[med-svn] [lamarc] 06/07: Update upstream source from tag 'upstream/2.1.10.1+dfsg'
Andreas Tille
tille at debian.org
Thu Jan 4 20:53:00 UTC 2018
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository lamarc.
commit dcf98f0fee781537d08731c1e79299ad1923902c
Merge: 19f8279 0f70698
Author: Andreas Tille <tille at debian.org>
Date: Thu Jan 4 21:33:25 2018 +0100
Update upstream source from tag 'upstream/2.1.10.1+dfsg'
Update to upstream version '2.1.10.1+dfsg'
with Debian dir d6b19119a2ba5ece2adeea93b5238b88e1214cb8
CONTENTS | 71 +
COPYING | 57 +
HISTORY | 97 +
INSTALL | 2 +
MAINTAINER.README | 179 +
Makefile.am | 22 +-
Makefile.in | 10162 +++++++++++++++++++
README | 61 +
aclocal.m4 | 1188 +++
config/{conf.h.in => conf.h} | 70 +-
config/conf.h.in | 5 +-
config/config.guess | 1447 +++
config/config.sub | 1555 +++
config/depcomp | 520 +
config/dynacounter.bash | 138 +
config/install-sh | 316 +
config/missing | 360 +
configure | 7765 ++++++++++++++
configure.ac | 4 +-
depcomp | 520 +
doc/html/changes.html | 15 +-
doc/html/compiling.html | 6 +-
doc/html/converter_cmd.html | 6 +-
doc/html/genetic_map.html | 6 +-
doc/html/index.html | 4 +-
doc/html/mapping.html | 4 +-
doc/html/menu.html | 11 +-
doc/html/panels.html | 8 +-
doc/pipeline.txt | 235 +
doc/wx-osx-notes.txt | 52 +
firstLinuxBuild.sh | 4 +
install-sh | 316 +
makedebug.sh | 26 +
makegcov.sh | 14 +
makeopt.sh | 17 +
missing | 360 +
projects/macos/MacOSPrefix.h | 37 +
projects/macos/MacOSPrefixDebug.h | 68 +
projects/macos/carb.r | 18 +
projects/macos/lam_conv make | Bin 0 -> 85969 bytes
projects/macos/lamarc make | Bin 0 -> 94970 bytes
projects/macos/make_mwerks.pl | 171 +
projects/macos/mwerks_xml_template | 1261 +++
projects/win32/README | 2 +
projects/win32/gui_lam_conv.vcproj | 324 +
projects/win32/lam_conv.vcproj | 183 +
projects/win32/lamarc.vcproj | 433 +
projects/win32/make_vcproj.pl | 174 +
projects/win32/vcproj_template | 126 +
scripts/buildDmg.sh | 134 +
scripts/pyParallel/README | 19 +
scripts/pyParallel/combine_regions.py | 191 +
scripts/pyParallel/combine_replicates.py | 164 +
scripts/pyParallel/divide_data.py | 108 +
scripts/pyParallel/parallelCommon.py | 239 +
.../binutils-2.15.91-20040904-1-src.tar.gz | Bin 0 -> 14507299 bytes
.../xmingw32/gcc-core-3.4.2-20040916-1-src.tar.gz | Bin 0 -> 14096017 bytes
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scripts/xmingw32/mingw-runtime-3.7.tar.gz | Bin 0 -> 343841 bytes
scripts/xmingw32/w32api-3.2.tar.gz | Bin 0 -> 1530078 bytes
scripts/xmingw32/xmingw32.bat.in | 59 +
scripts/xmingw32/xmingw32.mak | 285 +
scripts/xmingw32/xmingw32.sh.in | 53 +
src/BUGS | 453 -
src/bayeslike/bayesanalyzer_1d.cpp | 22 +-
src/bayeslike/bayesanalyzer_1d.h | 22 +-
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src/convParse/gc_loci_match.cpp | 22 +-
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src/convParse/gc_migrate.cpp | 22 +-
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src/menu/newmenu.h | 22 +-
src/menu/newmenuitems.cpp | 36 +-
src/menu/newmenuitems.h | 26 +-
src/menu/setmenuitem.cpp | 22 +-
src/menu/setmenuitem.h | 28 +-
src/menu/togglemenuitem.cpp | 22 +-
src/menu/togglemenuitem.h | 22 +-
src/menu/twodtable.cpp | 24 +-
src/menu/twodtable.h | 22 +-
src/postlike/analyzer.cpp | 22 +-
src/postlike/analyzer.h | 22 +-
src/postlike/derivatives.cpp | 22 +-
src/postlike/likelihood.cpp | 22 +-
