Subversion Logs

This is a list of recent commits to the development branch of the Bioconductor Subversion repository.

This list is also available as an RSS feed. (release branch)

Revision: 100191
Author: r.illa
Date: 2015-03-04T12:02:21+00:00
Paths:
Deleted  /trunk/madman/Rpacks/nucleR/Rpack
removed empty folder
Revision: 100190
Author: r.illa
Date: 2015-03-04T09:00:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/nucleR/DESCRIPTION
Modified  /trunk/madman/Rpacks/nucleR/NAMESPACE
Modified  /trunk/madman/Rpacks/nucleR/R/export.bed-methods.R
Modified  /trunk/madman/Rpacks/nucleR/R/importBAM.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 83518a3b30da41d1b9e8efaca4f762f3329988a8

    some fixes in NAMESPACE

Revision: 100189
Author: b.fischer
Date: 2015-03-04T08:41:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/mzR/DESCRIPTION
updated email address
Revision: 100188
Author: b.fischer
Date: 2015-03-04T08:39:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/RNAinteract/DESCRIPTION
updated email address
Revision: 100186
Author: j.schumann
Date: 2015-03-04T08:23:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCHIC/DESCRIPTION
new version
Revision: 100184
Author: j.schumann
Date: 2015-03-04T08:17:11+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowCyBar/DESCRIPTION
new version
Revision: 100182
Author: d.strbenac
Date: 2015-03-04T07:18:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/R/runTest.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/runTests.R
Modified  /trunk/madman/Rpacks/ClassifyR/R/utilities.R
Modified  /trunk/madman/Rpacks/ClassifyR/inst/NEWS.Rd
Fixed framework code which didn't work when multiple varieties were predicted.
Revision: 100179
Author: n.hayden
Date: 2015-03-04T01:38:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/Rhtslib/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: fdc83236061361564851b5f10d6a713b0cfc2497

    Add BugReports URL and GitHub URL

Revision: 100178
Author: n.hayden
Date: 2015-03-04T01:38:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/QuasR/DESCRIPTION
avoid linebreak on Rsamtools in Imports
Revision: 100176
Author: n.hayden
Date: 2015-03-04T01:16:10+00:00
Paths:
Modified  /trunk/madman/Rpacks/seqbias/DESCRIPTION
Modified  /trunk/madman/Rpacks/seqbias/src/motif.cpp
initialize pseudocount member outside of class def
Revision: 100174
Author: s.arora
Date: 2015-03-04T01:02:00+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makePazar.R
code update

Pazar Recipe
- add check to read in only csv files
- change rdataClass to GRanges

Revision: 100173
Author: s.arora
Date: 2015-03-04T01:01:44+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeChEA.R
code update

ChEA recipe
- change dispatch class to ChEA from Zip
- correct description ( 9 column file, not 3 columns!)


Revision: 100172
Author: j.storey
Date: 2015-03-04T01:00:09+00:00
Paths:
Modified  /trunk/madman/Rpacks/qvalue/DESCRIPTION
Modified  /trunk/madman/Rpacks/qvalue/NAMESPACE
Modified  /trunk/madman/Rpacks/qvalue/R/qvalue.R
Modified  /trunk/madman/Rpacks/qvalue/man/qplot.rd
Modified  /trunk/madman/Rpacks/qvalue/man/qsummary.rd
Deleted  /trunk/madman/Rpacks/qvalue/man/qvalue.gui.rd
Modified  /trunk/madman/Rpacks/qvalue/man/qvalue.rd
Modified  /trunk/madman/Rpacks/qvalue/man/qwrite.rd
Deleted  /trunk/madman/Rpacks/qvalue/vignettes/manual.pdf
Removed function requiring tcl/tk because it causes problems for many users.
Revision: 100171
Author: n.hayden
Date: 2015-03-04T00:58:52+00:00
Paths:
Added  /trunk/madman/Rpacks/Rhtslib/src/winlib/i386/libhts.a
Added  /trunk/madman/Rpacks/Rhtslib/src/winlib/x64/libhts.a
add Windows static libs from svn side
Revision: 100170
Author: n.hayden
Date: 2015-03-04T00:56:36+00:00
Paths:
Modified  /trunk/madman/Rpacks/bioc_3.1.manifest
add Rhtslib
Revision: 100169
Author: m.jiang
Date: 2015-03-04T00:52:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/src/protobuf-2.6.0.tgz
Commit made by the Bioconductor Git-SVN bridge.

