printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild clustalo 2>&1 The package 'clustalo' will be built without being installed. Reading build dependency for clustalo-1.2.1-3... Reading dependency for clustalo-1.2.1-3... Reading build conflict for clustalo-1.2.1-3... The package 'fink-package-precedence' will be installed. Reading dependency for fink-package-precedence-0.18-1... Reading runtime dependency for fink-package-precedence-0.18-1... 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 'libargtable2-dev' will be installed. Reading dependency for libargtable2-dev-2.13-2... Reading runtime dependency for libargtable2-dev-2.13-2... 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 'libargtable2-shlibs' will be installed. Reading dependency for libargtable2-shlibs-2.13-2... Reading runtime dependency for libargtable2-shlibs-2.13-2... 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: clustalo The following 11 additional packages will be installed: cloog-org2-shlibs fink-package-precedence gcc48-compiler gcc48-shlibs gmp5-shlibs isl-shlibs libargtable2-dev libargtable2-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/clustal-omega-1.2.1.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 5 1137k 5 59124 0 0 95728 0 0:00:12 --:--:-- 0:00:12 95669 22 1137k 22 261k 0 0 159k 0 0:00:07 0:00:01 0:00:06 159k 55 1137k 55 634k 0 0 238k 0 0:00:04 0:00:02 0:00:02 238k 100 1137k 100 1137k 0 0 324k 0 0:00:03 0:00:03 --:--:-- 324k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/fink-package-precedence_0.18-1_darwin-x86_64.deb Selecting previously deselected package fink-package-precedence. (Reading database ... 4296 files and directories currently installed.) Unpacking fink-package-precedence (from .../fink-package-precedence_0.18-1_darwin-x86_64.deb) ... Setting up fink-package-precedence (0.18-1) ... Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/dists/stable/main/binary-darwin-x86_64/libs/libargtable2-dev_2.13-2_darwin-x86_64.deb /sw/fink/debs/libargtable2-shlibs_2.13-2_darwin-x86_64.deb Selecting previously deselected package libargtable2-dev. (Reading database ... 4297 files and directories currently installed.) Unpacking libargtable2-dev (from .../libargtable2-dev_2.13-2_darwin-x86_64.deb) ... Selecting previously deselected package libargtable2-shlibs. Unpacking libargtable2-shlibs (from .../libargtable2-shlibs_2.13-2_darwin-x86_64.deb) ... Setting up libargtable2-shlibs (2.13-2) ... Setting up libargtable2-dev (2.13-2) ... Clearing dependency_libs of .la files being installed 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 ... 4341 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 ... 4370 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 ... 4383 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 ... 4384 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 ... 4387 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/dists/stable/main/binary-darwin-x86_64/languages/gcc48-compiler_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 Selecting previously deselected package gcc48-compiler. (Reading database ... 4388 files and directories currently installed.) Unpacking gcc48-compiler (from .../gcc48-compiler_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) ... 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 runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-clustalo-1.2.1-3 /sw/build.build dpkg-deb: building package `fink-buildlock-clustalo-1.2.1-3' in `/sw/build.build/fink-buildlock-clustalo-1.2.1-3_2014.07.29-16.46.30_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-clustalo-1.2.1-3_2014.07.29-16.46.30_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-clustalo-1.2.1-3. (Reading database ... 9808 files and directories currently installed.) Unpacking fink-buildlock-clustalo-1.2.1-3 (from .../fink-buildlock-clustalo-1.2.1-3_2014.07.29-16.46.30_darwin-x86_64.deb) ... Setting up fink-buildlock-clustalo-1.2.1-3 (2014.07.29-16.46.30) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.0ZE0I env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/clustal-omega-1.2.1.tar.gz clustal-omega-1.2.1/ clustal-omega-1.2.1/m4/ clustal-omega-1.2.1/m4/ltversion.m4 clustal-omega-1.2.1/m4/libtool.m4 clustal-omega-1.2.1/m4/lt~obsolete.m4 clustal-omega-1.2.1/m4/ax_openmp.m4 clustal-omega-1.2.1/m4/ltoptions.m4 clustal-omega-1.2.1/m4/ax_prefix_config_h.m4 clustal-omega-1.2.1/m4/ltsugar.m4 clustal-omega-1.2.1/configure clustal-omega-1.2.1/missing clustal-omega-1.2.1/TODO clustal-omega-1.2.1/src/ clustal-omega-1.2.1/src/clustal-omega.c clustal-omega-1.2.1/src/clustal-omega-config.h clustal-omega-1.2.1/src/clustal-omega.h clustal-omega-1.2.1/src/clustal/ clustal-omega-1.2.1/src/clustal/mbed.h clustal-omega-1.2.1/src/clustal/ktuple_pair.h clustal-omega-1.2.1/src/clustal/progress.c clustal-omega-1.2.1/src/clustal/pair_dist.c clustal-omega-1.2.1/src/clustal/symmatrix.h clustal-omega-1.2.1/src/clustal/seq.h clustal-omega-1.2.1/src/clustal/log.c clustal-omega-1.2.1/src/clustal/muscle_tree.h clustal-omega-1.2.1/src/clustal/seq.c clustal-omega-1.2.1/src/clustal/muscle_tree.c clustal-omega-1.2.1/src/clustal/tree.c clustal-omega-1.2.1/src/clustal/hhalign_wrapper.h clustal-omega-1.2.1/src/clustal/hhalign_wrapper.c clustal-omega-1.2.1/src/clustal/muscle_upgma.c clustal-omega-1.2.1/src/clustal/util.h clustal-omega-1.2.1/src/clustal/progress.h clustal-omega-1.2.1/src/clustal/list.h clustal-omega-1.2.1/src/clustal/list.c clustal-omega-1.2.1/src/clustal/tree.h clustal-omega-1.2.1/src/clustal/mbed.c clustal-omega-1.2.1/src/clustal/ktuple_pair.c clustal-omega-1.2.1/src/clustal/Makefile.in clustal-omega-1.2.1/src/clustal/util.c clustal-omega-1.2.1/src/clustal/queue.h clustal-omega-1.2.1/src/clustal/muscle_upgma.h clustal-omega-1.2.1/src/clustal/weights.h clustal-omega-1.2.1/src/clustal/Makefile.am clustal-omega-1.2.1/src/clustal/weights.c clustal-omega-1.2.1/src/clustal/pair_dist.h clustal-omega-1.2.1/src/clustal/log.h clustal-omega-1.2.1/src/clustal/symmatrix.c clustal-omega-1.2.1/src/hhalign/ clustal-omega-1.2.1/src/hhalign/hhhalfalignment.h clustal-omega-1.2.1/src/hhalign/hhdecl-C.h clustal-omega-1.2.1/src/hhalign/util-C.h clustal-omega-1.2.1/src/hhalign/hhhalfalignment-C.h clustal-omega-1.2.1/src/hhalign/hhfullalignment-C.h clustal-omega-1.2.1/src/hhalign/hhfunc-C.h clustal-omega-1.2.1/src/hhalign/hhutil-C.h clustal-omega-1.2.1/src/hhalign/hash-C.h clustal-omega-1.2.1/src/hhalign/hhalignment.h clustal-omega-1.2.1/src/hhalign/hhhit-C.h clustal-omega-1.2.1/src/hhalign/hhhmm-C.h clustal-omega-1.2.1/src/hhalign/general.h clustal-omega-1.2.1/src/hhalign/list.h clustal-omega-1.2.1/src/hhalign/hash.h clustal-omega-1.2.1/src/hhalign/Makefile.in clustal-omega-1.2.1/src/hhalign/list-C.h clustal-omega-1.2.1/src/hhalign/hhalign.h clustal-omega-1.2.1/src/hhalign/hhfullalignment.h clustal-omega-1.2.1/src/hhalign/hhfunc.h clustal-omega-1.2.1/src/hhalign/hhhit.h clustal-omega-1.2.1/src/hhalign/hhmatrices-C.h clustal-omega-1.2.1/src/hhalign/Makefile.am clustal-omega-1.2.1/src/hhalign/hhhitlist-C.h clustal-omega-1.2.1/src/hhalign/hhalign.cpp clustal-omega-1.2.1/src/hhalign/hhalignment-C.h clustal-omega-1.2.1/src/hhalign/hhhitlist.h clustal-omega-1.2.1/src/hhalign/hhhmm.h clustal-omega-1.2.1/src/Makefile.in clustal-omega-1.2.1/src/clustalo-api-test.c clustal-omega-1.2.1/src/main.cpp clustal-omega-1.2.1/src/config.h.in clustal-omega-1.2.1/src/mymain.h clustal-omega-1.2.1/src/squid/ clustal-omega-1.2.1/src/squid/COPYRIGHT clustal-omega-1.2.1/src/squid/shuffle.c clustal-omega-1.2.1/src/squid/stockholm.c clustal-omega-1.2.1/src/squid/sre_math.c clustal-omega-1.2.1/src/squid/alignio.c clustal-omega-1.2.1/src/squid/aligneval.c clustal-omega-1.2.1/src/squid/sre_random.c clustal-omega-1.2.1/src/squid/a2m.c clustal-omega-1.2.1/src/squid/sqio.c clustal-omega-1.2.1/src/squid/squid-1.9g.tar.gz clustal-omega-1.2.1/src/squid/types.c clustal-omega-1.2.1/src/squid/translate.c clustal-omega-1.2.1/src/squid/gsi64.h clustal-omega-1.2.1/src/squid/cluster.c clustal-omega-1.2.1/src/squid/stopwatch.h clustal-omega-1.2.1/src/squid/weight.c clustal-omega-1.2.1/src/squid/squidcore.c clustal-omega-1.2.1/src/squid/version.h