lp://qastaging/~noskcaj/ubuntu/utopic/infernal/ftbfs-fix
- Get this branch:
- bzr branch lp://qastaging/~noskcaj/ubuntu/utopic/infernal/ftbfs-fix
Branch merges
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Diff: 30156 lines (+24750/-861)352 files modifiedCOPYRIGHT (+1/-1)
INSTALL (+5/-5)
Makefile.in (+2/-2)
README (+2/-2)
RELEASE-NOTES (+171/-12)
configure (+23/-23)
configure.ac (+12/-12)
debian/changelog (+7/-0)
debian/control (+1/-1)
documentation/Makefile.in (+2/-2)
documentation/manpages/Makefile.in (+2/-2)
documentation/manpages/cmalign.man (+2/-2)
documentation/manpages/cmbuild.man (+2/-2)
documentation/manpages/cmcalibrate.man (+2/-2)
documentation/manpages/cmconvert.man (+2/-2)
documentation/manpages/cmemit.man (+2/-2)
documentation/manpages/cmfetch.man (+2/-2)
documentation/manpages/cmpress.man (+2/-2)
documentation/manpages/cmscan.man (+2/-2)
documentation/manpages/cmsearch.man (+2/-2)
documentation/manpages/cmsearch_dual.man (+2/-2)
documentation/manpages/cmstat.man (+2/-2)
documentation/manpages/infernal.man (+2/-2)
documentation/manpages/sse_cmsearch.man (+2/-2)
documentation/userguide/Makefile.in (+2/-2)
documentation/userguide/install.tex (+5/-5)
documentation/userguide/introduction.tex (+5/-6)
documentation/userguide/more.tex (+8/-11)
documentation/userguide/pipeline.tex (+2/-2)
documentation/userguide/tutorial.tex (+22/-21)
easel/00README (+2/-2)
easel/COPYRIGHT (+1/-1)
easel/INSTALL (+5/-5)
easel/Makefile.in (+2/-2)
easel/configure (+11/-11)
easel/configure.ac (+4/-4)
easel/devkit/sqc (+2/-3)
easel/documentation/Makefile.in (+2/-2)
easel/documentation/codestyle.tex (+10/-10)
easel/easel.c (+2/-2)
easel/easel.h (+2/-2)
easel/esl_alphabet.c (+2/-2)
easel/esl_alphabet.h (+2/-2)
easel/esl_buffer.c (+2/-2)
easel/esl_buffer.h (+2/-2)
easel/esl_cluster.c (+2/-2)
easel/esl_cluster.h (+2/-2)
easel/esl_config.h.in (+2/-2)
easel/esl_dirichlet.c (+2/-2)
easel/esl_dirichlet.h (+2/-2)
easel/esl_distance.c (+2/-2)
easel/esl_distance.h (+2/-2)
easel/esl_dmatrix.c (+2/-2)
easel/esl_dmatrix.h (+2/-2)
easel/esl_exponential.c (+2/-2)
easel/esl_exponential.h (+2/-2)
easel/esl_fileparser.c (+2/-2)
easel/esl_fileparser.h (+2/-2)
easel/esl_gamma.c (+2/-2)
easel/esl_gamma.h (+2/-2)
easel/esl_getopts.c (+2/-2)
easel/esl_getopts.h (+2/-2)
easel/esl_gev.c (+2/-2)
easel/esl_gev.h (+2/-2)
easel/esl_gumbel.c (+2/-2)
easel/esl_gumbel.h (+2/-2)
easel/esl_histogram.c (+2/-2)
easel/esl_histogram.h (+2/-2)
easel/esl_hmm.c (+2/-2)
easel/esl_hmm.h (+2/-2)
easel/esl_hyperexp.c (+2/-2)
easel/esl_hyperexp.h (+2/-2)
easel/esl_keyhash.c (+2/-2)
easel/esl_keyhash.h (+2/-2)
easel/esl_mem.c (+2/-2)
easel/esl_mem.h (+2/-2)
easel/esl_minimizer.c (+2/-2)
easel/esl_minimizer.h (+2/-2)
easel/esl_mixgev.c (+2/-2)
easel/esl_mixgev.h (+2/-2)
easel/esl_mpi.c (+2/-2)
easel/esl_mpi.h (+2/-2)
easel/esl_msa.c (+2/-2)
easel/esl_msa.h (+2/-2)
easel/esl_msacluster.c (+2/-2)
easel/esl_msacluster.h (+2/-2)
easel/esl_msafile.c (+2/-2)
easel/esl_msafile.h (+2/-2)
easel/esl_msafile2.c (+2/-2)
easel/esl_msafile2.h (+2/-2)
easel/esl_msafile_a2m.c (+2/-2)
easel/esl_msafile_a2m.h (+2/-2)
easel/esl_msafile_afa.c (+2/-2)
easel/esl_msafile_afa.h (+2/-2)
easel/esl_msafile_clustal.c (+2/-2)
easel/esl_msafile_clustal.h (+2/-2)
