printf ' ' | fink --no-use-binary-dist --yes --build-as-nobody rebuild muscle 2>&1 The package 'muscle' will be built without being installed. Reading build dependency for muscle-3.8.31-1... Reading dependency for muscle-3.8.31-1... Reading build conflict for muscle-3.8.31-1... The package 'dos2unix' will be installed. Reading dependency for dos2unix-6.0.5-1... Reading runtime dependency for dos2unix-6.0.5-1... The following package will be rebuilt: muscle The following additional package will be installed: dos2unix 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/muscle3.8.31_src.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 26 503k 26 134k 0 0 183k 0 0:00:02 --:--:-- 0:00:02 183k 100 503k 100 503k 0 0 320k 0 0:00:01 0:00:01 --:--:-- 320k Reading buildlock packages... All buildlocks accounted for. /sw/bin/dpkg-lockwait -i /sw/fink/debs/dos2unix_6.0.5-1_darwin-x86_64.deb Selecting previously deselected package dos2unix. (Reading database ... 4296 files and directories currently installed.) Unpacking dos2unix (from .../dos2unix_6.0.5-1_darwin-x86_64.deb) ... Setting up dos2unix (6.0.5-1) ... Setting runtime build-lock... dpkg-deb -b /sw/build.build/root-fink-buildlock-muscle-3.8.31-1 /sw/build.build dpkg-deb: building package `fink-buildlock-muscle-3.8.31-1' in `/sw/build.build/fink-buildlock-muscle-3.8.31-1_2014.07.30-21.32.33_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/build.build/fink-buildlock-muscle-3.8.31-1_2014.07.30-21.32.33_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-muscle-3.8.31-1. (Reading database ... 4313 files and directories currently installed.) Unpacking fink-buildlock-muscle-3.8.31-1 (from .../fink-buildlock-muscle-3.8.31-1_2014.07.30-21.32.33_darwin-x86_64.deb) ... Setting up fink-buildlock-muscle-3.8.31-1 (2014.07.30-21.32.33) ... sudo -u fink-bld [ENV] sh -c /tmp/fink.riQZK env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/muscle3.8.31_src.tar.gz muscle3.8.31/src/ muscle3.8.31/src/svnversion.h muscle3.8.31/src/aligntwoprofs.cpp muscle3.8.31/src/scoredist.cpp muscle3.8.31/src/glbalignle.cpp muscle3.8.31/src/fastdistkmer.cpp muscle3.8.31/src/phytofile.cpp muscle3.8.31/src/intmath.cpp muscle3.8.31/src/fastclust.cpp muscle3.8.31/src/aligngivenpathsw.cpp muscle3.8.31/src/enumopts.cpp muscle3.8.31/src/ppscore.cpp muscle3.8.31/src/scorepp.cpp muscle3.8.31/src/profdb.cpp muscle3.8.31/src/globalsosx.cpp muscle3.8.31/src/color.cpp muscle3.8.31/src/msadistkimura.h muscle3.8.31/src/phy3.cpp muscle3.8.31/src/globals.cpp muscle3.8.31/src/gotowt.cpp muscle3.8.31/src/params.cpp muscle3.8.31/src/distfunc.h muscle3.8.31/src/nwdasimple2.cpp muscle3.8.31/src/enums.h muscle3.8.31/src/muscle.h muscle3.8.31/src/msa2.cpp muscle3.8.31/src/vtml2.cpp muscle3.8.31/src/progress.cpp muscle3.8.31/src/glbaligndiag.cpp muscle3.8.31/src/pwpath.h muscle3.8.31/src/diffpaths.cpp muscle3.8.31/src/glbalign352.cpp muscle3.8.31/src/enumopts.h muscle3.8.31/src/distfunc.cpp muscle3.8.31/src/glbalign.cpp muscle3.8.31/src/readmx.cpp muscle3.8.31/src/scoremx.cpp muscle3.8.31/src/progalign.cpp muscle3.8.31/src/termgaps.cpp muscle3.8.31/src/phyfromfile.cpp muscle3.8.31/src/hydro.cpp muscle3.8.31/src/clustsetdf.h muscle3.8.31/src/distcalc.cpp muscle3.8.31/src/scoregaps.cpp muscle3.8.31/src/refinetree.cpp muscle3.8.31/src/gapscoredimer.h muscle3.8.31/src/refinesubfams.cpp muscle3.8.31/src/textfile.h muscle3.8.31/src/README.txt muscle3.8.31/src/fastdistkbit.cpp muscle3.8.31/src/refinetreee.cpp muscle3.8.31/src/seq.h muscle3.8.31/src/fastdistmafft.cpp