src/postlike/likelihood.h | 22 +-
src/postlike/maximizer.cpp | 24 +-
src/postlike/maximizer.h | 22 +-
src/postlike/maximizer_strings.cpp | 22 +-
src/postlike/maximizer_strings.h | 22 +-
src/postlike/plforces.cpp | 22 +-
src/postlike/plforces.h | 56 +-
src/postlike/plotstat.cpp | 22 +-
src/postlike/plotstat.h | 22 +-
src/postlike/profile.cpp | 22 +-
src/report/curvefiles.cpp | 22 +-
src/report/curvefiles.h | 22 +-
src/report/outputfile.cpp | 22 +-
src/report/outputfile.h | 22 +-
src/report/reportpage.cpp | 22 +-
src/report/reportpage.h | 26 +-
src/report/runreport.cpp | 22 +-
src/report/runreport.h | 22 +-
src/report/spreadsheet.cpp | 22 +-
src/report/spreadsheet.h | 22 +-
src/report/xml_report.cpp | 22 +-
src/report/xml_report.h | 22 +-
src/tools/mathx.cpp | 25 +-
src/tools/mathx.h | 22 +-
src/tools/random.cpp | 22 +-
src/tools/random.h | 22 +-
src/tools/rangex.cpp | 22 +-
src/tools/rangex.h | 22 +-
src/tools/stringx.cpp | 23 +-
src/tools/stringx.h | 22 +-
src/tools/timex.cpp | 22 +-
src/tools/timex.h | 22 +-
src/tools/tools.h | 22 +-
src/tools/vector_constants.cpp | 22 +-
src/tools/vector_constants.h | 27 +-
src/tools/vectorx.cpp | 22 +-
src/tools/vectorx.h | 22 +-
src/tree/argtree.cpp | 30 +-
src/tree/argtree.h | 22 +-
src/tree/arranger.cpp | 22 +-
src/tree/arranger.h | 28 +-
src/tree/arranger_types.cpp | 22 +-
src/tree/arranger_types.h | 22 +-
src/tree/arrangervec.cpp | 24 +-
src/tree/arrangervec.h | 22 +-
src/tree/branch.cpp | 22 +-
src/tree/branch.h | 30 +-
src/tree/branchbuffer.cpp | 22 +-
src/tree/branchbuffer.h | 22 +-
src/tree/branchtag.cpp | 22 +-
src/tree/branchtag.h | 22 +-
src/tree/chain.cpp | 22 +-
src/tree/chain.h | 22 +-
src/tree/chainstate.cpp | 22 +-
src/tree/chainstate.h | 22 +-
src/tree/collector.cpp | 24 +-
src/tree/collector.h | 26 +-
src/tree/collmanager.cpp | 22 +-
src/tree/collmanager.h | 22 +-
src/tree/fc_status.cpp | 26 +-
src/tree/fc_status.h | 26 +-
src/tree/individual.cpp | 22 +-
src/tree/individual.h | 22 +-
src/tree/intervaldata.cpp | 22 +-
src/tree/intervaldata.h | 22 +-
src/tree/newick.h | 24 +-
src/tree/parameter.cpp | 22 +-
src/tree/parameter.h | 22 +-
src/tree/partition.cpp | 22 +-
src/tree/partition.h | 22 +-
src/tree/prior.cpp | 41 +-
src/tree/prior.h | 22 +-
src/tree/range.cpp | 22 +-
src/tree/range.h | 32 +-
src/tree/rectree.cpp | 22 +-
src/tree/sticksum.h | 28 +-
src/tree/summary.cpp | 22 +-
src/tree/summary.h | 26 +-
src/tree/tempident.cpp | 22 +-
src/tree/tempident.h | 22 +-
src/tree/timelist.cpp | 22 +-
src/tree/timelist.h | 22 +-
src/tree/tree.cpp | 24 +-
src/tree/tree.h | 26 +-
src/tree/treesum.cpp | 22 +-
src/tree/treesum.h | 20 +-
src/ui_interface/chainparam_interface.cpp | 27 +-
src/ui_interface/chainparam_interface.h | 27 +-
src/ui_interface/constraint_interface.cpp | 27 +-
src/ui_interface/constraint_interface.h | 27 +-
src/ui_interface/data_interface.cpp | 27 +-
src/ui_interface/data_interface.h | 27 +-
src/ui_interface/datamodel_interface.cpp | 27 +-
src/ui_interface/datamodel_interface.h | 27 +-
src/ui_interface/force_interface.cpp | 27 +-
src/ui_interface/force_interface.h | 27 +-
src/ui_interface/front_end_warnings.cpp | 22 +-
src/ui_interface/front_end_warnings.h | 27 +-
src/ui_interface/prior_interface.cpp | 27 +-
src/ui_interface/prior_interface.h | 27 +-
src/ui_interface/profile_interface.cpp | 27 +-
