[med-svn] [probabel] 02/03: Merge tag 'upstream/0.4.4'
Lennart Karssen
lckarssen-guest at moszumanska.debian.org
Fri Nov 7 22:58:40 UTC 2014
This is an automated email from the git hooks/post-receive script.
lckarssen-guest pushed a commit to branch master
in repository probabel.
commit 79d572022224e17edfdfe1b95c9a38d7a08a84b6
Merge: fca5931 82d925a
Author: L.C. Karssen <lennart at karssen.org>
Date: Fri Nov 7 21:45:18 2014 +0100
Merge tag 'upstream/0.4.4'
Upstream version 0.4.4
Conflicts:
doc/Makefile.in
src/Makefile.in
Added new upstream bugfix release (v0.4.4).
Makefile.in | 738 -----------------------------------
aclocal.m4 | 154 ++++++--
checks/Makefile.in | 933 ---------------------------------------------
checks/R-tests/Makefile.in | 868 -----------------------------------------
configure | 268 ++++++-------
configure.ac | 12 +-
doc/ChangeLog | 11 +
doc/ProbABEL_manual.tex | 12 +-
doc/pacoxph.1 | 2 +-
doc/palinear.1 | 2 +-
doc/palogist.1 | 2 +-
doc/probabel.1 | 2 +-
doc/probabel.pl.1 | 2 +-
examples/Makefile.in | 629 ------------------------------
src/Makefile.am | 24 +-
src/config.h.in | 3 -
src/coxph_data.cpp | 46 ++-
src/main.cpp | 2 +-
18 files changed, 310 insertions(+), 3400 deletions(-)
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--abs_builddir = @abs_builddir@
--abs_srcdir = @abs_srcdir@
--abs_top_builddir = @abs_top_builddir@
--abs_top_srcdir = @abs_top_srcdir@
--ac_ct_CC = @ac_ct_CC@
--ac_ct_CXX = @ac_ct_CXX@
--am__include = @am__include@
--am__leading_dot = @am__leading_dot@
--am__quote = @am__quote@
--am__tar = @am__tar@
--am__untar = @am__untar@
--bindir = @bindir@
--build_alias = @build_alias@
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--libexecdir = @libexecdir@
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--localstatedir = @localstatedir@
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--AUTOMAKE_OPTIONS = foreign color-tests
--verified_results_dir = verified_results
--verified_results = $(verified_results_dir)/height_add.out.txt \
-- $(verified_results_dir)/height_ngp2_add.out.txt \
-- $(verified_results_dir)/height_ngp2_2df.out.txt \
-- $(verified_results_dir)/height_ngp2_domin.out.txt \
-- $(verified_results_dir)/height_ngp2_over_domin.out.txt \
-- $(verified_results_dir)/height_ngp2_recess.out.txt \
-- $(verified_results_dir)/height_base_add.out.txt
--
--input_files_dir = inputfiles
--phenofiles = $(input_files_dir)/height.txt \
-- $(input_files_dir)/logist_data.txt \
-- $(input_files_dir)/coxph_data.txt \
-- $(input_files_dir)/mmscore_pheno.PHE
--
--genofiles = $(input_files_dir)/test.mldose \
-- $(input_files_dir)/test.mlprob \
-- $(input_files_dir)/test.mlinfo \
-- $(input_files_dir)/test.map \
-- $(input_files_dir)/test.dose.fvi \
-- $(input_files_dir)/test.dose.fvd \
-- $(input_files_dir)/test.prob.fvi \
-- $(input_files_dir)/test.prob.fvd \
-- $(input_files_dir)/mmscore_gen.mlinfo \
-- $(input_files_dir)/mmscore_gen.mldose \
-- $(input_files_dir)/mmscore_gen.mlprob \
-- $(input_files_dir)/mmscore_gen.dose.fvi \
-- $(input_files_dir)/mmscore_gen.dose.fvd \
-- $(input_files_dir)/mmscore_gen.prob.fvi \
-- $(input_files_dir)/mmscore_gen.prob.fvd \
-- $(input_files_dir)/mmscore_InvSigma_aj.sex.age.dat
--