clustal-omega-1.2.1/src/squid/rk.c clustal-omega-1.2.1/src/squid/dayhoff.c clustal-omega-1.2.1/src/squid/eps.c clustal-omega-1.2.1/src/squid/seqencode.c clustal-omega-1.2.1/src/squid/msf.c clustal-omega-1.2.1/src/squid/stopwatch.c clustal-omega-1.2.1/src/squid/sqfuncs.h clustal-omega-1.2.1/src/squid/phylip.c clustal-omega-1.2.1/src/squid/clustalo.README clustal-omega-1.2.1/src/squid/revcomp.c clustal-omega-1.2.1/src/squid/selex.c clustal-omega-1.2.1/src/squid/LICENSE clustal-omega-1.2.1/src/squid/msa.c clustal-omega-1.2.1/src/squid/stack.c clustal-omega-1.2.1/src/squid/00README clustal-omega-1.2.1/src/squid/file.c clustal-omega-1.2.1/src/squid/getopt.c clustal-omega-1.2.1/src/squid/ssi.c clustal-omega-1.2.1/src/squid/rk.h clustal-omega-1.2.1/src/squid/clustal.c clustal-omega-1.2.1/src/squid/iupac.c clustal-omega-1.2.1/src/squid/gsi.c clustal-omega-1.2.1/src/squid/Makefile.in clustal-omega-1.2.1/src/squid/gki.h clustal-omega-1.2.1/src/squid/gsi.h clustal-omega-1.2.1/src/squid/msa.h clustal-omega-1.2.1/src/squid/stockholm.h clustal-omega-1.2.1/src/squid/gki.c clustal-omega-1.2.1/src/squid/ssi.h clustal-omega-1.2.1/src/squid/vectorops.h clustal-omega-1.2.1/src/squid/sre_string.c clustal-omega-1.2.1/src/squid/hsregex.c clustal-omega-1.2.1/src/squid/gsi64.c clustal-omega-1.2.1/src/squid/Makefile.am clustal-omega-1.2.1/src/squid/sre_ctype.c clustal-omega-1.2.1/src/squid/squid.h clustal-omega-1.2.1/src/squid/sqerror.c clustal-omega-1.2.1/src/squid/vectorops.c clustal-omega-1.2.1/src/squid/sre_random.h clustal-omega-1.2.1/src/Makefile.am clustal-omega-1.2.1/src/kmpp/ clustal-omega-1.2.1/src/kmpp/KmTree.h clustal-omega-1.2.1/src/kmpp/KmUtils.h clustal-omega-1.2.1/src/kmpp/KMeans.cpp clustal-omega-1.2.1/src/kmpp/KmTree.cpp clustal-omega-1.2.1/src/kmpp/KmUtils.cpp clustal-omega-1.2.1/src/kmpp/KMeans.h clustal-omega-1.2.1/src/kmpp/Makefile.in clustal-omega-1.2.1/src/kmpp/Makefile.am clustal-omega-1.2.1/src/mymain.c clustal-omega-1.2.1/config.guess clustal-omega-1.2.1/ltmain.sh clustal-omega-1.2.1/AUTHORS clustal-omega-1.2.1/install-sh clustal-omega-1.2.1/clustalo.pc.in clustal-omega-1.2.1/README clustal-omega-1.2.1/Doxyfile.in clustal-omega-1.2.1/Doxyfile clustal-omega-1.2.1/aclocal.m4 clustal-omega-1.2.1/NEWS clustal-omega-1.2.1/config.sub clustal-omega-1.2.1/Makefile.in clustal-omega-1.2.1/depcomp clustal-omega-1.2.1/ChangeLog clustal-omega-1.2.1/INSTALL clustal-omega-1.2.1/Makefile.am clustal-omega-1.2.1/configure.ac clustal-omega-1.2.1/COPYING sudo -u fink-bld [ENV] sh -c /tmp/fink.WVwoj ./configure --prefix=/sw configure: Welcome to Clustal Omega - version 1.2.1 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 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 style of include used by make... GNU checking for gcc... 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 gcc-fsf-4.8 accepts -g... yes checking for gcc-fsf-4.8 option to accept ISO C89... none needed checking dependency style of gcc-fsf-4.8... gcc3 checking how to run the C preprocessor... 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 minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... i386-apple-darwin13.3.0 checking host system type... i386-apple-darwin13.3.0 checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... /usr/bin/sed checking for fgrep... /usr/bin/grep -F checking for ld used by gcc-fsf-4.8... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... no checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... 196608 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... yes checking for /usr/bin/ld option to reload object files... -r checking for objdump... no checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from gcc-fsf-4.8 object... ok checking for dsymutil... dsymutil checking for nmedit... nmedit checking for lipo... lipo checking for otool... otool checking for otool64... no checking for -single_module linker flag... yes checking for -exported_symbols_list linker flag... yes checking for dlfcn.h... yes checking for objdir... .libs checking if gcc-fsf-4.8 supports -fno-rtti -fno-exceptions... no checking for gcc-fsf-4.8 option to produce PIC... -fno-common -DPIC checking if gcc-fsf-4.8 PIC flag -fno-common -DPIC works... yes checking if gcc-fsf-4.8 static flag -static works... no checking if gcc-fsf-4.8 supports -c -o file.o... yes checking if gcc-fsf-4.8 supports -c -o file.o... (cached) yes checking whether the gcc-fsf-4.8 linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.3.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... (cached) gcc-fsf-4.8 checking whether we are using the GNU C compiler... (cached) yes checking whether gcc-fsf-4.8 accepts -g... (cached) yes checking for gcc-fsf-4.8 option to accept ISO C89... (cached) none needed checking dependency style of gcc-fsf-4.8... (cached) gcc3 checking how to run the C preprocessor... gcc-fsf-4.8 -E checking whether we are using the GNU C++ compiler... yes checking whether g++-fsf-4.8 accepts -g... yes checking dependency style of g++-fsf-4.8... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++-fsf-4.8 accepts -g... (cached) yes checking dependency style of g++-fsf-4.8... (cached) gcc3 checking how to run the C++ preprocessor... g++-fsf-4.8 -E checking for ld used by g++-fsf-4.8... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... no checking whether the g++-fsf-4.8 linker (/usr/bin/ld) supports shared libraries... yes checking for g++-fsf-4.8 option to produce PIC... -fno-common -DPIC checking if g++-fsf-4.8 PIC flag -fno-common -DPIC works... yes checking if g++-fsf-4.8 static flag -static works... no checking if g++-fsf-4.8 supports -c -o file.o... yes checking if g++-fsf-4.8 supports -c -o file.o... (cached) yes checking whether the g++-fsf-4.8 linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin13.3.0 dyld checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... g++-fsf-4.8 -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking ctype.h usability... yes checking ctype.h presence... yes checking for ctype.h... yes checking float.h usability... yes checking float.h presence... yes checking for float.h... yes checking limits.h usability... yes checking limits.h presence... yes checking for limits.h... yes checking math.h usability... yes checking math.h presence... yes checking for math.h... yes checking for memory.h... (cached) yes checking stdarg.h usability... yes checking stdarg.h presence... yes checking for stdarg.h... yes checking stdio.h usability... yes checking stdio.h presence... yes checking for stdio.h... yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking time.h usability... yes checking time.h presence... yes checking for time.h... 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 log in -lm... yes checking for log2 in -lm... yes checking argtable2.h usability... yes checking argtable2.h presence... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... -fopenmp checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... 