[med-svn] [eigensoft] branch master updated (b7b2db8 -> 62810ca)
Andreas Tille
tille at debian.org
Mon Jul 18 20:16:45 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository eigensoft.
from b7b2db8 Remove dubious file, upload to unstable
new 6460cc8 Adapt watch file to match new upstream version
new aa2f41f New upstream version
new dc81bb2 Imported Upstream version 6.1.2+dgsg
new 6ce0873 Merge tag 'upstream/6.1.2+dgsg'
new af4c479 fix typo
new a34f862 Imported Upstream version 6.1.2+dfsg
new a40e8b5 Merge tag 'upstream/6.1.2+dfsg'
new 7185360 Upstream has changed to BSD license - upload to main
new 62810ca Adapt patches
The 9 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:
EIGENSTRAT/README | 42 +-
EIGENSTRAT/example.pcaselection.chisq | 8 +
EIGENSTRAT/example.pcaselection.par | 5 +
LICENSE.txt | 32 +
POPGEN/README | 16 +-
README | 41 +-
bin/{evec2pca-ped.perl => evec2pca-ped.pl} | 0
bin/{evec2pca.perl => evec2pca.pl} | 0
bin/fixgreen | 25 -
bin/{gc.perl => gc.pl} | 0
bin/ploteig | 168 -
bin/{smarteigenstrat.perl => smarteigenstrat.pl} | 0
bin/{smartpca.perl => smartpca.pl} | 0
debian/changelog | 7 +
debian/control | 3 +-
debian/copyright | 13 +-
debian/patches/blas.patch | 19 +-
debian/patches/hardening.patch | 23 -
debian/patches/libm.patch | 9 +
debian/patches/perlPath.patch | 20 -
debian/patches/series | 8 +-
debian/rules | 3 -
debian/watch | 4 +-
include/LICENSE.txt | 32 +
include/admutils.h | 393 +-
include/backup/kjg_fpca.h | 71 -
include/backup/kjg_geno.h | 137 -
include/backup/kjg_gsl.h | 73 -
include/badpairs.h | 28 +-
include/egsubs.h | 19 +-
include/eigqpsubs.h | 360 +-
include/eigsubs.h | 25 +-
include/exclude.h | 10 +-
include/getpars.h | 55 +-
include/globals.h | 2 +-
include/gval.h | 26 +-
include/kjg_fpca.h | 12 +-
include/kjg_geno.h | 137 -
include/kjg_gsl.h | 43 +-
include/lapacke.h | 16305 ---------------------
include/ldsubs.h | 62 +-
include/linsubs.h | 30 +-
include/mcio.h | 355 +-
include/mcmcpars.h | 49 +-
include/not-thread-h | 49 -
include/old.h | 43 -
include/packit.h | 12 +-
include/qpsubs.h | 373 +-
include/ranmath.h | 89 +-
include/regsubs.h | 36 +-
include/smartsubs.h | 7 +-
include/sortit.h | 34 +-
include/statsubs.h | 228 +-
include/strsubs.h | 201 +-
include/twtable.h | 12 +
include/vsubs.h | 486 +-
include/workqueue.h | 21 +-
include/xpsubs.h | 65 +-
include/xsearch.h | 42 +-
src/LICENSE.txt | 32 +
src/Makefile | 49 +-
src/admutils.c | 1894 +--
src/baseprog.c | 421 +-
src/convertf.c | 1728 ++-
src/egsubs.c | 260 +-
src/eigensrc/LICENSE.txt | 32 +
src/eigensrc/eigenstrat.c | 637 +-
src/eigensrc/eigenstratQTL.c | 609 +-
src/eigensrc/eigsubs.c | 338 +-
src/eigensrc/eigx.c | 325 +-
src/eigensrc/exclude.c | 146 +-
src/eigensrc/fffpca.c | 5448 +++----
src/eigensrc/newpca.c | 5460 +++----
src/eigensrc/old.c | 3213 ----
src/eigensrc/oldfffpca.c | 3231 ----
src/eigensrc/pcatoy.c | 47 +-
src/eigensrc/q1 | 105 -
src/eigensrc/qdiff | 1000 --
src/eigensrc/qq2.c | 29 -
src/eigensrc/qqq.c | 3139 ----
src/eigensrc/smarteigenstrat.c | 821 +-