--input_files = $(phenofiles) $(genofiles) run_diff.sh test_all.sh
--check_SCRIPTS = $(am__append_1) $(am__append_2) $(am__append_3)
--AM_TESTS_ENVIRONMENT = \
-- PA_BINDIR=$(top_builddir)/src
--
--TESTS = $(check_SCRIPTS)
--EXTRA_DIST = $(verified_results) $(input_files) $(check_SCRIPTS)
--
--##################################################
--# Files that need to be cleaned up after testing
--##################################################
--cleanfiles_bt = logist_add.out.txt logist_fv_add.out.txt \
--logist_prob_2df.out.txt logist_prob_fv_2df.out.txt \
--logist_prob_fv_domin.out.txt logist_prob_add.out.txt \
--logist_prob_fv_add.out.txt logist_prob_over_domin.out.txt \
--logist_prob_domin.out.txt logist_prob_fv_recess.out.txt \
--logist_prob_fv_over_domin.out.txt logist_prob_recess.out.txt
--
--cleanfiles_qt = linear_base_add.out.txt linear_base_fv_add.out.txt \
--linear_allcov_add.out.txt linear_allcov_fv_add.out.txt \
--linear_int1_add.out.txt linear_int1_fv_add.out.txt \
--linear_robust_add.out.txt linear_robust_fv_add.out.txt \
--linear_robust_int1_add.out.txt linear_robust_int1_fv_add.out.txt \
--linear_ngp2_add.out.txt linear_ngp2_fv_add.out.txt \
--linear_ngp2_domin.out.txt linear_ngp2_fv_domin.out.txt \
--linear_ngp2_over_domin.out.txt linear_ngp2_fv_over_domin.out.txt \
--linear_ngp2_recess.out.txt linear_ngp2_fv_recess.out.txt \
--linear_ngp2_2df.out.txt linear_ngp2_fv_2df.out.txt \
--linear_ngp2_allcov_add.out.txt linear_ngp2_allcov_fv_add.out.txt \
--linear_ngp2_allcov_domin.out.txt linear_ngp2_allcov_fv_domin.out.txt \
--linear_ngp2_allcov_over_domin.out.txt \
--linear_ngp2_allcov_fv_over_domin.out.txt \
--linear_ngp2_allcov_recess.out.txt linear_ngp2_allcov_fv_recess.out.txt \
--linear_ngp2_allcov_recess.out.txt linear_ngp2_allcov_fv_recess.out.txt \
--linear_ngp2_int1_add.out.txt linear_ngp2_int1_fv_add.out.txt \
--linear_ngp2_int1_domin.out.txt linear_ngp2_int1_fv_domin.out.txt \
--linear_ngp2_int1_over_domin.out.txt \
--linear_ngp2_int1_fv_over_domin.out.txt linear_ngp2_int1_recess.out.txt \
--linear_ngp2_int1_fv_recess.out.txt linear_ngp2_int1_2df.out.txt \
--linear_ngp2_int1_fv_2df.out.txt linear_ngp2_robust_add.out.txt \
--linear_ngp2_robust_fv_add.out.txt linear_ngp2_robust_domin.out.txt \
--linear_ngp2_robust_fv_domin.out.txt \
--linear_ngp2_robust_over_domin.out.txt \
--linear_ngp2_robust_fv_over_domin.out.txt \
--linear_ngp2_robust_recess.out.txt linear_ngp2_robust_fv_recess.out.txt \
--linear_ngp2_robust_2df.out.txt linear_ngp2_robust_fv_2df.out.txt \
--linear_ngp2_robust_int1_add.out.txt \
--linear_ngp2_robust_int1_fv_add.out.txt \
--linear_ngp2_robust_int1_domin.out.txt \
--linear_ngp2_robust_int1_fv_domin.out.txt \
--linear_ngp2_robust_int1_over_domin.out.txt \
--linear_ngp2_robust_int1_fv_over_domin.out.txt \
--linear_ngp2_robust_int1_recess.out.txt \
--linear_ngp2_robust_int1_fv_recess.out.txt \
--linear_ngp2_robust_int1_2df.out.txt \
--linear_ngp2_robust_int1_fv_2df.out.txt \
--linear_ngp2_allcov_fv_2df.out.txt linear_ngp2_robust_fv_add.out.txt \
--linear_ngp2_allcov_2df.out.txt
--
--cleanfiles_mms = mmscore_dose_add.out.txt mmscore_dose_fv_add.out.txt \
--mmscore_prob_fv_over_domin.out.txt mmscore_prob_fv_domin.out.txt \
--mmscore_prob_over_domin.out.txt mmscore_prob_fv_add.out.txt \