Commit id: e6fa436b5e7caf6ba46a13015b466c0ec99da7e3

    Merge branch 'trunk'


Commit id: 047ea8c7b9affda38ad1c3bd3baf193ff07d13dc

    fix check error on mac by removing test-driver and compile files from pb source

Revision: 100168
Author: s.arora
Date: 2015-03-04T00:51:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHubResource-class.R
code update

- add column names for ChEA and Pazar Files
- remove the 12th column for Pazar Files as it contains only NA
- make GRanges from Pazar Files

Revision: 100166
Author: n.hayden
Date: 2015-03-04T00:49:47+00:00
Paths:
Added  /trunk/madman/Rpacks/Rhtslib/.gitattributes
Added  /trunk/madman/Rpacks/Rhtslib/.gitignore
Added  /trunk/madman/Rpacks/Rhtslib/.gitmodules
Added  /trunk/madman/Rpacks/Rhtslib/DESCRIPTION
Added  /trunk/madman/Rpacks/Rhtslib/NAMESPACE
Added  /trunk/madman/Rpacks/Rhtslib/R
Added  /trunk/madman/Rpacks/Rhtslib/R/zzz.R
Added  /trunk/madman/Rpacks/Rhtslib/README.md
Added  /trunk/madman/Rpacks/Rhtslib/cleanup
Added  /trunk/madman/Rpacks/Rhtslib/configure
Added  /trunk/madman/Rpacks/Rhtslib/man
Added  /trunk/madman/Rpacks/Rhtslib/man/Rhtslib-package.Rd
Added  /trunk/madman/Rpacks/Rhtslib/man/pkgconfig.Rd
Added  /trunk/madman/Rpacks/Rhtslib/src
Added  /trunk/madman/Rpacks/Rhtslib/src/Makevars
Added  /trunk/madman/Rpacks/Rhtslib/src/Makevars.win
Added  /trunk/madman/Rpacks/Rhtslib/src/Rhtslib.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/.gitattributes
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/.gitignore
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/.travis.yml
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/INSTALL
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/LICENSE
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/Makefile.am
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/README
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/README.md
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/aclocal.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/bgzf.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/bgzf_faidx_config.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/bgzip.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/configure.ac
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_codecs.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_codecs.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_decode.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_decode.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_encode.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_encode.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_index.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_index.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_io.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_io.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_samtools.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_samtools.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_stats.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_stats.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/cram_structs.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/files.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/mFILE.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/mFILE.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/md5.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/md5.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/misc.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/open_trace_file.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/open_trace_file.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/os.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/pooled_alloc.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/pooled_alloc.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/rANS_byte.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/rANS_static.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/rANS_static.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/sam_header.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/sam_header.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/string_alloc.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/string_alloc.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/thread_pool.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/thread_pool.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/vlen.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/vlen.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/zfio.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/cram/zfio.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/faidx.5
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/faidx.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/hfile.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/hfile_internal.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/hfile_net.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/hts.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htsfile.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/bgzf.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/faidx.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/hfile.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/hts.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/hts_defs.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/kfunc.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/khash.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/khash_str2int.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/klist.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/knetfile.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/kseq.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/ksort.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/kstring.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/regidx.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/sam.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/synced_bcf_reader.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/tbx.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/vcf.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/vcf_sweep.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib/vcfutils.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib.mk
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib.pc.in
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/htslib_vars.mk
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/kfunc.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/knetfile.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/kstring.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/.gitignore
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/Makefile.am
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/alloca.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/alloca.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/arpa_inet.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/close.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/dup2.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/errno.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/fcntl.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/fcntl.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/fd-hook.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/fd-hook.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/fdatasync.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/fileblocks.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/fsync.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/getdtablesize.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/getpagesize.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/gettimeofday.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/inttypes.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/msvc-inval.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/msvc-inval.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/msvc-nothrow.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/msvc-nothrow.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/netdb.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/recv.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/send.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/signal.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/stat-size.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/stdalign.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/stddef.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/stdint.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/stdlib.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/string.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/sys_select.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/sys_socket.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/sys_socket.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/sys_stat.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/sys_time.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/sys_types.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/sys_uio.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/time.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/unistd.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/unistd.in.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/lib/w32sock.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/.gitignore