2 checking size of unsigned int... 4 checking size of unsigned long... 8 checking size of unsigned long long... 8 checking for stroul... no checking for strtoull... yes checking for ftello... yes checking for fseeko... yes checking for ftello64... no checking for fseeko64... no checking for ftell64... no checking for fseek64... no checking for off_t... yes checking size of fpos_t... 8 checking if malloc debugging is wanted... no checking whether to build with debug information... no configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating clustalo.pc config.status: creating Doxyfile config.status: creating src/clustal/Makefile config.status: creating src/hhalign/Makefile config.status: creating src/kmpp/Makefile config.status: creating src/squid/Makefile config.status: creating src/config.h config.status: executing src/clustal-omega-config.h commands config.status: creating src/clustal-omega-config.h - prefix CLUSTAL_OMEGA for src/config.h defines config.status: executing depfiles commands config.status: executing libtool commands make Making all in src /Applications/Xcode.app/Contents/Developer/usr/bin/make all-recursive Making all in hhalign /bin/sh ../../libtool --tag=CXX --mode=compile g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -MT hhalign.lo -MD -MP -MF .deps/hhalign.Tpo -c -o hhalign.lo hhalign.cpp libtool: compile: g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -MT hhalign.lo -MD -MP -MF .deps/hhalign.Tpo -c hhalign.cpp -fno-common -DPIC -o .libs/hhalign.o In file included from hhalign.cpp:62:0: hhutil-C.h: In function 'void ReadDefaultsFile(int&, char**)': hhutil-C.h:516:53: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ hhutil-C.h:521:56: warning: ISO C++ does not support variable-length array types [-Wvla] argv_conf[argc_conf]=new(char[strlen(c_first)+1]); ^ In file included from hhalign.cpp:70:0: hhhmm-C.h: In member function 'HMM& HMM::operator=(HMM&)': hhhmm-C.h:188:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(q.sname[k])+1]); ^ hhhmm-C.h:193:40: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(q.seq[k])+1]); ^ hhhmm-C.h: In member function 'int HMM::Read(FILE*, char*)': hhhmm-C.h:329:48: warning: ISO C++ does not support variable-length array types [-Wvla] char *cur_seq = new(char[par.maxColCnt]); //Sequence currently read in ^ hhhmm-C.h:360:43: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k-1]=new(char[strlen(cur_seq)+1]); ^ hhhmm-C.h:367:43: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new (char[strlen(line+1)+1]); //+1 for terminating '\0' ^ hhhmm-C.h:463:40: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+1]); ^ hhhmm-C.h: In member function 'int HMM::ReadHMMer(FILE*, char*)': hhhmm-C.h:735:59: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:756:59: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:777:59: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:859:55: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1035:46: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm-C.h:1037:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h:1040:29: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm-C.h:1058:44: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm-C.h:1062:27: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h: In member function 'int HMM::ReadHMMer3(FILE*, char*)': hhhmm-C.h:1237:77: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nsa_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1258:77: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_pred] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1279:77: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_conf] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1349:69: warning: ISO C++ does not support variable-length array types [-Wvla] seq[nss_dssp] = new(char[/*MAXRES*/par.maxResLen+2]); ^ hhhmm-C.h:1529:49: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k+1]=new(char[strlen(longname)+1]); ^ hhhmm-C.h:1531:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h:1534:32: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k+1]=new(char[L+2]); ^ hhhmm-C.h:1552:47: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k]=new(char[strlen(longname)+1]); ^ hhhmm-C.h:1554:30: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[L+2]); ^ hhhmm-C.h: In member function 'void HMM::InsertCalibration(char*)': hhhmm-C.h:2109:39: warning: ISO C++ does not support variable-length array types [-Wvla] char** lines = new(char*[3*L+100000]); ^ hhhmm-C.h:2138:44: warning: ISO C++ does not support variable-length array types [-Wvla] lines[nline]=new(char[strlen(line)+1]); ^ In file included from hhalign.cpp:71:0: hhalignment-C.h: In constructor 'Alignment::Alignment(int, int)': hhalignment-C.h:80:30: warning: ISO C++ does not support variable-length array types [-Wvla] sname = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:81:28: warning: ISO C++ does not support variable-length array types [-Wvla] seq = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:82:22: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int[maxres]); ^ hhalignment-C.h:83:26: warning: ISO C++ does not support variable-length array types [-Wvla] X = new(char*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:84:40: warning: ISO C++ does not support variable-length array types [-Wvla] I = new(short unsigned int*[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:85:28: warning: ISO C++ does not support variable-length array types [-Wvla] keep = new(char[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:86:31: warning: ISO C++ does not support variable-length array types [-Wvla] display = new(char[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:87:27: warning: ISO C++ does not support variable-length array types [-Wvla] wg = new(float[maxseq+2]); /* MR1 */ ^ hhalignment-C.h:88:28: warning: ISO C++ does not support variable-length array types [-Wvla] nseqs = new(int[maxres+2]); /* MR1 */ ^ hhalignment-C.h: In member function 'void Alignment::Read(FILE*, char*, char*)': hhalignment-C.h:141:40: warning: ISO C++ does not support variable-length array types [-Wvla] char *cur_seq=new(char[par.maxColCnt]); ^ hhalignment-C.h:183:61: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment-C.h:185:59: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment-C.h:187:73: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ In file included from hhalign.cpp:71:0: hhalignment-C.h:236:58: warning: ISO C++ does not support variable-length array types [-Wvla] sname[k] = new(char[strlen(cur_name)+1]); ^ hhalignment-C.h:351:45: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment-C.h:353:43: warning: ISO C++ does not support variable-length array types [-Wvla] X[k]=new(char[strlen(cur_seq)+2]); ^ hhalignment-C.h:355:57: warning: ISO C++ does not support variable-length array types [-Wvla] I[k]=new(short unsigned int[strlen(cur_seq)+2]); ^ hhalignment-C.h: In member function 'void Alignment::Compress(const char*)': hhalignment-C.h:423:43: warning: ISO C++ does not support variable-length array types [-Wvla] h = new(/*short*/ unsigned int[N_in+2]); /* short -> overflow, FS, r235 -> r236 */ ^ hhalignment-C.h:555:52: warning: ISO C++ does not support variable-length array types [-Wvla] percent_gaps = new(float[par.maxColCnt]); ^ hhalignment-C.h:561:47: warning: ISO C++ does not support variable-length array types [-Wvla] if (nres==NULL) nres=new(int[N_in]); ^ hhalignment-C.h:783:50: warning: ISO C++ does not support variable-length array types [-Wvla] match_state = new(char[par.maxColCnt]); ^ hhalignment-C.h: In member function 'int Alignment::FilterForDisplay(int, int, int, float, int)': hhalignment-C.h:945:35: warning: ISO C++ does not support variable-length array types [-Wvla] char *dummy = new(char[N_in+1]); ^ hhalignment-C.h: In member function 'int Alignment::Filter2(char*, int, int, float, int, int, int)': hhalignment-C.h:1008:30: warning: ISO C++ does not support variable-length array types [-Wvla] char* in=new(char[N_in+1]); // in[k]=1: seq k has been accepted; in[k]=0: seq k has not yet been accepted at current seqid ^ hhalignment-C.h:1009:32: warning: ISO C++ does not support variable-length array types [-Wvla] char* inkk=new(char[N_in+1]); // inkk[k]=1 iff in[ksort[k]]=1 else 0; ^ hhalignment-C.h:1010:27: warning: ISO C++ does not support variable-length array types [-Wvla] int* Nmax=new(int[L+2]); // position-dependent maximum-sequence-identity threshold for filtering /* MR1, used to be called idmax*/ ^ hhalignment-C.h:1011:31: warning: ISO C++ does not support variable-length array types [-Wvla] int* idmaxwin=new(int[L+2]); // minimum value of idmax[i-WFIL,i+WFIL] ^ hhalignment-C.h:1012:36: warning: ISO C++ does not support variable-length array types [-Wvla] int* seqid_prev=new(int[N_in+1]); // maximum-sequence-identity threshold used in previous round of filtering (with lower seqid) ^ hhalignment-C.h:1013:24: warning: ISO C++ does not support variable-length array types [-Wvla] int* N=new(int[L+2]); // N[i] number of already accepted sequences at position i ^ hhalignment-C.h:1042:32: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment-C.h:1043:32: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment-C.h:1056:31: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment-C.h:1070:32: warning: ISO C++ does not support variable-length array types [-Wvla] ksort=new(int[N_in]); // never reuse alignment object for new alignment with more sequences ^ hhalignment-C.h: In member function 'int Alignment::HomologyFilter(int, float, float)': hhalignment-C.h:1313:33: warning: ISO C++ does not support variable-length array types [-Wvla] char* coreseq=new(char[N_in]); // coreseq[k]=1 if sequence belongs to core of alignment (i.e. it is very similar to query) ^ hhalignment-C.h: In member function 'int Alignment::FilterWithCoreHMM(char*, float, HMM&)': hhalignment-C.h:1364:36: warning: ISO C++ does not support variable-length array types [-Wvla] float** logodds=new(float*[L+1]); // log-odds ratios for HMM qcore ^ hhalignment-C.h:1373:32: warning: ISO C++ does not support variable-length array types [-Wvla] first=new(int[N_in]);// first non-gap position in sequence k ^ hhalignment-C.h:1374:32: warning: ISO C++ does not support variable-length array types [-Wvla] last =new(int[N_in]);// last non-gap position in sequence k ^ hhalignment-C.h:1387:31: warning: ISO C++ does not support variable-length array types [-Wvla] nres=new(int[N_in]); ^ hhalignment-C.h: In member function 'void Alignment::FrequenciesAndTransitions(HMM&, char*)': hhalignment-C.h:1669:49: warning: ISO C++ does not support variable-length array types [-Wvla] q.seq[q.ncons]=new(char[L+2]); ^ hhalignment-C.h:1676:64: warning: ISO C++ does not support variable-length array types [-Wvla] q.sname[q.nfirst]=new(char[strlen(name)+11]); ^ hhalignment-C.h:1680:50: warning: ISO C++ does not support variable-length array types [-Wvla] q.seq[q.nfirst]=new(char[L+2]); ^ hhalignment-C.h:1738:61: warning: ISO C++ does not support variable-length array types [-Wvla] q.sname[nn]=new(char[strlen(sname[k])+1]); ^ hhalignment-C.h:1741:57: warning: ISO C++ does not support variable-length array types [-Wvla] q.seq[nn]=new(char[strlen(seq[k])+1]); ^ hhalignment-C.h: In member function 'void Alignment::Amino_acid_frequencies_and_transitions_from_M_state(HMM&, char*)': hhalignment-C.h:1828:41: warning: ISO C++ does not support variable-length array types [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:1835:25: warning: ISO C++ does not support variable-length array types [-Wvla] wi = new(float[N_in+2]); ^ hhalignment-C.h:1844:20: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::Transitions_from_I_state(HMM&, char*)': hhalignment-C.h:2054:43: warning: ISO C++ does not support variable-length array types [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:2062:27: warning: ISO C++ does not support variable-length array types [-Wvla] wi = new(float[N_in+2]); ^ hhalignment-C.h:2073:22: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::Transitions_from_D_state(HMM&, char*)': hhalignment-C.h:2256:43: warning: ISO C++ does not support variable-length array types [-Wvla] float *Neff = new(float[par.maxResLen]); // diversity of subalignment i ^ hhalignment-C.h:2265:27: warning: ISO C++ does not support variable-length array types [-Wvla] wi = new(float[N_in+2]); /* FIXME: FS */ ^ hhalignment-C.h:2275:22: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::MergeMasterSlave(Hit&, char*)': hhalignment-C.h:2546:31: warning: ISO C++ does not support variable-length array types [-Wvla] int* imatch=new(int[hit.j2+1]); ^ hhalignment-C.h:2678:34: warning: ISO C++ does not support variable-length array types [-Wvla] char* new_seq=new(char[2*maxcol]); ^ hhalignment-C.h:2691:23: warning: ISO C++ does not support variable-length array types [-Wvla] seq[N_in]=new(char[h]); ^ hhalignment-C.h:2694:21: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[h]); ^ hhalignment-C.h:2696:35: warning: ISO C++ does not support variable-length array types [-Wvla] I[N_in]=new(short unsigned int[h]); ^ hhalignment-C.h:2698:47: warning: ISO C++ does not support variable-length array types [-Wvla] sname[N_in]=new(char[strlen(Tali.sname[k])+1]); ^ hhalignment-C.h: In member function 'void Alignment::AddSequence(char*, int*)': hhalignment-C.h:2729:23: warning: ISO C++ does not support variable-length array types [-Wvla] X[N_in]=new(char[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::GetPositionSpecificWeights(float**)': hhalignment-C.h:2779:19: warning: ISO C++ does not support variable-length array types [-Wvla] n = new(int*[L+2]); ^ hhalignment-C.h: In member function 'void Alignment::Transfer(char**, int)': hhalignment-C.h:2896:59: warning: ISO C++ does not support variable-length array types [-Wvla] I[k] = new(short unsigned int[iLen+2+GOOD_MEASURE]); ^ hhalignment-C.h:2897:45: warning: ISO C++ does not support variable-length array types [-Wvla] X[k] = new(char[iLen+2+GOOD_MEASURE]); ^ hhalignment-C.h:2898:47: warning: ISO C++ does not support variable-length array types [-Wvla] seq[k] = new(char[iLen+2+GOOD_MEASURE]); ^ In file included from hhalign.cpp:72:0: hhhit-C.h: In member function 'void Hit::AllocateBacktraceMatrix(int, int)': hhhit-C.h:179:20: warning: ISO C++ does not support variable-length array types [-Wvla] bMM=new(char*[Nq]); ^ hhhit-C.h:180:20: warning: ISO C++ does not support variable-length array types [-Wvla] bMI=new(char*[Nq]); ^ hhhit-C.h:181:20: warning: ISO C++ does not support variable-length array types [-Wvla] bIM=new(char*[Nq]); ^ hhhit-C.h:182:20: warning: ISO C++ does not support variable-length array types [-Wvla] bDG=new(char*[Nq]); ^ hhhit-C.h:183:20: warning: ISO C++ does not support variable-length array types [-Wvla] bGD=new(char*[Nq]); ^ hhhit-C.h:184:25: warning: ISO C++ does not support variable-length array types [-Wvla] cell_off=new(char*[Nq]); ^ hhhit-C.h:187:26: warning: ISO C++ does not support variable-length array types [-Wvla] bMM[i]=new(char[Nt]); ^ hhhit-C.h:188:26: warning: ISO C++ does not support variable-length array types [-Wvla] bMI[i]=new(char[Nt]); ^ hhhit-C.h:189:26: warning: ISO C++ does not support variable-length array types [-Wvla] bIM[i]=new(char[Nt]); ^ hhhit-C.h:190:26: warning: ISO C++ does not support variable-length array types [-Wvla] bGD[i]=new(char[Nt]); ^ hhhit-C.h:191:26: warning: ISO C++ does not support variable-length array types [-Wvla] bDG[i]=new(char[Nt]); ^ hhhit-C.h:192:31: warning: ISO C++ does not support variable-length array types [-Wvla] cell_off[i]=new(char[Nt]); ^ hhhit-C.h: In member function 'void Hit::AllocateForwardMatrix(int, int)': hhhit-C.h:239:23: warning: ISO C++ does not support variable-length array types [-Wvla] F_MM=new(double*[Nq]); ^ hhhit-C.h:240:23: warning: ISO C++ does not support variable-length array types [-Wvla] F_MI=new(double*[Nq]); ^ hhhit-C.h:241:23: warning: ISO C++ does not support variable-length array types [-Wvla] F_DG=new(double*[Nq]); ^ hhhit-C.h:242:23: warning: ISO C++ does not support variable-length array types [-Wvla] F_IM=new(double*[Nq]); ^ hhhit-C.h:243:23: warning: ISO C++ does not support variable-length array types [-Wvla] F_GD=new(double*[Nq]); ^ hhhit-C.h:244:25: warning: ISO C++ does not support variable-length array types [-Wvla] scale=new(double[Nq+1]); // need Nq+3? ^ hhhit-C.h:247:31: warning: ISO C++ does not support variable-length array types [-Wvla] F_MM[i] = new(double[Nt]); ^ hhhit-C.h:248:31: warning: ISO C++ does not support variable-length array types [-Wvla] F_MI[i] = new(double[Nt]); ^ hhhit-C.h:249:31: warning: ISO C++ does not support variable-length array types [-Wvla] F_DG[i] = new(double[Nt]); ^ hhhit-C.h:250:31: warning: ISO C++ does not support variable-length array types [-Wvla] F_IM[i] = new(double[Nt]); ^ hhhit-C.h:251:31: warning: ISO C++ does not support variable-length array types [-Wvla] F_GD[i] = new(double[Nt]); ^ hhhit-C.h: In member function 'void Hit::AllocateBackwardMatrix(int, int)': hhhit-C.h:296:23: warning: ISO C++ does not support variable-length array types [-Wvla] B_MM=new(double*[Nq]); ^ hhhit-C.h:303:31: warning: ISO C++ does not support variable-length array types [-Wvla] B_MM[i] = new(double[Nt]); ^ hhhit-C.h: In member function 'void Hit::Viterbi(HMM&, HMM&, float**)': hhhit-C.h:376:42: warning: ISO C++ does not support variable-length array types [-Wvla] float *sMM = new(float[par.maxResLen]); // sMM[i][j] = score of best alignment up to indices (i,j) ending in (Match,Match) ^ hhhit-C.h:377:42: warning: ISO C++ does not support variable-length array types [-Wvla] float *sGD = new(float[par.maxResLen]); // sGD[i][j] = score of best alignment up to indices (i,j) ending in (Gap,Delete) ^ hhhit-C.h:378:42: warning: ISO C++ does not support variable-length array types [-Wvla] float *sDG = new(float[par.maxResLen]); // sDG[i][j] = score of best alignment up to indices (i,j) ending in (Delete,Gap) ^ hhhit-C.h:379:42: warning: ISO C++ does not support variable-length array types [-Wvla] float *sIM = new(float[par.maxResLen]); // sIM[i][j] = score of best alignment up to indices (i,j) ending in (Ins,Match) ^ hhhit-C.h:380:42: warning: ISO C++ does not support variable-length array types [-Wvla] float *sMI = new(float[par.maxResLen]); // sMI[i][j] = score of best alignment up to indices (i,j) ending in (Match,Ins) ^ hhhit-C.h: In member function 'void Hit::Backtrace(HMM&, HMM&)': hhhit-C.h:1126:40: warning: ISO C++ does not support variable-length array types [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1127:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1128:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h: In member function 'void Hit::StochasticBacktrace(HMM&, HMM&, char)': hhhit-C.h:1228:40: warning: ISO C++ does not support variable-length array types [-Wvla] double* scale_cum = new(double[q.L+2]); ^ hhhit-C.h:1247:39: warning: ISO C++ does not support variable-length array types [-Wvla] double* sumF=new(double[q.L+t.L]); ^ hhhit-C.h:1371:40: warning: ISO C++ does not support variable-length array types [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1372:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1373:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h: In member function 'void Hit::BacktraceMAC(HMM&, HMM&)': hhhit-C.h:1475:40: warning: ISO C++ does not support variable-length array types [-Wvla] if (t.Xcons) Xcons = new( char[q.L+2]); // for template consensus sequence aligned to query ^ hhhit-C.h:1476:30: warning: ISO C++ does not support variable-length array types [-Wvla] S = new( float[nsteps+1]); ^ hhhit-C.h:1477:30: warning: ISO C++ does not support variable-length array types [-Wvla] S_ss = new( float[nsteps+1]); ^ hhhit-C.h:1478:37: warning: ISO C++ does not support variable-length array types [-Wvla] P_posterior = new( float[nsteps+1]); ^ hhhit-C.h: In member function 'void Hit::InitializeBacktrace(HMM&, HMM&)': hhhit-C.h:1683:54: warning: ISO C++ does not support variable-length array types [-Wvla] longname=new(char[strlen(t.longname)+1])(); ^ hhhit-C.h:1684:50: warning: ISO C++ does not support variable-length array types [-Wvla] name =new(char[strlen(t.name)+1])(); ^ hhhit-C.h:1685:50: warning: ISO C++ does not support variable-length array types [-Wvla] file =new(char[strlen(t.file)+1])(); ^ hhhit-C.h:1696:43: warning: ISO C++ does not support variable-length array types [-Wvla] sname=new(char*[t.n_display])(); // Call Compare only once with irep=1 ^ hhhit-C.h:1697:43: warning: ISO C++ does not support variable-length array types [-Wvla] seq =new(char*[t.n_display])(); // Call Compare only once with irep=1 ^ hhhit-C.h:1730:34: warning: ISO C++ does not support variable-length array types [-Wvla] this->i = new( int[i2+j2+2])(); ^ hhhit-C.h:1731:34: warning: ISO C++ does not support variable-length array types [-Wvla] this->j = new( int[i2+j2+2])(); ^ hhhit-C.h:1732:35: warning: ISO C++ does not support variable-length array types [-Wvla] states = new( char[i2+j2+2])(); ^ In file included from hhalign.cpp:73:0: hhhalfalignment-C.h: In constructor 'HalfAlignment::HalfAlignment(int)': hhhalfalignment-C.h:66:25: warning: ISO C++ does not support variable-length array types [-Wvla] h = new(int[maxseqdis]); //h[k] = next position of sequence k to be written ^ hhhalfalignment-C.h:67:27: warning: ISO C++ does not support variable-length array types [-Wvla] s = new(char*[maxseqdis]); //s[k][h] = character in column h, sequence k of output alignment ^ hhhalfalignment-C.h:68:26: warning: ISO C++ does not support variable-length array types [-Wvla] l = new(int*[maxseqdis]); //counts non-gap residues: l[k][i] = index of last residue AT OR BEFORE match state i in seq k ^ hhhalfalignment-C.h:69:26: warning: ISO C++ does not support variable-length array types [-Wvla] m = new(int*[maxseqdis]); //counts positions: m[k][i] = position of match state i in string seq[k] ^ In file included from hhalign.cpp:74:0: hhfullalignment-C.h: In member function 'void FullAlignment::PrintHHR(FILE*, Hit&)': hhfullalignment-C.h:359:39: warning: ISO C++ does not support variable-length array types [-Wvla] lq = new(short unsigned int[qa->n+2]); ^ hhfullalignment-C.h:360:39: warning: ISO C++ does not support variable-length array types [-Wvla] lt = new(short unsigned int[ta->n+2]); ^ In file included from hhalign.cpp:75:0: hhhitlist-C.h: In member function 'void HitList::TransitiveScoring()': hhhitlist-C.h:1285:20: warning: ISO C++ does not support variable-length array types [-Wvla] Z = new(float*[N]); ^ hhhitlist-C.h:1288:26: warning: ISO C++ does not support variable-length array types [-Wvla] Z[k] = new(float[N]); ^ hhhitlist-C.h:1293:20: warning: ISO C++ does not support variable-length array types [-Wvla] C = new(float*[N]); ^ hhhitlist-C.h:1296:26: warning: ISO C++ does not support variable-length array types [-Wvla] C[k] = new(float[N]); ^ hhhitlist-C.h:1303:20: warning: ISO C++ does not support variable-length array types [-Wvla] Zq = new(float[N]); ^ hhhitlist-C.h:1304:21: warning: ISO C++ does not support variable-length array types [-Wvla] Ztq = new(float[N]); ^ hhhitlist-C.h:1305:21: warning: ISO C++ does not support variable-length array types [-Wvla] Zrq = new(float[N]); ^ hhhitlist-C.h:1306:22: warning: ISO C++ does not support variable-length array types [-Wvla] fold = new(char*[N]); ^ hhhitlist-C.h:1307:21: warning: ISO C++ does not support variable-length array types [-Wvla] fam = new(char*[N]); ^ hhhitlist-C.h:1308:22: warning: ISO C++ does not support variable-length array types [-Wvla] Prob = new(float[N]); ^ hhhitlist-C.h:1309:18: warning: ISO C++ does not support variable-length array types [-Wvla] ll = new(int[N]); ^ hhhitlist-C.h:1310:19: warning: ISO C++ does not support variable-length array types [-Wvla] w = new(float[N]); ^ hhhitlist-C.h:1373:37: warning: ISO C++ does not support variable-length array types [-Wvla] double** Csub = new(double*[M]); ^ hhhitlist-C.h:1374:37: warning: ISO C++ does not support variable-length array types [-Wvla] double** Cinv = new(double*[M]); ^ hhhitlist-C.h:1377:27: warning: ISO C++ does not support variable-length array types [-Wvla] Csub[m] = new(double[M]); ^ hhhitlist-C.h:1378:27: warning: ISO C++ does not support variable-length array types [-Wvla] Cinv[m] = new(double[M]); ^ hhhitlist-C.h:1453:34: warning: ISO C++ does not support variable-length array types [-Wvla] double** Csub = new(double*[M]); ^ hhhitlist-C.h:1456:31: warning: ISO C++ does not support variable-length array types [-Wvla] Csub[m] = new(double[M]); ^ hhhitlist-C.h:1470:38: warning: ISO C++ does not support variable-length array types [-Wvla] double** Cinv = new(double*[M]); ^ hhhitlist-C.h:1471:51: warning: ISO C++ does not support variable-length array types [-Wvla] for (m=0; m/dev/null 2>&1 mv -f .deps/hhalign.Tpo .deps/hhalign.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++-fsf-4.8 -fno-strict-aliasing -DCLUSTALO -DCLUSTALO_NOFILE -DDEFAULT_FILTER=90 -fopenmp -O3 -g -O2 -L/sw/lib -o libhhalign.la hhalign.lo -largtable2 -lm libtool: link: ar cru .libs/libhhalign.a .libs/hhalign.o libtool: link: ranlib .libs/libhhalign.a libtool: link: ( cd ".libs" && rm -f "libhhalign.la" && ln -s "../libhhalign.la" "libhhalign.la" ) Making all in squid /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT a2m.lo -MD -MP -MF .deps/a2m.Tpo -c -o a2m.lo a2m.c /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT aligneval.lo -MD -MP -MF .deps/aligneval.Tpo -c -o aligneval.lo aligneval.c /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT alignio.lo -MD -MP -MF .deps/alignio.Tpo -c -o alignio.lo alignio.c /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT clustal.lo -MD -MP -MF .deps/clustal.Tpo -c -o clustal.lo clustal.c /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c -o cluster.lo cluster.c /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT dayhoff.lo -MD -MP -MF .deps/dayhoff.Tpo -c -o dayhoff.lo dayhoff.c /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT eps.lo -MD -MP -MF .deps/eps.Tpo -c -o eps.lo eps.c /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT file.lo -MD -MP -MF .deps/file.Tpo -c -o file.lo file.