--mmscore_prob_fv_recess.out.txt mmscore_prob_domin.out.txt \
--mmscore_prob_recess.out.txt mmscore_prob_add.out.txt \
--mmscore_prob_2df.out.txt mmscore_prob_fv_2df.out.txt
--
--cleanfiles_cox = coxph_dose_add.out.txt coxph_dose_fv_add.out.txt \
--coxph_prob_fv_over_domin.out.txt coxph_prob_fv_domin.out.txt \
--coxph_prob_over_domin.out.txt coxph_prob_fv_add.out.txt \
--coxph_prob_fv_recess.out.txt coxph_prob_domin.out.txt \
--coxph_prob_recess.out.txt coxph_prob_add.out.txt \
--coxph_prob_2df.out.txt coxph_prob_fv_2df.out.txt
--
--dose_files = chr1.chunk1.dose chr1.chunk2.dose chr2.chunk1.dose \
-- chr2.chunk2.dose chr1.dose chr2.dose
--
--prob_files = $(dose_files:.dose=.prob)
--map_files = $(dose_files:.dose=.map)
--info_files = $(dose_files:.dose=.info)
--output_files = height_add.out.txt height_2df.out.txt \
-- height_domin.out.txt height_over_domin.out.txt height_recess.out.txt \
-- height_ngp2_recess.out.txt height_ngp2_domin.out.txt \
-- height_ngp2_over_domin.out.txt height_ngp2_2df.out.txt \
-- height_ngp2_add.out.txt height_base_add.out.txt
--
--other_files = probabel probabel_config.cfg
--cleanfiles_probabel_check = height.PHE $(dose_files) $(prob_files) \
-- $(map_files) $(info_files) $(output_files) $(other_files)
--
--cleanfiles_dose_check = test.mldose
--CLEANFILES = $(cleanfiles_probabel_check) $(cleanfiles_dose_check) \
-- $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) $(cleanfiles_cox)
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--logist_prob_domin.out.txt logist_prob_fv_recess.out.txt \
--logist_prob_fv_over_domin.out.txt logist_prob_recess.out.txt
--
--cleanfiles_qt = linear_base_add.out.txt linear_base_fv_add.out.txt \
--linear_allcov_add.out.txt linear_allcov_fv_add.out.txt \
--linear_int1_add.out.txt linear_int1_fv_add.out.txt \
--linear_robust_add.out.txt linear_robust_fv_add.out.txt \
--linear_robust_int1_add.out.txt linear_robust_int1_fv_add.out.txt \
--linear_ngp2_add.out.txt linear_ngp2_fv_add.out.txt \
--linear_ngp2_domin.out.txt linear_ngp2_fv_domin.out.txt \
--linear_ngp2_over_domin.out.txt linear_ngp2_fv_over_domin.out.txt \
--linear_ngp2_recess.out.txt linear_ngp2_fv_recess.out.txt \
--linear_ngp2_2df.out.txt linear_ngp2_fv_2df.out.txt \
--linear_ngp2_allcov_add.out.txt linear_ngp2_allcov_fv_add.out.txt \
--linear_ngp2_allcov_domin.out.txt linear_ngp2_allcov_fv_domin.out.txt \
--linear_ngp2_allcov_over_domin.out.txt \
--linear_ngp2_allcov_fv_over_domin.out.txt \
--linear_ngp2_allcov_recess.out.txt linear_ngp2_allcov_fv_recess.out.txt \
--linear_ngp2_allcov_recess.out.txt linear_ngp2_allcov_fv_recess.out.txt \
--linear_ngp2_int1_add.out.txt linear_ngp2_int1_fv_add.out.txt \
--linear_ngp2_int1_domin.out.txt linear_ngp2_int1_fv_domin.out.txt \
--linear_ngp2_int1_over_domin.out.txt \
--linear_ngp2_int1_fv_over_domin.out.txt linear_ngp2_int1_recess.out.txt \
--linear_ngp2_int1_fv_recess.out.txt linear_ngp2_int1_2df.out.txt \
--linear_ngp2_int1_fv_2df.out.txt linear_ngp2_robust_add.out.txt \
--linear_ngp2_robust_fv_add.out.txt linear_ngp2_robust_domin.out.txt \
--linear_ngp2_robust_fv_domin.out.txt \
--linear_ngp2_robust_over_domin.out.txt \
--linear_ngp2_robust_fv_over_domin.out.txt \