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/00gnulib.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/absolute-header.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/alloca.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/arpa_inet_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/close.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/dup2.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/errno_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/extensions.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/extern-inline.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/fcntl-o.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/fcntl.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/fcntl_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/fdatasync.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/fileblocks.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/fsync.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/getdtablesize.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/getpagesize.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/gettimeofday.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/gnulib-cache.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/gnulib-common.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/gnulib-comp.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/gnulib-tool.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/include_next.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/inttypes-pri.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/inttypes.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/longlong.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/msvc-inval.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/msvc-nothrow.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/multiarch.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/netdb_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/off_t.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/signal_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/socketlib.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/socklen.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/sockpfaf.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/ssize_t.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/stat-size.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/stdalign.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/stddef_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/stdint.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/stdlib_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/string_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/sys_select_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/sys_socket_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/sys_stat_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/sys_time_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/sys_types_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/sys_uio_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/time_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/unistd_h.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/warn-on-use.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/m4/wchar_t.m4
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/regidx.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/run_tests.sh
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/sam.5
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/sam.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/snippet
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/snippet/.gitignore
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/snippet/_Noreturn.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/snippet/arg-nonnull.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/snippet/c++defs.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/snippet/warn-on-use.h
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/synced_bcf_reader.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/tabix.1
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/tabix.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/tbx.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/.gitignore
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/Makefile.am
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/auxf#values.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/auxf.fa
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/auxf.fa.fai
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/c1#bounds.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/c1#clip.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/c1#pad1.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/c1#pad2.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/c1#pad3.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/c1.fa
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/c1.fa.fai
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#1.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#2.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#5.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#5b.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#large_seq.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#tag_depadded.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#tag_padded.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#unmap.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#unmap1.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce#unmap2.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce.fa
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/ce.fa.fai
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/compare_sam.pl
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/fieldarith.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/fieldarith.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/hfile.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/sam.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/test-regidx.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/test-vcf-api.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/test-vcf-api.out
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/test-vcf-sweep.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/test-vcf-sweep.out
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/test.pl
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/test_view.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/test_view.pl
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx#blank.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx#large_aux.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx#large_aux2.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx#minimal.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx#pair.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx#rg.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx#triplet.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx#unsorted.sam
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx.fa
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/test/xx.fa.fai
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/vcf.5
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/vcf.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/vcf_sweep.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/vcfutils.c
Added  /trunk/madman/Rpacks/Rhtslib/src/htslib/version.h
Added  /trunk/madman/Rpacks/Rhtslib/src/winlib
Added  /trunk/madman/Rpacks/Rhtslib/src/winlib/i386
Added  /trunk/madman/Rpacks/Rhtslib/src/winlib/x64
Added  /trunk/madman/Rpacks/Rhtslib/tools
Added  /trunk/madman/Rpacks/Rhtslib/tools/Makefile.in
Added  /trunk/madman/Rpacks/Rhtslib/tools/config.guess
Added  /trunk/madman/Rpacks/Rhtslib/tools/config.h.in
Added  /trunk/madman/Rpacks/Rhtslib/tools/config.sub
Added  /trunk/madman/Rpacks/Rhtslib/tools/configure
Added  /trunk/madman/Rpacks/Rhtslib/tools/depcomp
Added  /trunk/madman/Rpacks/Rhtslib/tools/install-sh
Added  /trunk/madman/Rpacks/Rhtslib/tools/lib_Makefile.in
Added  /trunk/madman/Rpacks/Rhtslib/tools/missing
Added  /trunk/madman/Rpacks/Rhtslib/tools/test_Makefile.in
Added  /trunk/madman/Rpacks/Rhtslib/vignettes
Added  /trunk/madman/Rpacks/Rhtslib/vignettes/Rhtslib.Rmd
setting up git-svn bridge
Revision: 100165
Author: n.hayden
Date: 2015-03-04T00:46:11+00:00
Paths:
Added  /trunk/madman/Rpacks/Rhtslib
prep for initializing bridge for Rhtslib
Revision: 100159
Author: s.arora
Date: 2015-03-03T23:43:13+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makePazar.R
code update