muscle3.8.31/src/phy.cpp muscle3.8.31/src/spfast.cpp muscle3.8.31/src/make.out muscle3.8.31/src/cons.cpp muscle3.8.31/src/globalslinux.cpp muscle3.8.31/src/pwpath.cpp muscle3.8.31/src/html.cpp muscle3.8.31/src/edgelist.h muscle3.8.31/src/profile.h muscle3.8.31/src/muscle.vcproj muscle3.8.31/src/objscoreda.cpp muscle3.8.31/src/savebest.cpp muscle3.8.31/src/typetostr.cpp muscle3.8.31/src/pam200mafft.cpp muscle3.8.31/src/traceback.cpp muscle3.8.31/src/difftreese.cpp muscle3.8.31/src/glbalignns.cpp muscle3.8.31/src/make.err muscle3.8.31/src/globalsother.cpp muscle3.8.31/src/msf.cpp muscle3.8.31/src/nucmx.cpp muscle3.8.31/src/distcalc.h muscle3.8.31/src/scorehistory.cpp muscle3.8.31/src/anchors.cpp muscle3.8.31/src/diffobjscore.cpp muscle3.8.31/src/subfams.cpp muscle3.8.31/src/releases.txt muscle3.8.31/src/henikoffweight.cpp muscle3.8.31/src/nwdasimple.cpp muscle3.8.31/src/tomhydro.cpp muscle3.8.31/src/diaglist.h muscle3.8.31/src/refine.cpp muscle3.8.31/src/aligntwomsas.cpp muscle3.8.31/src/muscle21 muscle3.8.31/src/clustsetmsa.h muscle3.8.31/src/nwsmall.cpp muscle3.8.31/src/fastdistjones.cpp muscle3.8.31/src/cluster.cpp muscle3.8.31/src/refinehoriz.cpp muscle3.8.31/src/alpha.cpp muscle3.8.31/src/glbalignss.cpp muscle3.8.31/src/msa.h muscle3.8.31/src/fastscorepath2.cpp muscle3.8.31/src/muscle.cpp muscle3.8.31/src/posgap.cpp muscle3.8.31/src/glbalignsimple.cpp muscle3.8.31/src/local.cpp muscle3.8.31/src/dpreglist.cpp muscle3.8.31/src/refinew.cpp muscle3.8.31/src/phyfromclust.cpp muscle3.8.31/src/aligngivenpath.cpp muscle3.8.31/src/finddiagsn.cpp muscle3.8.31/src/globalswin32.cpp muscle3.8.31/src/dpregionlist.h muscle3.8.31/src/domuscle.cpp muscle3.8.31/src/drawtree.cpp muscle3.8.31/src/blosumla.cpp muscle3.8.31/src/bittraceback.cpp muscle3.8.31/src/unixio.h muscle3.8.31/src/glbalndimer.cpp muscle3.8.31/src/muscleout.cpp muscle3.8.31/src/sptest.cpp muscle3.8.31/src/nwdasmall.cpp muscle3.8.31/src/phy2.cpp muscle3.8.31/src/progressivealign.cpp muscle3.8.31/src/mhack.cpp muscle3.8.31/src/textfile.cpp muscle3.8.31/src/phy4.cpp muscle3.8.31/src/makerootmsab.cpp muscle3.8.31/src/msadistmafft.h muscle3.8.31/src/seq.cpp muscle3.8.31/src/tracebacksw.cpp muscle3.8.31/src/onexception.cpp muscle3.8.31/src/options.cpp muscle3.8.31/src/Makefile muscle3.8.31/src/fasta.cpp muscle3.8.31/src/edgelist.cpp muscle3.8.31/src/profile.cpp muscle3.8.31/src/outweights.cpp muscle3.8.31/src/realigndiffse.cpp muscle3.8.31/src/tree.h muscle3.8.31/src/setblosumweights.cpp muscle3.8.31/src/intmath.h muscle3.8.31/src/seqvect.cpp muscle3.8.31/src/clustset.h muscle3.8.31/src/msadistkimura.cpp muscle3.8.31/src/subfam.cpp muscle3.8.31/src/estring.h muscle3.8.31/src/fasta2.cpp muscle3.8.31/src/version.txt muscle3.8.31/src/henikoffweightpb.cpp muscle3.8.31/src/distpwkimura.cpp muscle3.8.31/src/profilefrommsa.cpp muscle3.8.31/src/stabilize.cpp muscle3.8.31/src/sw.cpp muscle3.8.31/src/validateids.cpp muscle3.8.31/src/gonnet.cpp muscle3.8.31/src/clust.cpp muscle3.8.31/src/timing.h muscle3.8.31/src/glbalignspn.cpp muscle3.8.31/src/diaglist.cpp muscle3.8.31/src/clwwt.cpp muscle3.8.31/src/scorehistory.h muscle3.8.31/src/usage.cpp muscle3.8.31/src/dosp.cpp muscle3.8.31/src/objscore.cpp muscle3.8.31/src/redblack.cpp muscle3.8.31/src/msadist.h muscle3.8.31/src/physeq.cpp muscle3.8.31/src/types.h muscle3.8.31/src/estring.cpp muscle3.8.31/src/muscle21.vcproj muscle3.8.31/src/mpam200.cpp muscle3.8.31/src/nwrec.cpp muscle3.8.31/src/seqvect.h muscle3.8.31/src/msa.cpp muscle3.8.31/src/fastdist.cpp muscle3.8.31/src/makerootmsa.cpp