src/eigensrc/smartpca.c | 5464 +++----
src/eigensrc/smartrel.c | 2729 ++--
src/eigensrc/smartsubs.c | 159 +-
src/eigensrc/twstats.c | 223 +-
src/eigx.c | 325 +-
src/exclude.c | 146 +-
src/gval.c | 36 +-
src/gval.h | 13 -
src/h2d.c | 146 +-
src/ksrc/LICENSE.txt | 32 +
src/ksrc/kjg_fpca.c | 38 +-
src/ksrc/kjg_gsl.c | 67 +-
src/mcio.c | 8631 ++++++-----
src/mergeit.c | 824 +-
src/mmakefile | 99 -
src/nicksrc/LICENSE.txt | 32 +
src/nicksrc/Makefile | 6 +-
src/nicksrc/gauss.c | 61 +-
src/nicksrc/gds.c | 1075 +-
src/nicksrc/getpars.c | 699 +-
src/nicksrc/linsubs.c | 532 +-
src/nicksrc/sortit.c | 362 +-
src/nicksrc/statsubs.c | 3519 +++--
src/nicksrc/strsubs.c | 2427 +--
src/nicksrc/twtable.c | 94 +
src/nicksrc/vsubs.c | 2728 ++--
src/nicksrc/xsearch.c | 458 +-
src/oldgval.c | 226 -
src/oldmakefile | 74 -
src/oldmcio.c | 4924 -------
src/pca.c | 510 +-
src/pcaselection.c | 344 +
src/qpsubs.c | 6098 ++++----
src/qq | 2 -
src/qqq.c | 5239 ++++---
src/regsubs.c | 766 +-
src/smartpca.gmon.out | Bin 143681 -> 0 bytes
src/smartpca.gmon.profile | 863 --
src/smarttables/twtable | 164 -
src/twsubs.c | 385 +-
121 files changed, 36341 insertions(+), 63511 deletions(-)
create mode 100644 EIGENSTRAT/example.pcaselection.chisq
create mode 100644 EIGENSTRAT/example.pcaselection.par
create mode 100644 LICENSE.txt
mode change 100755 => 100644 README
rename bin/{evec2pca-ped.perl => evec2pca-ped.pl} (100%)
rename bin/{evec2pca.perl => evec2pca.pl} (100%)
delete mode 100755 bin/fixgreen
rename bin/{gc.perl => gc.pl} (100%)
delete mode 100755 bin/ploteig
rename bin/{smarteigenstrat.perl => smarteigenstrat.pl} (100%)
rename bin/{smartpca.perl => smartpca.pl} (100%)
delete mode 100644 debian/patches/hardening.patch
create mode 100644 debian/patches/libm.patch
delete mode 100644 debian/patches/perlPath.patch
create mode 100644 include/LICENSE.txt
delete mode 100644 include/backup/kjg_fpca.h
delete mode 100644 include/backup/kjg_geno.h
delete mode 100644 include/backup/kjg_gsl.h
delete mode 100644 include/kjg_geno.h
delete mode 100644 include/lapacke.h
delete mode 100644 include/not-thread-h
delete mode 100644 include/old.h
create mode 100644 include/twtable.h
create mode 100644 src/LICENSE.txt
create mode 100644 src/eigensrc/LICENSE.txt
delete mode 100644 src/eigensrc/old.c
delete mode 100644 src/eigensrc/oldfffpca.c
delete mode 100644 src/eigensrc/q1
delete mode 100644 src/eigensrc/qdiff
delete mode 100644 src/eigensrc/qq2.c
delete mode 100644 src/eigensrc/qqq.c
delete mode 100644 src/gval.h
create mode 100644 src/ksrc/LICENSE.txt
delete mode 100644 src/mmakefile
create mode 100644 src/nicksrc/LICENSE.txt
create mode 100644 src/nicksrc/twtable.c
delete mode 100644 src/oldgval.c
delete mode 100644 src/oldmakefile
delete mode 100644 src/oldmcio.c
create mode 100644 src/pcaselection.c
delete mode 100644 src/qq
delete mode 100644 src/smartpca.gmon.out
delete mode 100644 src/smartpca.gmon.profile
delete mode 100644 src/smarttables/twtable
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