaRNA" || ./install-sh -c -d "/sw/build.build/root-viennarna-1.8.5-205/sw/share/ViennaRNA" /usr/bin/install -c -m 644 vienna13.par default.par '/sw/build.build/root-viennarna-1.8.5-205/sw/share/ViennaRNA' sudo -u fink-bld [ENV] sh -c /tmp/fink.qDSKS /bin/mkdir -p /sw/build.build/root-viennarna-1.8.5-205/sw/share/podfiles for i in `find /sw/build.build/root-viennarna-1.8.5-205/sw -name perllocal.pod`; do /bin/cat $i | sed -e s,/sw/build.build/root-viennarna-1.8.5-205/sw/lib/perl5,/sw/lib/perl5, >> /sw/build.build/root-viennarna-1.8.5-205/sw/share/podfiles/perllocal.viennarna.pod; /bin/rm -rf $i; done; /usr/bin/install -d -m 700 /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna /bin/cp -r AUTHORS /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna/ /bin/cp -r ChangeLog /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna/ /bin/cp -r COPYING /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna/ /bin/cp -r INSTALL /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna/ /bin/cp -r INSTALL.configure /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna/ /bin/cp -r NEWS /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna/ /bin/cp -r README /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna/ /bin/cp -r THANKS /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna/ /bin/chmod -R go=u-w /sw/build.build/root-viennarna-1.8.5-205/sw/share/doc/viennarna /bin/rm -f /sw/build.build/root-viennarna-1.8.5-205/sw/info/dir /sw/build.build/root-viennarna-1.8.5-205/sw/info/dir.old /sw/build.build/root-viennarna-1.8.5-205/sw/share/info/dir /sw/build.build/root-viennarna-1.8.5-205/sw/share/info/dir.old /bin/rm -rf /sw/build.build/root-viennarna-dev-1.8.5-205 /bin/mkdir -p /sw/build.build/root-viennarna-dev-1.8.5-205/sw /bin/mkdir -p /sw/build.build/root-viennarna-dev-1.8.5-205/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-viennarna-dev-1.8.5-205 sudo -u fink-bld [ENV] sh -c /tmp/fink.JabVI /usr/bin/install -d -m 755 /sw/build.build/root-viennarna-dev-1.8.5-205/sw/include /bin/mv /sw/build.build/root-viennarna-1.8.5-205/sw/include/*.h /sw/build.build/root-viennarna-dev-1.8.5-205/sw/include/ /usr/bin/install -d -m 755 /sw/build.build/root-viennarna-dev-1.8.5-205/sw/include/ViennaRNA /bin/mv /sw/build.build/root-viennarna-1.8.5-205/sw/include/ViennaRNA/*.h /sw/build.build/root-viennarna-dev-1.8.5-205/sw/include/ViennaRNA/ /usr/bin/install -d -m 755 /sw/build.build/root-viennarna-dev-1.8.5-205/sw/lib /bin/mv /sw/build.build/root-viennarna-1.8.5-205/sw/lib/*.a /sw/build.build/root-viennarna-dev-1.8.5-205/sw/lib/ /bin/rm -f /sw/build.build/root-viennarna-dev-1.8.5-205/sw/info/dir /sw/build.build/root-viennarna-dev-1.8.5-205/sw/info/dir.old /sw/build.build/root-viennarna-dev-1.8.5-205/sw/share/info/dir /sw/build.build/root-viennarna-dev-1.8.5-205/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing package script postinst... Writing package script postrm... Writing package script prerm... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-viennarna-1.8.5-205 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `viennarna' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/viennarna_1.8.5-205_darwin-x86_64.deb'. Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-viennarna-dev-1.8.5-205 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `viennarna-dev' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/viennarna-dev_1.8.5-205_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-viennarna-1.8.5-205 (Reading database ... 9832 files and directories currently installed.) Removing fink-buildlock-viennarna-1.8.5-205 ...