easel/esl_msafile_phylip.c (+2/-2)
easel/esl_msafile_phylip.h (+2/-2)
easel/esl_msafile_psiblast.c (+2/-2)
easel/esl_msafile_psiblast.h (+2/-2)
easel/esl_msafile_selex.c (+2/-2)
easel/esl_msafile_selex.h (+2/-2)
easel/esl_msafile_stockholm.c (+2/-2)
easel/esl_msafile_stockholm.h (+2/-2)
easel/esl_msashuffle.c (+2/-2)
easel/esl_msashuffle.h (+2/-2)
easel/esl_msaweight.c (+2/-2)
easel/esl_msaweight.h (+2/-2)
easel/esl_normal.c (+2/-2)
easel/esl_normal.h (+2/-2)
easel/esl_paml.c (+2/-2)
easel/esl_paml.h (+2/-2)
easel/esl_random.c (+2/-2)
easel/esl_random.h (+2/-2)
easel/esl_randomseq.c (+2/-2)
easel/esl_randomseq.h (+2/-2)
easel/esl_ratematrix.c (+2/-2)
easel/esl_ratematrix.h (+2/-2)
easel/esl_recorder.c (+2/-2)
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easel/esl_regexp.c (+2/-2)
easel/esl_regexp.h (+2/-2)
easel/esl_rootfinder.c (+2/-2)
easel/esl_rootfinder.h (+2/-2)
easel/esl_scorematrix.c (+2/-2)
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easel/esl_sqio.h (+2/-2)
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easel/esl_weibull.c (+2/-2)
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easel/esl_workqueue.c (+2/-2)
easel/esl_workqueue.h (+2/-2)
easel/esl_wuss.c (+2/-2)
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easel/interface_gsl.c (+2/-2)
easel/interface_lapack.c (+2/-2)
easel/miniapps/Makefile.in (+2/-2)
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easel/miniapps/esl-alimanip.c (+2/-2)
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easel/miniapps/esl-alistat.c (+2/-2)
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easel/miniapps/esl-reformat.c (+2/-2)
easel/miniapps/esl-selectn.c (+2/-2)
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easel/miniapps/esl-ssdraw.c (+2/-2)
easel/miniapps/esl-weight.c (+2/-2)
easel/testsuite/Makefile.in (+2/-2)
hmmer/COPYRIGHT (+1/-1)
hmmer/INSTALL (+5/-5)
hmmer/Makefile.in (+2/-2)
hmmer/README (+2/-2)
hmmer/configure (+16/-16)
hmmer/configure.ac (+8/-8)
hmmer/documentation/Makefile.in (+2/-2)
hmmer/documentation/man/Makefile.in (+2/-2)
hmmer/documentation/userguide/Makefile.in (+2/-2)
hmmer/profmark/Makefile.in (+2/-2)
hmmer/profmark/create-profmark.c (+2/-2)
hmmer/src/Makefile.in (+2/-2)
hmmer/src/alimask.c (+2/-2)
hmmer/src/build.c (+2/-2)
hmmer/src/cachedb.c (+2/-2)
hmmer/src/cachedb.h (+2/-2)
hmmer/src/emit.c (+2/-2)
hmmer/src/evalues.c (+2/-2)
hmmer/src/exactmatch.c (+2/-2)
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hmmer/src/generic_fwdback_chk.c (+2/-2)
hmmer/src/generic_msv.c (+2/-2)
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hmmer/src/generic_optacc.c (+2/-2)
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hmmer/src/generic_viterbi.c (+2/-2)
hmmer/src/generic_vtrace.c (+2/-2)
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hmmer/src/hmmbuild.c (+2/-2)
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hmmer/src/hmmconvert.c (+2/-2)
hmmer/src/hmmdmstr.c (+2/-2)
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hmmer/src/hmmemit.c (+2/-2)
hmmer/src/hmmer.c (+2/-2)
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hmmer/src/hmmlogo.c (+2/-2)
hmmer/src/hmmpgmd.c (+2/-2)
hmmer/src/hmmpgmd.h (+2/-2)
hmmer/src/hmmpgmd2msa.c (+2/-2)
hmmer/src/hmmpress.c (+2/-2)