src/ui_interface/profile_interface.h | 27 +-
src/ui_interface/setget.h | 87 +-
src/ui_interface/setgetmachine.cpp | 27 +-
src/ui_interface/setgetmachine.h | 22 +-
src/ui_interface/traitmodel_interface.cpp | 27 +-
src/ui_interface/traitmodel_interface.h | 27 +-
src/ui_interface/ui_constants.cpp | 27 +-
src/ui_interface/ui_constants.h | 27 +-
src/ui_interface/ui_id.cpp | 27 +-
src/ui_interface/ui_id.h | 27 +-
src/ui_interface/ui_interface.cpp | 27 +-
src/ui_interface/ui_interface.h | 27 +-
src/ui_interface/ui_regid.cpp | 27 +-
src/ui_interface/ui_regid.h | 27 +-
src/ui_interface/ui_strings.cpp | 22 +-
src/ui_interface/ui_strings.h | 27 +-
src/ui_interface/ui_warnings.cpp | 22 +-
src/ui_interface/ui_warnings.h | 27 +-
src/ui_interface/userparam_interface.cpp | 27 +-
src/ui_interface/userparam_interface.h | 27 +-
src/ui_util/undoredochain.cpp | 27 +-
src/ui_util/undoredochain.h | 27 +-
src/ui_vars/report_strings.cpp | 22 +-
src/ui_vars/report_strings.h | 22 +-
src/ui_vars/ui_vars.cpp | 27 +-
src/ui_vars/ui_vars.h | 27 +-
src/ui_vars/ui_vars_chainparams.cpp | 27 +-
src/ui_vars/ui_vars_chainparams.h | 27 +-
src/ui_vars/ui_vars_component.cpp | 27 +-
src/ui_vars/ui_vars_component.h | 27 +-
src/ui_vars/ui_vars_datamodel.cpp | 27 +-
src/ui_vars/ui_vars_datamodel.h | 27 +-
src/ui_vars/ui_vars_datapackplus.cpp | 22 +-
src/ui_vars/ui_vars_datapackplus.h | 27 +-
src/ui_vars/ui_vars_forces.cpp | 27 +-
src/ui_vars/ui_vars_forces.h | 27 +-
src/ui_vars/ui_vars_prior.cpp | 27 +-
src/ui_vars/ui_vars_prior.h | 27 +-
src/ui_vars/ui_vars_traitmodels.cpp | 27 +-
src/ui_vars/ui_vars_traitmodels.h | 27 +-
src/ui_vars/ui_vars_userparams.cpp | 27 +-
src/ui_vars/ui_vars_userparams.h | 27 +-
src/xml/lamarc_input_schema.h | 22 +-
src/xml/lamarcschema.cpp | 22 +-
src/xml/parsetreeschema.cpp | 22 +-
src/xml/parsetreeschema.h | 22 +-
src/xml/parsetreetodata.cpp | 22 +-
src/xml/parsetreetodata.h | 22 +-
src/xml/parsetreetosettings.cpp | 22 +-
src/xml/parsetreetosettings.h | 22 +-
src/xml/parsetreewalker.cpp | 22 +-
src/xml/parsetreewalker.h | 22 +-
src/xml/tixml_base.cpp | 23 +-
src/xml/tixml_base.h | 22 +-
src/xml/toxml.cpp | 22 +-
src/xml/toxml.h | 22 +-
src/xml/xml.cpp | 22 +-
src/xml/xml.h | 22 +-
src/xml/xml_strings.cpp | 22 +-
src/xml/xml_strings.h | 22 +-
tools/README | 2 +
tools/apache-forrest-0.7.tar.gz | Bin 0 -> 21917527 bytes
website/apacheInput/skinconf.xml | 446 +
website/apacheInput/xdocs/documentation/index.xml | 15 +
website/apacheInput/xdocs/download/index.xml | 15 +
website/apacheInput/xdocs/images/icon.png | Bin 0 -> 696 bytes
website/apacheInput/xdocs/images/lamarc.gif | Bin 0 -> 1359 bytes
website/apacheInput/xdocs/index.xml | 55 +
website/apacheInput/xdocs/more/index.xml | 26 +
.../xdocs/publications/beerli-felsenstein-2001.pdf | Bin 0 -> 137971 bytes
.../xdocs/publications/evolution2000-pb-mkk.pdf | 1340 +++
.../xdocs/publications/fluctuate1.1.pdf | Bin 0 -> 1914419 bytes
.../apacheInput/xdocs/publications/g_explain.pdf | Bin 0 -> 39859 bytes
.../apacheInput/xdocs/publications/genetics763.pdf | Bin 0 -> 210247 bytes
website/apacheInput/xdocs/publications/index.xml | 75 +
.../xdocs/publications/metro-hastings.pdf | Bin 0 -> 2579896 bytes
website/apacheInput/xdocs/site.xml | 59 +
website/apacheInput/xdocs/tabs.xml | 42 +
662 files changed, 41963 insertions(+), 3877 deletions(-)
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