--linear_ngp2_robust_recess.out.txt linear_ngp2_robust_fv_recess.out.txt \
--linear_ngp2_robust_2df.out.txt linear_ngp2_robust_fv_2df.out.txt \
--linear_ngp2_robust_int1_add.out.txt \
--linear_ngp2_robust_int1_fv_add.out.txt \
--linear_ngp2_robust_int1_domin.out.txt \
--linear_ngp2_robust_int1_fv_domin.out.txt \
--linear_ngp2_robust_int1_over_domin.out.txt \
--linear_ngp2_robust_int1_fv_over_domin.out.txt \
--linear_ngp2_robust_int1_recess.out.txt \
--linear_ngp2_robust_int1_fv_recess.out.txt \
--linear_ngp2_robust_int1_2df.out.txt \
--linear_ngp2_robust_int1_fv_2df.out.txt \
--linear_ngp2_allcov_fv_2df.out.txt linear_ngp2_robust_fv_add.out.txt \
--linear_ngp2_allcov_2df.out.txt
--
--cleanfiles_mms = mmscore_dose_add.out.txt mmscore_dose_fv_add.out.txt \
--mmscore_prob_fv_over_domin.out.txt mmscore_prob_fv_domin.out.txt \
--mmscore_prob_over_domin.out.txt mmscore_prob_fv_add.out.txt \
--mmscore_prob_fv_recess.out.txt mmscore_prob_domin.out.txt \
--mmscore_prob_recess.out.txt mmscore_prob_add.out.txt \
--mmscore_prob_2df.out.txt mmscore_prob_fv_2df.out.txt
--
--cleanfiles_cox = coxph_dose_add.out.txt coxph_dose_fv_add.out.txt \
--coxph_prob_fv_over_domin.out.txt coxph_prob_fv_domin.out.txt \
--coxph_prob_over_domin.out.txt coxph_prob_fv_add.out.txt \
--coxph_prob_fv_recess.out.txt coxph_prob_domin.out.txt \
--coxph_prob_recess.out.txt coxph_prob_add.out.txt \
--coxph_prob_2df.out.txt coxph_prob_fv_2df.out.txt
--
--CLEANFILES = $(cleanfiles_bt) $(cleanfiles_qt) $(cleanfiles_mms) \
-- $(cleanfiles_cox)
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--phenofiles = height.txt \
-- logist_data.txt \
-- mmscore_pheno.PHE \
-- coxph_data.txt
--
--gtdatadir = gtdata
--genofiles = $(gtdatadir)/test.mldose \
-- $(gtdatadir)/test.mlprob \
-- $(gtdatadir)/test.mlinfo \
-- $(gtdatadir)/test.map \
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-- $(gtdatadir)/test.dose.fvd \
-- $(gtdatadir)/test.prob.fvi \
-- $(gtdatadir)/test.prob.fvd \
-- $(gtdatadir)/mmscore_gen.mlinfo \
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-- $(gtdatadir)/mmscore_gen.mlprob \
-- $(gtdatadir)/mmscore_gen.dose.fvi \
-- $(gtdatadir)/mmscore_gen.dose.fvd \
-- $(gtdatadir)/mmscore_gen.prob.fvi \
-- $(gtdatadir)/mmscore_gen.prob.fvd
--
--additional_files = mmscore.R \
-- mmscore_InvSigma_aj.sex.age.dat \
-- README
--
--example_scripts = example_qt.sh \
-- example_bt.sh \
-- example_cox.sh \
-- example_mmscore.sh
--
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--cleanfiles_example_qt = height_allcov_fv_add.out.txt \
-- height_base_add.out.txt \
-- height_base_fv_add.out.txt \
-- height_int1_fv_add.out.txt \
-- height_ngp2_2df.out.txt \
-- height_ngp2_add.out.txt \
-- height_ngp2_allcov_fv_2df.out.txt \
-- height_ngp2_allcov_fv_add.out.txt \
-- height_ngp2_allcov_fv_domin.out.txt \
-- height_ngp2_allcov_fv_over_domin.out.txt \
-- height_ngp2_allcov_fv_recess.out.txt \
-- height_ngp2_domin.out.txt \
-- height_ngp2_fv_2df.out.txt \
-- height_ngp2_fv_add.out.txt \
-- height_ngp2_fv_domin.out.txt \
-- height_ngp2_fv_over_domin.out.txt \
-- height_ngp2_fv_recess.out.txt \
-- height_ngp2_int1_fv_2df.out.txt \
-- height_ngp2_int1_fv_add.out.txt \
-- height_ngp2_int1_fv_domin.out.txt \
-- height_ngp2_int1_fv_over_domin.out.txt \
