[med-svn] [probabel] 02/03: Merge tag 'upstream/0.4.4'

[Lennart Karssen]

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 <lenn...@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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--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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--R_test_files = run_models_in_R_palinear.R run_model_linear.R  \
-- run_models_in_R_palogist.R run_model_logist.R                        \
-- run_models_in_R_pacox.R run_model_coxph.R                    \
-- initial_checks.R
--
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--
--##################################################
--# 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
--
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-- $(cleanfiles_cox)
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--phenofiles = height.txt                               \
-- logist_data.txt                              \
-- mmscore_pheno.PHE                            \
-- coxph_data.txt
--
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--genofiles = $(gtdatadir)/test.mldose          \
-- $(gtdatadir)/test.mlprob                     \
-- $(gtdatadir)/test.mlinfo                     \
-- $(gtdatadir)/test.map                                \
-- $(gtdatadir)/test.dose.fvi                   \
-- $(gtdatadir)/test.dose.fvd                   \
-- $(gtdatadir)/test.prob.fvi                   \
-- $(gtdatadir)/test.prob.fvd                   \
-- $(gtdatadir)/mmscore_gen.mlinfo              \
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-- $(gtdatadir)/mmscore_gen.mlprob              \
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-- $(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
--
--exampledir = $(pkgdatadir)/examples
--dist_example_DATA = $(phenofiles) $(additional_files)
--dist_example_SCRIPTS = $(example_scripts)
--gdatadir = $(pkgdatadir)/examples/gtdata
--dist_gdata_DATA = $(genofiles)
--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) $(cleanfiles_example_mmscore)
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--      dir='$(DESTDIR)$(exampledir)'; $(am__uninstall_files_from_dir)
--install-dist_gdataDATA: $(dist_gdata_DATA)
--      @$(NORMAL_INSTALL)
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--      if test -n "$$list"; then \
--        echo " $(MKDIR_P) '$(DESTDIR)$(gdatadir)'"; \
--        $(MKDIR_P) "$(DESTDIR)$(gdatadir)" || exit 1; \
--      fi; \
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--        if test -f "$$p"; then d=; else d="$(srcdir)/"; fi; \
--        echo "$$d$$p"; \
--      done | $(am__base_list) | \
--      while read files; do \
--        echo " $(INSTALL_DATA) $$files '$(DESTDIR)$(gdatadir)'"; \
--        $(INSTALL_DATA) $$files "$(DESTDIR)$(gdatadir)" || exit $$?; \
--      done
--
--uninstall-dist_gdataDATA:
--      @$(NORMAL_UNINSTALL)
--      @list='$(dist_gdata_DATA)'; test -n "$(gdatadir)" || list=; \
--      files=`for p in $$list; do echo $$p; done | sed -e 's|^.*/||'`; \
--      dir='$(DESTDIR)$(gdatadir)'; $(am__uninstall_files_from_dir)
--tags TAGS:
--
--ctags CTAGS:
--
--cscope cscopelist:
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--      topsrcdirstrip=`echo "$(top_srcdir)" | sed 's/[].[^$$\\*]/\\\\&/g'`; \
--      list='$(DISTFILES)'; \
--        dist_files=`for file in $$list; do echo $$file; done | \
--        sed -e "s|^$$srcdirstrip/||;t" \
--            -e "s|^$$topsrcdirstrip/|$(top_builddir)/|;t"`; \
--      case $$dist_files in \
--        */*) $(MKDIR_P) `echo "$$dist_files" | \
--                         sed '/\//!d;s|^|$(distdir)/|;s,/[^/]*$$,,' | \
--                         sort -u` ;; \
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--          if test -d "$(distdir)/$$file"; then \
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--        else \
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--          || exit 1; \
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$(CONFIG_CLEAN_VPATH_FILES)
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--
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--
--
--# 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:

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