[med-svn] [probabel] branch master updated (8777b9b -> 9a74b8c)
Lennart Karssen
lckarssen-guest at moszumanska.debian.org
Mon Jan 13 17:00:33 UTC 2014
This is an automated email from the git hooks/post-receive script.
lckarssen-guest pushed a change to branch master
in repository probabel.
from 8777b9b Upload to unstable
new 9a74b8c Imported upstream release 0.4.2 and updated debian/* accordingly.
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 +
compile | 143 --
configure | 321 +--
configure.ac | 29 +-
debian/changelog | 7 +
debian/patches/series | 5 -
debian/rules | 7 +-
depcomp | 630 ------
doc/ChangeLog | 29 +
doc/INSTALL | 15 +-
doc/Makefile.am | 2 +-
doc/Makefile.in | 546 -----
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 +-
install-sh | 520 -----
missing | 461 ++---
src/Makefile.am | 27 +-
src/Makefile.in | 2100 --------------------
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 ++
105 files changed, 7105 insertions(+), 8007 deletions(-)
create mode 100644 checks/R-tests/Makefile.am
create mode 100644 checks/R-tests/Makefile.in
create mode 100644 checks/R-tests/initial_checks.R
create mode 100755 checks/R-tests/run_R_test_pacox.sh
create mode 100755 checks/R-tests/run_R_test_palinear.sh
create mode 100755 checks/R-tests/run_R_test_palogist.sh
create mode 100644 checks/R-tests/run_model_coxph.R
create mode 100644 checks/R-tests/run_model_linear.R
create mode 100644 checks/R-tests/run_model_logist.R
create mode 100644 checks/R-tests/run_models_in_R_pacox.R
create mode 100644 checks/R-tests/run_models_in_R_palinear.R
create mode 100644 checks/R-tests/run_models_in_R_palogist.R
rename checks/{check_probabel.pl_chunk.sh => check_probabel_chunk.sh} (91%)
delete mode 100755 compile
delete mode 100755 depcomp
delete mode 100644 doc/Makefile.in
create mode 100644 doc/probabel.1
create mode 100644 doc/probabel.pl.1
delete mode 100755 install-sh
delete mode 100644 src/Makefile.in
create mode 100644 src/main_functions_dump.cpp
create mode 100644 src/main_functions_dump.h
rename src/{probabel.pl => probabel} (90%)
mode change 100755 => 100644
create mode 100755 test-driver
--
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