This is an automated email from the git hooks/post-receive script. lckarssen-guest pushed a commit to branch master in repository probabel.
commit a6319b946f81cf08505bfd850f319b5322dbeeeb Merge: 8777b9b 7b2d0e3 Author: L.C. Karssen <[email protected]> Date: Wed Jan 15 11:30:26 2014 +0100 Merge tag 'upstream/0.4.2' Upstream version 0.4.2 Makefile.am | 2 +- Makefile.in | 297 ++--- aclocal.m4 | 564 +++++----- checks/Makefile.am | 93 +- checks/Makefile.in | 767 ++++++++----- checks/R-tests/Makefile.am | 103 ++ checks/R-tests/Makefile.in | 867 +++++++++++++++ checks/R-tests/initial_checks.R | 93 ++ checks/R-tests/run_R_test_pacox.sh | 11 + checks/R-tests/run_R_test_palinear.sh | 11 + checks/R-tests/run_R_test_palogist.sh | 11 + checks/R-tests/run_model_coxph.R | 98 ++ checks/R-tests/run_model_linear.R | 29 + checks/R-tests/run_model_logist.R | 23 + checks/R-tests/run_models_in_R_pacox.R | 109 ++ checks/R-tests/run_models_in_R_palinear.R | 129 +++ checks/R-tests/run_models_in_R_palogist.R | 129 +++ checks/check_dose_input.sh | 2 +- ...robabel.pl_chunk.sh => check_probabel_chunk.sh} | 18 +- checks/inputfiles/test.dose.fvd | Bin 4000 -> 4800 bytes checks/inputfiles/test.dose.fvi | Bin 6608 -> 6640 bytes checks/inputfiles/test.map | 1 + checks/inputfiles/test.mldose | 400 +++---- checks/inputfiles/test.mlinfo | 1 + checks/inputfiles/test.mlprob | 400 +++---- checks/inputfiles/test.prob.fvd | Bin 8000 -> 9600 bytes checks/inputfiles/test.prob.fvi | Bin 6768 -> 6832 bytes checks/test_bt.sh | 23 +- checks/test_cox.sh | 20 +- checks/test_mms.sh | 23 +- checks/test_qt.sh | 139 +-- checks/verified_results/height_base_add.out.txt | 1 + configure | 321 +++--- configure.ac | 29 +- doc/ChangeLog | 29 + doc/INSTALL | 15 +- doc/Makefile.am | 2 +- doc/Makefile.in | 132 ++- doc/ProbABEL_manual.tex | 39 +- doc/pacoxph.1 | 2 +- doc/palinear.1 | 4 +- doc/palogist.1 | 4 +- doc/probabel.1 | 91 ++ doc/probabel.pl.1 | 91 ++ examples/Makefile.am | 81 ++ examples/Makefile.in | 191 +++- examples/example_bt.sh | 24 +- examples/example_cox.sh | 24 +- examples/example_qt.sh | 72 +- missing | 461 +++----- src/Makefile.am | 27 +- src/Makefile.in | 332 ++++-- src/command_line_settings.cpp | 31 +- src/command_line_settings.h | 6 +- src/config.h.in | 7 - src/coxfit2.c | 1 - src/coxph_data.cpp | 206 +++- src/coxph_data.h | 25 +- src/data.cpp | 33 +- src/data.h | 34 +- src/eigen_mematrix.cpp | 43 +- src/eigen_mematrix.h | 6 +- src/extract-snp.cpp | 10 +- src/fvlib/AbstractMatrix.cpp | 12 +- src/fvlib/AbstractMatrix.h | 113 +- src/fvlib/CastUtils.cpp | 295 ++--- src/fvlib/CastUtils.h | 141 +-- src/fvlib/FileVector.cpp | 1145 +++++++++++--------- src/fvlib/FileVector.h | 209 ++-- src/fvlib/FilteredMatrix.cpp | 117 +- src/fvlib/FilteredMatrix.h | 173 +-- src/fvlib/Logger.cpp | 7 +- src/fvlib/Logger.h | 30 +- src/fvlib/RealHandlerWrapper.cpp | 21 +- src/fvlib/RealHandlerWrapper.h | 10 +- src/fvlib/ReusableFileHandle.cpp | 31 +- src/fvlib/ReusableFileHandle.h | 28 +- src/fvlib/Transposer.cpp | 237 ++-- src/fvlib/Transposer.h | 38 +- src/fvlib/convert_util.cpp | 567 +++++----- src/fvlib/convert_util.h | 10 +- src/fvlib/frutil.cpp | 238 ++-- src/fvlib/frutil.h | 86 +- src/gendata.cpp | 3 +- src/gendata.h | 4 +- src/main.cpp | 497 ++------- src/main_functions_dump.cpp | 428 ++++++++ src/main_functions_dump.h | 38 + src/maskedmatrix.h | 6 +- src/mematrix.h | 2 +- src/phedata.cpp | 30 +- src/phedata.h | 2 +- src/{probabel.pl => probabel} | 25 +- src/reg1.cpp | 87 +- src/reg1.h | 6 +- src/regdata.cpp | 88 +- src/regdata.h | 12 +- src/usage.cpp | 18 +- test-driver | 127 +++ 99 files changed, 7406 insertions(+), 4212 deletions(-) -- Alioth's /git/debian-med/git-commit-notice on /srv/git.debian.org/git/debian-med/probabel.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