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hmmer/src/hmmsim.c (+2/-2)
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hmmer/src/impl_dummy/vitfilter.c (+2/-2)
hmmer/src/impl_dummy/vitscore.c (+2/-2)
hmmer/src/impl_sse/Makefile.in (+2/-2)
hmmer/src/impl_sse/decoding.c (+2/-2)
hmmer/src/impl_sse/fm.c (+2/-2)
hmmer/src/impl_sse/fwdback.c (+2/-2)
hmmer/src/impl_sse/impl_sse.h (+2/-2)
hmmer/src/impl_sse/io.c (+2/-2)
hmmer/src/impl_sse/mpi.c (+2/-2)
hmmer/src/impl_sse/msvfilter.c (+2/-2)
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hmmer/src/impl_sse/optacc.c (+2/-2)
hmmer/src/impl_sse/p7_omx.c (+2/-2)
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hmmer/src/impl_sse/stotrace.c (+2/-2)
hmmer/src/impl_sse/vitfilter.c (+2/-2)
hmmer/src/impl_sse/vitscore.c (+2/-2)
hmmer/src/impl_vmx/Makefile.in (+2/-2)
hmmer/src/impl_vmx/decoding.c (+2/-2)
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hmmer/src/impl_vmx/p7_oprofile.c (+2/-2)
hmmer/src/impl_vmx/stotrace.c (+2/-2)
hmmer/src/impl_vmx/vitfilter.c (+2/-2)
hmmer/src/impl_vmx/vitscore.c (+2/-2)
hmmer/src/jackhmmer.c (+2/-2)
hmmer/src/logsum.c (+2/-2)
hmmer/src/modelconfig.c (+2/-2)
hmmer/src/modelstats.c (+2/-2)
hmmer/src/mpisupport.c (+2/-2)
hmmer/src/nhmmer.c (+2/-2)
hmmer/src/p7_alidisplay.c (+2/-2)
hmmer/src/p7_bg.c (+2/-2)
hmmer/src/p7_builder.c (+2/-2)
hmmer/src/p7_config.h.in (+2/-2)
hmmer/src/p7_gmx.c (+2/-2)
hmmer/src/p7_gmxchk.c (+2/-2)
hmmer/src/p7_gmxchk.h (+2/-2)
hmmer/src/p7_hmm.c (+2/-2)
hmmer/src/p7_hmmcache.c (+2/-2)
hmmer/src/p7_hmmcache.h (+2/-2)
hmmer/src/p7_hmmfile.c (+2/-2)
hmmer/src/p7_hmmwindow.c (+2/-2)
hmmer/src/p7_msvdata.c (+2/-2)
hmmer/src/p7_null3.c (+2/-2)
hmmer/src/p7_pipeline.c (+2/-2)
hmmer/src/p7_prior.c (+2/-2)
hmmer/src/p7_profile.c (+2/-2)
hmmer/src/p7_tophits.c (+2/-2)
hmmer/src/p7_trace.c (+2/-2)
hmmer/src/phmmer.c (+2/-2)
hmmer/src/seqmodel.c (+2/-2)
hmmer/src/tracealign.c (+2/-2)
hmmer/testsuite/Makefile.in (+2/-2)
hmmer/testsuite/testsuite.sqc (+2/-2)
rmark/Makefile.in (+2/-2)
src/Makefile.in (+2/-2)
src/bandcyk-montecarlo-test.c (+2/-2)
src/bandcyk-truncation-test.c (+2/-2)
src/cm.c (+2/-2)
src/cm_alidisplay.c (+2/-2)
src/cm_dispatch.h (+2/-2)
src/cm_dpalign.c (+5/-5)
src/cm_dpalign_trunc.c (+2/-2)
src/cm_dpsearch.c (+2/-2)
src/cm_dpsearch_trunc.c (+2/-2)
src/cm_dpsmall.c (+2/-2)
src/cm_file.c (+8/-3)
src/cm_modelconfig.c (+2/-2)
src/cm_modelmaker.c (+2/-2)
src/cm_p7_modelmaker.c (+2/-2)
src/cm_pipeline.c (+62/-15)
src/cm_qdband.c (+2/-2)
src/cm_submodel.c (+2/-2)
src/cm_tophits.c (+2/-2)
src/cmalign.c (+2/-2)
src/cmbuild.c (+2/-2)
src/cmcalibrate.c (+2/-2)
src/cmconvert.c (+12/-3)
src/cmemit.c (+2/-2)
src/cmfetch.c (+2/-2)
src/cmpress.c (+2/-2)
src/cmscan.c (+16/-16)
src/cmsearch.c (+17/-17)
src/cmstat.c (+2/-2)
src/cp9-test.c (+2/-2)
src/cp9.c (+2/-2)
src/cp9_dp.c (+2/-2)
src/cp9_trace.c (+2/-2)
src/display.c (+2/-2)
src/eweight.c (+2/-2)
src/hmmband.c (+2/-2)
src/hmmband.h (+2/-2)
src/impl_sse/Makefile.in (+2/-2)
src/impl_sse/impl_sse.h (+2/-2)
src/impl_sse/sse_cm_dpsearch.c (+2/-2)
src/impl_sse/sse_cm_dpsmall.c (+2/-2)
src/impl_sse/sse_cmcons_mscyk.c (+2/-2)
src/infernal.h (+8/-3)
src/sa-Makefile.in (+2/-2)
src/sub_cm-test.c (+2/-2)
testsuite/Makefile.in (+2/-2)
testsuite/bug-i43.cm (+23623/-0)