-- height_ngp2_int1_fv_recess.out.txt \
-- height_ngp2_over_domin.out.txt \
-- height_ngp2_recess.out.txt \
-- height_ngp2_robust_fv_2df.out.txt \
-- height_ngp2_robust_fv_add.out.txt \
-- height_ngp2_robust_fv_domin.out.txt \
-- height_ngp2_robust_fv_over_domin.out.txt \
-- height_ngp2_robust_fv_recess.out.txt \
-- height_ngp2_robust_int1_fv_2df.out.txt \
-- height_ngp2_robust_int1_fv_add.out.txt \
-- height_ngp2_robust_int1_fv_domin.out.txt \
-- height_ngp2_robust_int1_fv_over_domin.out.txt \
-- height_ngp2_robust_int1_fv_recess.out.txt \
-- height_robust_fv_add.out.txt \
-- height_robust_int1_fv_add.out.txt
--
--cleanfiles_example_bt = logist_add.out.txt \
-- logist_fv_add.out.txt \
-- logist_prob_2df.out.txt \
-- logist_prob_add.out.txt \
-- logist_prob_domin.out.txt \
-- logist_prob_fv_2df.out.txt \
-- logist_prob_fv_add.out.txt \
-- logist_prob_fv_domin.out.txt \
-- logist_prob_fv_over_domin.out.txt \
-- logist_prob_fv_recess.out.txt \
-- logist_prob_over_domin.out.txt \
-- logist_prob_recess.out.txt
--
--cleanfiles_example_cox = coxph_dose_add.out.txt \
-- coxph_dose_fv_add.out.txt \
-- coxph_prob_2df.out.txt \
-- coxph_prob_add.out.txt \
-- coxph_prob_domin.out.txt \
-- coxph_prob_fv_2df.out.txt \
-- coxph_prob_fv_add.out.txt \
-- coxph_prob_fv_domin.out.txt \
-- coxph_prob_fv_over_domin.out.txt \
-- coxph_prob_fv_recess.out.txt \
-- coxph_prob_over_domin.out.txt \
-- coxph_prob_recess.out.txt
--
--cleanfiles_example_mmscore = mmscore_dose_add.out.txt \
-- mmscore_dose_fv_add.out.txt \
-- mmscore_prob_2df.out.txt \
-- mmscore_prob_add.out.txt \
-- mmscore_prob_domin.out.txt \
-- mmscore_prob_fv_2df.out.txt \
-- mmscore_prob_fv_add.out.txt \
-- mmscore_prob_fv_domin.out.txt \
-- mmscore_prob_fv_over_domin.out.txt \
-- mmscore_prob_fv_recess.out.txt \
-- mmscore_prob_over_domin.out.txt \
-- mmscore_prob_recess.out.txt
--
--CLEANFILES = $(cleanfiles_example_qt) $(cleanfiles_example_bt) \
-- $(cleanfiles_example_cox) $(cleanfiles_example_mmscore)
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--ps: ps-am
--
--ps-am:
--
--uninstall-am: uninstall-dist_exampleDATA uninstall-dist_exampleSCRIPTS \
-- uninstall-dist_gdataDATA
--
--.MAKE: install-am install-strip
--
--.PHONY: all all-am check check-am clean clean-generic cscopelist-am \
-- ctags-am distclean distclean-generic distdir dvi dvi-am html \
-- html-am info info-am install install-am install-data \
-- install-data-am install-dist_exampleDATA \
-- install-dist_exampleSCRIPTS install-dist_gdataDATA install-dvi \
-- install-dvi-am install-exec install-exec-am install-html \
-- install-html-am install-info install-info-am install-man \
-- install-pdf install-pdf-am install-ps install-ps-am \
-- install-strip installcheck installcheck-am installdirs \
-- maintainer-clean maintainer-clean-generic mostlyclean \
-- mostlyclean-generic pdf pdf-am ps ps-am tags-am uninstall \
-- uninstall-am uninstall-dist_exampleDATA \
-- uninstall-dist_exampleSCRIPTS uninstall-dist_gdataDATA
--
--
--# Tell versions [3.59,3.63) of GNU make to not export all variables.
--# Otherwise a system limit (for SysV at least) may be exceeded.
--.NOEXPORT:
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/probabel.git
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