muscle3.8.31/src/setgscweights.cpp muscle3.8.31/src/main.cpp muscle3.8.31/src/cluster.h muscle3.8.31/src/writescorefile.cpp muscle3.8.31/src/objscore2.cpp muscle3.8.31/src/alpha.h muscle3.8.31/src/upgma2.cpp muscle3.8.31/src/maketree.cpp muscle3.8.31/src/gonnet.h muscle3.8.31/src/clust.h muscle3.8.31/src/enumtostr.cpp muscle3.8.31/src/dpreglist.h muscle3.8.31/src/tracebackopt.cpp muscle3.8.31/src/setnewhandler.cpp muscle3.8.31/src/threewaywt.cpp muscle3.8.31/src/blosum62.cpp muscle3.8.31/src/refinevert.cpp muscle3.8.31/src/aln.cpp muscle3.8.31/src/objscore.h muscle3.8.31/src/difftrees.cpp muscle3.8.31/src/glbalignsp.cpp muscle3.8.31/src/treefrommsa.cpp muscle3.8.31/src/fastdistnuc.cpp muscle3.8.31/src/gatest.cpp muscle3.8.31/src/params.h muscle3.8.31/src/finddiags.cpp muscle3.8.31/src/glbalignla.cpp muscle3.8.31/src/realigndiffs.cpp muscle3.8.31/src/svnmods.h muscle3.8.31/src/mk sudo -u fink-bld [ENV] sh -c /tmp/fink.bsUdU [ -r /sw/fink/dists/stable/main/finkinfo/sci/muscle.patch ] sudo -u fink-bld [ENV] sh -c /tmp/fink.YyD2d dos2unix src/globalsosx.cpp dos2unix: converting file src/globalsosx.cpp to Unix format... patch -p1 < /sw/fink/dists/stable/main/finkinfo/sci/muscle.patch patching file src/globalsosx.cpp sudo -u fink-bld [ENV] sh -c /tmp/fink.IQjU_ cd src; make chmod +x ./mk ./mk ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured ./mk: line 8: /dev/tty: Device not configured subfams.cpp:44:25: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare] for (unsigned i = 0; i < uNodeCount; ++i) ~ ^ ~~~~~~~~~~ 1 warning generated. In file included from treefrommsa.cpp:5: In file included from ./clustsetmsa.h:8: ./msadist.h:22:10: warning: 10 enumeration values not handled in switch: 'DISTANCE_Undefined', 'DISTANCE_Kmer6_6', 'DISTANCE_Kmer20_3'... [-Wswitch] switch(m_Distance) ^ 1 warning generated. -rwxr-xr-x 1 fink-bld fink-bld 346K Jul 30 21:33 muscle 19957 347 muscle /bin/rm -rf /sw/build.build/root-muscle-3.8.31-1 /bin/mkdir -p /sw/build.build/root-muscle-3.8.31-1/sw /bin/mkdir -p /sw/build.build/root-muscle-3.8.31-1/DEBIAN /usr/sbin/chown -R fink-bld:fink-bld /sw/build.build/root-muscle-3.8.31-1 sudo -u fink-bld [ENV] sh -c /tmp/fink.o_UtR /tmp/fink.yKMzj #!/bin/sh -ev mkdir -p /sw/build.build/root-muscle-3.8.31-1/sw/bin cp -p src/muscle /sw/build.build/root-muscle-3.8.31-1/sw/bin/ cat > LICENSE << EOF MUSCLE v3.8.31 by Robert C. Edgar http://www.drive5.com/muscle This software is donated to the public domain. Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97. EOF sudo -u fink-bld [ENV] sh -c /tmp/fink.Jhhp4 /usr/bin/install -d -m 700 /sw/build.build/root-muscle-3.8.31-1/sw/share/doc/muscle /bin/cp -r LICENSE /sw/build.build/root-muscle-3.8.31-1/sw/share/doc/muscle/ /bin/cp -r src/README.txt /sw/build.build/root-muscle-3.8.31-1/sw/share/doc/muscle/ /bin/chmod -R go=u-w /sw/build.build/root-muscle-3.8.31-1/sw/share/doc/muscle /bin/rm -f /sw/build.build/root-muscle-3.8.31-1/sw/info/dir /sw/build.build/root-muscle-3.8.31-1/sw/info/dir.old /sw/build.build/root-muscle-3.8.31-1/sw/share/info/dir /sw/build.build/root-muscle-3.8.31-1/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-muscle-3.8.31-1 /sw/fink/10.9/stable/main/binary-darwin-x86_64/sci dpkg-deb: building package `muscle' in `/sw/fink/10.9/stable/main/binary-darwin-x86_64/sci/muscle_3.8.31-1_darwin-x86_64.deb'. Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-muscle-3.8.31-1 (Reading database ... 4314 files and directories currently installed.) Removing fink-buildlock-muscle-3.8.31-1 ...