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT aligneval.lo -MD -MP -MF .deps/aligneval.Tpo -c aligneval.c -fno-common -DPIC -o .libs/aligneval.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT alignio.lo -MD -MP -MF .deps/alignio.Tpo -c alignio.c -fno-common -DPIC -o .libs/alignio.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT a2m.lo -MD -MP -MF .deps/a2m.Tpo -c a2m.c -fno-common -DPIC -o .libs/a2m.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT clustal.lo -MD -MP -MF .deps/clustal.Tpo -c clustal.c -fno-common -DPIC -o .libs/clustal.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c cluster.c -fno-common -DPIC -o .libs/cluster.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT dayhoff.lo -MD -MP -MF .deps/dayhoff.Tpo -c dayhoff.c -fno-common -DPIC -o .libs/dayhoff.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT eps.lo -MD -MP -MF .deps/eps.Tpo -c eps.c -fno-common -DPIC -o .libs/eps.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT file.lo -MD -MP -MF .deps/file.Tpo -c file.c -fno-common -DPIC -o .libs/file.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT eps.lo -MD -MP -MF .deps/eps.Tpo -c eps.c -o eps.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT dayhoff.lo -MD -MP -MF .deps/dayhoff.Tpo -c dayhoff.c -o dayhoff.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT a2m.lo -MD -MP -MF .deps/a2m.Tpo -c a2m.c -o a2m.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT file.lo -MD -MP -MF .deps/file.Tpo -c file.c -o file.o >/dev/null 2>&1 mv -f .deps/eps.Tpo .deps/eps.Plo /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c -o getopt.lo getopt.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT clustal.lo -MD -MP -MF .deps/clustal.Tpo -c clustal.c -o clustal.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT aligneval.lo -MD -MP -MF .deps/aligneval.Tpo -c aligneval.c -o aligneval.o >/dev/null 2>&1 mv -f .deps/a2m.Tpo .deps/a2m.Plo mv -f .deps/dayhoff.Tpo .deps/dayhoff.Plo /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT gki.lo -MD -MP -MF .deps/gki.Tpo -c -o gki.lo gki.c /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT gsi.lo -MD -MP -MF .deps/gsi.Tpo -c -o gsi.lo gsi.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -fno-common -DPIC -o .libs/getopt.o mv -f .deps/file.Tpo .deps/file.Plo libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT cluster.lo -MD -MP -MF .deps/cluster.Tpo -c cluster.c -o cluster.o >/dev/null 2>&1 /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT 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/bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT hsregex.lo -MD -MP -MF .deps/hsregex.Tpo -c -o hsregex.lo hsregex.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT getopt.lo -MD -MP -MF .deps/getopt.Tpo -c getopt.c -o getopt.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT hsregex.lo -MD -MP -MF .deps/hsregex.Tpo -c hsregex.c -fno-common -DPIC -o .libs/hsregex.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT gki.lo -MD -MP -MF .deps/gki.Tpo -c gki.c -o gki.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT gsi.lo -MD -MP -MF .deps/gsi.Tpo -c gsi.c -o gsi.o >/dev/null 2>&1 mv -f .deps/aligneval.Tpo .deps/aligneval.Plo /bin/sh ../../libtool --tag=CC 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-DCLUSTALO -O3 -g -O2 -MT KmUtils.lo -MD -MP -MF .deps/KmUtils.Tpo -c KmUtils.cpp -o KmUtils.o >/dev/null 2>&1 libtool: compile: g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT KmTree.lo -MD -MP -MF .deps/KmTree.Tpo -c KmTree.cpp -o KmTree.o >/dev/null 2>&1 mv -f .deps/KmUtils.Tpo .deps/KmUtils.Plo mv -f .deps/KmTree.Tpo .deps/KmTree.Plo libtool: compile: g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -DCLUSTALO -O3 -g -O2 -MT KMeans.lo -MD -MP -MF .deps/KMeans.Tpo -c KMeans.cpp -o KMeans.o >/dev/null 2>&1 mv -f .deps/KMeans.Tpo .deps/KMeans.Plo /bin/sh ../../libtool --tag=CXX --mode=link g++-fsf-4.8 -DCLUSTALO -O3 -g -O2 -L/sw/lib -o libkmpp.la KMeans.lo KmTree.lo KmUtils.lo -largtable2 -lm libtool: link: ar cru .libs/libkmpp.a .libs/KMeans.o .libs/KmTree.o .libs/KmUtils.o libtool: link: ranlib .libs/libkmpp.a libtool: link: ( cd ".libs" && rm -f "libkmpp.la" && ln -s "../libkmpp.la" "libkmpp.la" ) Making all in clustal /bin/sh 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libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT hhalign_wrapper.lo -MD -MP -MF .deps/hhalign_wrapper.Tpo -c hhalign_wrapper.c -fno-common -DPIC -o .libs/hhalign_wrapper.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT muscle_tree.lo -MD -MP -MF .deps/muscle_tree.Tpo -c muscle_tree.c -fno-common -DPIC -o .libs/muscle_tree.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT muscle_upgma.lo -MD -MP -MF .deps/muscle_upgma.Tpo -c muscle_upgma.c -fno-common -DPIC -o .libs/muscle_upgma.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT mbed.lo -MD -MP -MF .deps/mbed.Tpo -c mbed.c -fno-common -DPIC -o .libs/mbed.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT log.lo -MD -MP -MF .deps/log.Tpo -c log.c -fno-common -DPIC -o .libs/log.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT pair_dist.lo -MD -MP -MF .deps/pair_dist.Tpo -c pair_dist.c -fno-common -DPIC -o .libs/pair_dist.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT list.lo -MD -MP -MF .deps/list.Tpo -c list.c -o list.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT log.lo -MD -MP -MF .deps/log.Tpo -c log.c -o log.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT muscle_upgma.lo -MD -MP -MF .deps/muscle_upgma.Tpo -c muscle_upgma.c -o muscle_upgma.o >/dev/null 2>&1 mv -f .deps/list.Tpo .deps/list.Plo /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT progress.lo -MD -MP -MF .deps/progress.Tpo -c -o progress.lo progress.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT progress.lo -MD -MP -MF .deps/progress.Tpo -c progress.c -fno-common -DPIC -o .libs/progress.o mv -f .deps/log.Tpo .deps/log.Plo /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT seq.lo -MD -MP -MF .deps/seq.Tpo -c -o seq.lo seq.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT pair_dist.lo -MD -MP -MF .deps/pair_dist.Tpo -c pair_dist.c -o pair_dist.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT seq.lo -MD -MP -MF .deps/seq.Tpo -c seq.c -fno-common -DPIC -o .libs/seq.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT progress.lo -MD -MP -MF .deps/progress.Tpo -c progress.c -o progress.o >/dev/null 2>&1 mv -f .deps/muscle_upgma.Tpo .deps/muscle_upgma.Plo /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT symmatrix.lo -MD -MP -MF .deps/symmatrix.Tpo -c -o symmatrix.lo symmatrix.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT ktuple_pair.lo -MD -MP -MF .deps/ktuple_pair.Tpo -c ktuple_pair.c -o ktuple_pair.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT symmatrix.lo -MD -MP -MF .deps/symmatrix.Tpo -c symmatrix.c -fno-common -DPIC -o .libs/symmatrix.o mv -f .deps/progress.Tpo .deps/progress.Plo /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT tree.lo -MD -MP -MF .deps/tree.Tpo -c -o tree.lo tree.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT mbed.lo -MD -MP -MF .deps/mbed.Tpo -c mbed.c -o mbed.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT tree.lo -MD -MP -MF .deps/tree.Tpo -c tree.c -fno-common -DPIC -o .libs/tree.o mv -f .deps/pair_dist.Tpo .deps/pair_dist.Plo /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT util.lo -MD -MP -MF .deps/util.Tpo -c -o util.lo util.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT util.lo -MD -MP -MF .deps/util.Tpo -c util.c -fno-common -DPIC -o .libs/util.o libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT tree.lo -MD -MP -MF .deps/tree.Tpo -c tree.c -o tree.