testsuite/bug-i43.fa (+2/-0)
testsuite/bug-i43.pl (+34/-0)
testsuite/dev_testsuite.sqc (+1/-0)
testsuite/testsuite.sqc (+1/-0)
Branch information
- Owner:
- Jackson Doak
- Status:
- Development
Recent revisions
- 10. By Charles Plessy
-
* Team upload.
* New upstream release.
* Removed i386 architecture as some processors do not provide SSE2.
* Conforms with Policy 3.9.5. - 9. By Charles Plessy
-
* Team upload.
* Build-depends on libperl4-corelibs- perl (Closes: #724119).
* debian/control: removed myself from Uploaders. - 8. By Andreas Tille
-
* New upstream source
* debian/source/ format: 3.0 (quilt)
* debian/control:
- cme fix dpkg-control
- debhelper 9
- do not Build-Depend: quilt since source format implies this
- The package builds only on architectures with SSE instructions.
Quoting from build log on armel:
configure: WARNING: Infernal 1.1 requires VMX or SSE capability for
parallel instructions.
configure: error: It appears your platform has neither and will not
support Infernal.
So all non i386/amd64 architectures were excluded
Closes: #718742
- use anonscm in Vcs fields
* debian/rules:
- remove redundant setting for flags which is handled by debhelper 9
automatically
- use xz compression
* debian/copyright: DEP5 - 7. By Steffen Möller
-
* New upstream version - aiming to support RNAWorld BOINC project,
with many thanks and regards to Yoyo!
- cmscore no longer available
* Bumped policy to 3.9.4 (no changes needed)
- introduced hardening, with it build dep on
dpkg-dev (>= 1.16.1~) - 6. By Steffen Möller
-
* Series of mall fixes (Closes: #643407).
* source/format 3.0
* Policy to 3.9.2
* added infernal-dbg
* corrected upstream's email address - 4. By Charles Plessy
-
* Switch to CDBS to benefit from automagical config.{sub,guess}
update (debian/rules). Closes: #550253.
* debian/control:
- Depend on cdbs, downgraded requirement on debhelper from 7.1 to 7.
- Transferred bibliographic information from the package description
to debian/upstream- metadata. yaml.
- Clarified the short description of the documentation package.
* Removed debian/infernal. dirs, not needed.
* Edited README.source, removing mention that infernal is in contrib.
* debian/copyright points at the version 3 of the GPL. - 3. By Andreas Tille
-
[ Charles Plessy ]
* Updated my email address.[ Andreas Tille ]
* New upstream version
* debian/control:
- Standards-Version: 3.8.3 (no changes needed)
- Added myself to uploaders
- s/Debian-Med/Debian Med/
- Build-Depends: debhelper (>= 7.1) autotools-dev
- Package: infernal-doc
* debian/rules rewritten to make use of short dh
* debian/copyright:
- added myself to Copyright holders of debian/*
- squid is not part of the upstream tarball anymore so this
paragraph was deleted
- files/Userguide.pdf: Copied comment about PDF = source from
README.Debian
* debian/infernal- doc.doc- base
* debian/infernal. install: install src/{trcyk, truncyk_ check} to
/usr/bin* TODO: Convince upstream to release libeazel which is also used in
hmmer as a separate library instead of copying the code into
different projects
Branch metadata
- Branch format:
- Branch format 7
- Repository format:
- Bazaar repository format 2a (needs bzr 1.16 or later)
- Stacked on:
- lp://qastaging/ubuntu/utopic/infernal