[med-svn] [probabel] branch upstream updated (634e1db -> 7b2d0e3)
Lennart Karssen
lckarssen-guest at moszumanska.debian.org
Wed Jan 15 13:30:06 UTC 2014
This is an automated email from the git hooks/post-receive script.
lckarssen-guest pushed a change to branch upstream
in repository probabel.
from 634e1db Imported Upstream version 0.4.1
new 7b2d0e3 Imported Upstream version 0.4.2
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 +
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(-)
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%)
create mode 100644 doc/probabel.1
create mode 100644 doc/probabel.pl.1
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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