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT muscle_tree.lo -MD -MP -MF .deps/muscle_tree.Tpo -c muscle_tree.c -o muscle_tree.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT symmatrix.lo -MD -MP -MF .deps/symmatrix.Tpo -c symmatrix.c -o symmatrix.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT util.lo -MD -MP -MF .deps/util.Tpo -c util.c -o util.o >/dev/null 2>&1 libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT seq.lo -MD -MP -MF .deps/seq.Tpo -c seq.c -o seq.o >/dev/null 2>&1 mv -f .deps/tree.Tpo .deps/tree.Plo /bin/sh ../../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT weights.lo -MD -MP -MF .deps/weights.Tpo -c -o weights.lo weights.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT weights.lo -MD -MP -MF .deps/weights.Tpo -c weights.c -fno-common -DPIC -o .libs/weights.o mv -f .deps/ktuple_pair.Tpo .deps/ktuple_pair.Plo libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT hhalign_wrapper.lo -MD -MP -MF .deps/hhalign_wrapper.Tpo -c hhalign_wrapper.c -o hhalign_wrapper.o >/dev/null 2>&1 mv -f .deps/util.Tpo .deps/util.Plo mv -f .deps/symmatrix.Tpo .deps/symmatrix.Plo libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I../../src -I/sw/include -fopenmp -O3 -g -O2 -MT weights.lo -MD -MP -MF .deps/weights.Tpo -c weights.c -o weights.o >/dev/null 2>&1 mv -f .deps/mbed.Tpo .deps/mbed.Plo mv -f .deps/weights.Tpo .deps/weights.Plo mv -f .deps/seq.Tpo .deps/seq.Plo mv -f .deps/muscle_tree.Tpo .deps/muscle_tree.Plo mv -f .deps/hhalign_wrapper.Tpo .deps/hhalign_wrapper.Plo /bin/sh ../../libtool --tag=CC --mode=link gcc-fsf-4.8 -fopenmp -O3 -g -O2 -L/sw/lib -o libclustal.la hhalign_wrapper.lo ktuple_pair.lo list.lo log.lo muscle_upgma.lo muscle_tree.lo mbed.lo pair_dist.lo progress.lo seq.lo symmatrix.lo tree.lo util.lo weights.lo -largtable2 -lm libtool: link: ar cru .libs/libclustal.a .libs/hhalign_wrapper.o .libs/ktuple_pair.o .libs/list.o .libs/log.o .libs/muscle_upgma.o .libs/muscle_tree.o .libs/mbed.o .libs/pair_dist.o .libs/progress.o .libs/seq.o .libs/symmatrix.o .libs/tree.o .libs/util.o .libs/weights.o libtool: link: ranlib .libs/libclustal.a libtool: link: ( cd ".libs" && rm -f "libclustal.la" && ln -s "../libclustal.la" "libclustal.la" ) /bin/sh ../libtool --tag=CC --mode=compile gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -O3 -fopenmp -g -O2 -MT clustal-omega.lo -MD -MP -MF .deps/clustal-omega.Tpo -c -o clustal-omega.lo clustal-omega.c g++-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -O3 -fopenmp -g -O2 -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -O3 -fopenmp -g -O2 -MT mymain.o -MD -MP -MF .deps/mymain.Tpo -c -o mymain.o mymain.c libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -O3 -fopenmp -g -O2 -MT clustal-omega.lo -MD -MP -MF .deps/clustal-omega.Tpo -c clustal-omega.c -fno-common -DPIC -o .libs/clustal-omega.o mv -f .deps/main.Tpo .deps/main.Po mv -f .deps/mymain.Tpo .deps/mymain.Po libtool: compile: gcc-fsf-4.8 -DHAVE_CONFIG_H -I. -I/sw/include -O3 -fopenmp -g -O2 -MT clustal-omega.lo -MD -MP -MF .deps/clustal-omega.Tpo -c clustal-omega.c -o clustal-omega.o >/dev/null 2>&1 mv -f .deps/clustal-omega.Tpo .deps/clustal-omega.Plo /bin/sh ../libtool --tag=CC --mode=link gcc-fsf-4.8 -O3 -fopenmp -g -O2 -static -L/sw/lib -o libclustalo.la -rpath /sw/lib clustal-omega.lo clustal/libclustal.la hhalign/libhhalign.la squid/libsquid.la kmpp/libkmpp.la -largtable2 -lm libtool: link: (cd .libs/libclustalo.lax/libclustal.a && ar x "/sw/build.build/clustalo-1.2.1-3/clustal-omega-1.2.1/src/clustal/.libs/libclustal.a") libtool: link: (cd .libs/libclustalo.lax/libhhalign.a && ar x "/sw/build.build/clustalo-1.2.1-3/clustal-omega-1.2.1/src/hhalign/.libs/libhhalign.a") libtool: link: (cd .libs/libclustalo.lax/libsquid.a && ar x "/sw/build.build/clustalo-1.2.1-3/clustal-omega-1.2.1/src/squid/.libs/libsquid.a") libtool: link: (cd .libs/libclustalo.lax/libkmpp.a && ar x "/sw/build.build/clustalo-1.2.1-3/clustal-omega-1.2.1/src/kmpp/.libs/libkmpp.a") libtool: link: ar cru .libs/libclustalo.a clustal-omega.o .libs/libclustalo.lax/libclustal.a/hhalign_wrapper.o .libs/libclustalo.lax/libclustal.a/ktuple_pair.o .libs/libclustalo.lax/libclustal.a/list.o .libs/libclustalo.lax/libclustal.a/log.o .libs/libclustalo.lax/libclustal.a/mbed.o .libs/libclustalo.lax/libclustal.a/muscle_tree.o .libs/libclustalo.lax/libclustal.a/muscle_upgma.o .libs/libclustalo.lax/libclustal.a/pair_dist.o .libs/libclustalo.lax/libclustal.a/progress.o .libs/libclustalo.lax/libclustal.a/seq.o .libs/libclustalo.lax/libclustal.a/symmatrix.o .libs/libclustalo.lax/libclustal.a/tree.o .libs/libclustalo.lax/libclustal.a/util.o .libs/libclustalo.lax/libclustal.a/weights.o .libs/libclustalo.lax/libhhalign.a/hhalign.o .libs/libclustalo.lax/libsquid.a/a2m.o .libs/libclustalo.lax/libsquid.a/aligneval.o .libs/libclustalo.lax/libsquid.a/alignio.o .libs/libclustalo.lax/libsquid.a/clustal.o .libs/libclustalo.lax/libsquid.a/cluster.o .libs/libclustalo.lax/libsquid.a/dayhoff.o .libs/libclustalo.lax/libsquid.a/eps.o .libs/libclustalo.lax/libsquid.a/file.o .libs/libclustalo.lax/libsquid.a/getopt.o .libs/libclustalo.lax/libsquid.a/gki.o .libs/libclustalo.lax/libsquid.a/gsi.o .libs/libclustalo.lax/libsquid.a/gsi64.o .libs/libclustalo.lax/libsquid.a/hsregex.o .libs/libclustalo.lax/libsquid.a/iupac.o .libs/libclustalo.lax/libsquid.a/msa.o .libs/libclustalo.lax/libsquid.a/msf.o .libs/libclustalo.lax/libsquid.a/phylip.o .libs/libclustalo.lax/libsquid.a/revcomp.o .libs/libclustalo.lax/libsquid.a/rk.o .libs/libclustalo.lax/libsquid.a/selex.o .libs/libclustalo.lax/libsquid.a/seqencode.o .libs/libclustalo.lax/libsquid.a/shuffle.o .libs/libclustalo.lax/libsquid.a/sqerror.o .libs/libclustalo.lax/libsquid.a/sqio.o .libs/libclustalo.lax/libsquid.a/squidcore.o .libs/libclustalo.lax/libsquid.a/sre_ctype.o .libs/libclustalo.lax/libsquid.a/sre_math.o .libs/libclustalo.lax/libsquid.a/sre_random.o .libs/libclustalo.lax/libsquid.a/sre_string.o .libs/libclustalo.lax/libsquid.a/ssi.o .libs/libclustalo.lax/libsquid.a/stack.o .libs/libclustalo.lax/libsquid.a/stockholm.o .libs/libclustalo.lax/libsquid.a/stopwatch.o .libs/libclustalo.lax/libsquid.a/translate.o .libs/libclustalo.lax/libsquid.a/types.o .libs/libclustalo.lax/libsquid.a/vectorops.o .libs/libclustalo.lax/libsquid.a/weight.o .libs/libclustalo.lax/libkmpp.a/KMeans.o .libs/libclustalo.lax/libkmpp.a/KmTree.o .libs/libclustalo.lax/libkmpp.a/KmUtils.o /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libclustalo.a(gsi64.o) has no symbols libtool: link: ranlib .libs/libclustalo.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: .libs/libclustalo.a(gsi64.o) has no symbols libtool: link: rm -fr .libs/libclustalo.lax libtool: link: ( cd ".libs" && rm -f "libclustalo.la" && ln -s "../libclustalo.la" "libclustalo.la" ) /bin/sh ../libtool --tag=CXX --mode=link g++-fsf-4.8 -O3 -fopenmp -g -O2 -L/sw/lib -o clustalo main.o mymain.o libclustalo.la -largtable2 -lm libtool: link: g++-fsf-4.8 -O3 -fopenmp -g -O2 -o clustalo main.o mymain.o -L/sw/lib ./.libs/libclustalo.a /sw/lib/libargtable2.dylib -lm make[1]: Nothing to be done for `all-am'. /bin/rm -rf /sw/build.build/root-clustalo-1.2.1-3 /bin/mkdir -p /sw/build.build/root-clustalo-1.2.1-3/sw /bin/mkdir -p /sw/build.build/root-clustalo-1.2.1-3/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-clustalo-1.2.1-3 sudo -u fink-bld [ENV] sh -c /tmp/fink.b_Jfe fink-package-precedence . Scanning /\.Plo,\.Po$/ dependency files... ./src/.deps/clustal-omega.Plo ./src/.deps/main.Po ./src/.deps/mymain.Po ./src/clustal/.deps/hhalign_wrapper.Plo ./src/clustal/.deps/ktuple_pair.Plo ./src/clustal/.deps/list.Plo ./src/clustal/.deps/log.Plo ./src/clustal/.deps/mbed.Plo ./src/clustal/.deps/muscle_tree.Plo ./src/clustal/.deps/muscle_upgma.Plo ./src/clustal/.deps/pair_dist.Plo ./src/clustal/.deps/progress.Plo ./src/clustal/.deps/seq.Plo ./src/clustal/.deps/symmatrix.Plo ./src/clustal/.deps/tree.Plo ./src/clustal/.deps/util.Plo ./src/clustal/.deps/weights.Plo ./src/hhalign/.deps/hhalign.Plo ./src/kmpp/.deps/KMeans.Plo ./src/kmpp/.deps/KmTree.Plo ./src/kmpp/.deps/KmUtils.Plo ./src/squid/.deps/a2m.Plo ./src/squid/.deps/aligneval.Plo ./src/squid/.deps/alignio.Plo ./src/squid/.deps/clustal.Plo ./src/squid/.deps/cluster.Plo ./src/squid/.deps/dayhoff.Plo ./src/squid/.deps/eps.Plo ./src/squid/.deps/file.Plo ./src/squid/.deps/getopt.Plo ./src/squid/.deps/gki.Plo ./src/squid/.deps/gsi.Plo ./src/squid/.deps/gsi64.Plo ./src/squid/.deps/hsregex.Plo ./src/squid/.deps/iupac.Plo ./src/squid/.deps/msa.Plo ./src/squid/.deps/msf.Plo ./src/squid/.deps/phylip.Plo ./src/squid/.deps/revcomp.Plo ./src/squid/.deps/rk.Plo ./src/squid/.deps/selex.Plo ./src/squid/.deps/seqencode.Plo ./src/squid/.deps/shuffle.Plo ./src/squid/.deps/sqerror.Plo ./src/squid/.deps/sqio.Plo ./src/squid/.deps/squidcore.Plo ./src/squid/.deps/sre_ctype.Plo ./src/squid/.deps/sre_math.Plo ./src/squid/.deps/sre_random.Plo ./src/squid/.deps/sre_string.Plo ./src/squid/.deps/ssi.Plo ./src/squid/.deps/stack.Plo ./src/squid/.deps/stockholm.Plo ./src/squid/.deps/stopwatch.Plo ./src/squid/.deps/translate.Plo ./src/squid/.deps/types.Plo ./src/squid/.deps/vectorops.Plo ./src/squid/.deps/weight.Plo Looking for incorrect headers in 58 dependency files... Determining fink providers of 88 headers... 1 - 88 Found use of headers from 2 fink packages: gcc48-compiler libargtable2-dev Scanning binaries for incorrect dyld linking... make install DESTDIR=/sw/build.build/root-clustalo-1.2.1-3 Making install in src Making install in hhalign make[3]: Nothing to be done for `install-exec-am'. test -z "/sw/include/clustalo/hhalign" || ../.././install-sh -c -d "/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/hhalign" /usr/bin/install -c -m 644 'general.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/hhalign/general.h' /usr/bin/install -c -m 644 'hhfunc.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/hhalign/hhfunc.h' Making install in squid make[3]: Nothing to be done for `install-exec-am'. test -z "/sw/include/clustalo/squid" || ../.././install-sh -c -d "/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid" /usr/bin/install -c -m 644 'gki.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/gki.h' /usr/bin/install -c -m 644 'gsi64.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/gsi64.h' /usr/bin/install -c -m 644 'msa.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/msa.h' /usr/bin/install -c -m 644 'rk.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/rk.h' /usr/bin/install -c -m 644 'squid.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/squid.h' /usr/bin/install -c -m 644 'stopwatch.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/stopwatch.h' /usr/bin/install -c -m 644 'sqfuncs.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/sqfuncs.h' /usr/bin/install -c -m 644 'sre_random.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/sre_random.h' /usr/bin/install -c -m 644 'ssi.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/ssi.h' /usr/bin/install -c -m 644 'stockholm.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/stockholm.h' /usr/bin/install -c -m 644 'vectorops.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/vectorops.h' /usr/bin/install -c -m 644 'version.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/squid/version.h' Making install in kmpp make[3]: Nothing to be done for `install-exec-am'. make[3]: Nothing to be done for `install-data-am'. Making install in clustal make[3]: Nothing to be done for `install-exec-am'. test -z "/sw/include/clustalo/clustal" || ../.././install-sh -c -d "/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal" /usr/bin/install -c -m 644 'hhalign_wrapper.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/hhalign_wrapper.h' /usr/bin/install -c -m 644 'ktuple_pair.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/ktuple_pair.h' /usr/bin/install -c -m 644 'log.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/log.h' /usr/bin/install -c -m 644 'mbed.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/mbed.h' /usr/bin/install -c -m 644 'muscle_tree.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/muscle_tree.h' /usr/bin/install -c -m 644 'pair_dist.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/pair_dist.h' /usr/bin/install -c -m 644 'progress.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/progress.h' /usr/bin/install -c -m 644 'seq.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/seq.h' /usr/bin/install -c -m 644 'symmatrix.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/symmatrix.h' /usr/bin/install -c -m 644 'tree.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/tree.h' /usr/bin/install -c -m 644 'util.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/util.h' /usr/bin/install -c -m 644 'weights.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/clustal/weights.h' test -z "/sw/lib" || .././install-sh -c -d "/sw/build.build/root-clustalo-1.2.1-3/sw/lib" /bin/sh ../libtool --mode=install /usr/bin/install -c 'libclustalo.la' '/sw/build.build/root-clustalo-1.2.1-3/sw/lib/libclustalo.la' libtool: install: /usr/bin/install -c .libs/libclustalo.lai /sw/build.build/root-clustalo-1.2.1-3/sw/lib/libclustalo.la libtool: install: /usr/bin/install -c .libs/libclustalo.a /sw/build.build/root-clustalo-1.2.1-3/sw/lib/libclustalo.a libtool: install: chmod 644 /sw/build.build/root-clustalo-1.2.1-3/sw/lib/libclustalo.a libtool: install: ranlib /sw/build.build/root-clustalo-1.2.1-3/sw/lib/libclustalo.a /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: /sw/build.build/root-clustalo-1.2.1-3/sw/lib/libclustalo.a(gsi64.o) has no symbols libtool: install: warning: remember to run `libtool --finish /sw/lib' test -z "/sw/bin" || .././install-sh -c -d "/sw/build.build/root-clustalo-1.2.1-3/sw/bin" /bin/sh ../libtool --mode=install /usr/bin/install -c 'clustalo' '/sw/build.build/root-clustalo-1.2.1-3/sw/bin/clustalo' libtool: install: /usr/bin/install -c clustalo /sw/build.build/root-clustalo-1.2.1-3/sw/bin/clustalo test -z "/sw/include/clustalo/" || .././install-sh -c -d "/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo/" /usr/bin/install -c -m 644 'clustal-omega-config.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo//clustal-omega-config.h' /usr/bin/install -c -m 644 'clustal-omega.h' '/sw/build.build/root-clustalo-1.2.1-3/sw/include/clustalo//clustal-omega.h' make[2]: Nothing to be done for `install-exec-am'. test -z "/sw/share/doc/clustal-omega" || ./install-sh -c -d "/sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustal-omega" /usr/bin/install -c -m 644 'README' '/sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustal-omega/README' test -z "/sw/lib/pkgconfig" || ./install-sh -c -d "/sw/build.build/root-clustalo-1.2.1-3/sw/lib/pkgconfig" /usr/bin/install -c -m 644 'clustalo.pc' '/sw/build.build/root-clustalo-1.2.1-3/sw/lib/pkgconfig/clustalo.pc' rm -rf /sw/build.build/root-clustalo-1.2.1-3/sw/include /sw/build.build/root-clustalo-1.2.1-3/sw/lib sudo -u fink-bld [ENV] sh -c /tmp/fink.AVgBA /usr/bin/install -d -m 700 /sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustalo /bin/cp -r AUTHORS /sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustalo/ /bin/cp -r COPYING /sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustalo/ /bin/cp -r ChangeLog /sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustalo/ /bin/cp -r README /sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustalo/ /bin/cp -r TODO /sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustalo/ /bin/chmod -R go=u-w /sw/build.build/root-clustalo-1.2.1-3/sw/share/doc/clustalo /bin/rm -f /sw/build.build/root-clustalo-1.2.1-3/sw/info/dir /sw/build.build/root-clustalo-1.2.1-3/sw/info/dir.old /sw/build.build/root-clustalo-1.2.1-3/sw/share/info/dir /sw/build.build/root-clustalo-1.2.1-3/sw/share/info/dir.old Reverting ownership of install dir to root Writing control file... Writing md5sums file... env LANG=C LC_ALL=C dpkg-deb -b root-clustalo-1.2.1-3 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `clustalo' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/clustalo_1.2.1-3_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-clustalo-1.2.1-3 (Reading database ... 9809 files and directories currently installed.) Removing fink-buildlock-clustalo-1.2.1-3 ...