Pazar file recipe update
- better code to parse filename and sourceUrl
- remove duplicate code for Tags
- change dispatchClass to Pazar

Revision: 100157
Author: s.arora
Date: 2015-03-03T23:38:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeBioPaxImporter.R
code update

BioPAX files recipe update
- use sub instead of gsub
- more descriptive with the DataProvider
- rDataClass is biopax

Revision: 100155
Author: s.arora
Date: 2015-03-03T23:32:59+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHubResource-class.R
code update

- formatting
- have own method for Pazar files (instead of csv)
- header=FALSE for all files
- tempdir() instead of tempdir


Revision: 100154
Author: m.carlson
Date: 2015-03-03T23:27:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/NAMESPACE
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
Adds a couple more tests to the constructor. (more to come)
Revision: 100151
Author: b.phipson
Date: 2015-03-03T23:05:07+00:00
Paths:
Modified  /trunk/madman/Rpacks/missMethyl/vignettes/missMethyl.Rnw
Fixed typo in vignette.
Revision: 100150
Author: m.jiang
Date: 2015-03-03T22:43:17+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowWorkspace/DESCRIPTION
Modified  /trunk/madman/Rpacks/flowWorkspace/configure
Modified  /trunk/madman/Rpacks/flowWorkspace/configure.ac
Modified  /trunk/madman/Rpacks/flowWorkspace/src/protobuf-2.6.0.tgz
Commit made by the Bioconductor Git-SVN bridge.

Commit id: b1b1c69977bfd9a18f8e5a0c915b9ed9b1813be3

    Merge branch 'trunk'


Commit id: dbdf601b60faa4a8e112a2807e04b6081a049e35

    Fix R CMD check warnings: 1. rename lt~obsolete.m4 as lt-obsolete.m4 to since R complains about the non-portable filename 2. disable return type check by adding -Wno-return-type flag to Makefile.am due to 'control reaches end of non-void function' warning when compiling extension_set.cc

Revision: 100148
Author: v.obenchain
Date: 2015-03-03T22:35:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/MinimumDistance/DESCRIPTION
Modified  /trunk/madman/Rpacks/MinimumDistance/R/methods-MinDistExperiment.R
follow replacement of 'rowData' with 'rowRanges'
Revision: 100147
Author: d.tenenbaum
Date: 2015-03-03T22:33:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/CNEr/DESCRIPTION
Modified  /trunk/madman/Rpacks/eiR/DESCRIPTION
bump version to propagate previous change
Revision: 100144
Author: v.obenchain
Date: 2015-03-03T22:17:35+00:00
Paths:
Modified  /trunk/madman/Rpacks/roar/DESCRIPTION
Modified  /trunk/madman/Rpacks/roar/R/RoarDataset-accessors.R
Modified  /trunk/madman/Rpacks/roar/inst/unitTests/test_roar.R
Modified  /trunk/madman/Rpacks/roar/inst/unitTests/test_roar_results.R
follow replacement of 'rowData' with 'rowRanges'
Revision: 100143
Author: v.obenchain
Date: 2015-03-03T22:17:01+00:00
Paths:
Modified  /trunk/madman/Rpacks/SGSeq/DESCRIPTION
Modified  /trunk/madman/Rpacks/SGSeq/R/annotation.R
Modified  /trunk/madman/Rpacks/SGSeq/R/counts.R
Modified  /trunk/madman/Rpacks/SGSeq/R/graphs.R
Modified  /trunk/madman/Rpacks/SGSeq/R/main.R
Modified  /trunk/madman/Rpacks/SGSeq/R/plots.R
Modified  /trunk/madman/Rpacks/SGSeq/R/slots-methods.R
Modified  /trunk/madman/Rpacks/SGSeq/vignettes/SGSeq.Rnw
follow replacement of 'rowData' with 'rowRanges'
Revision: 100142
Author: j.hester
Date: 2015-03-03T22:14:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/epivizr/R/EpivizFeatureData-class.R
Modified  /trunk/madman/Rpacks/epivizr/R/register-methods.R
Modified  /trunk/madman/Rpacks/epivizr/vignettes/IntroToEpivizr.Rmd
Use rowRanges method rather than deprecated rowData method
Revision: 100137
Author: m.aryee
Date: 2015-03-03T21:46:02+00:00
Paths:
Modified  /trunk/madman/Rpacks/bumphunter/DESCRIPTION
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 5435801557b8bb60be8e6264491b69372dfe928e

    Fixed Martin's last name and bumped version

Revision: 100135
Author: m.aryee
Date: 2015-03-03T21:42:41+00:00
Paths:
Modified  /trunk/madman/Rpacks/bumphunter/R/smooth.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: ce7bb86408967bd233d8f6cfabdd8d44bf8f9868

    locfitByCluster no longer fails if all coefficients in a cluster are NA

Revision: 100134
Author: s.arora
Date: 2015-03-03T21:28:06+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHub/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHub/R/AnnotationHubResource-class.R
code update

- add client methods for ChEA, Pazar and BioPAX files
Revision: 100130
Author: s.gogarten
Date: 2015-03-03T21:16:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/GWASTools/inst/unitTests/gdsSubset_test.R
fix unit test bug with new gdsfmt
Revision: 100129
Author: s.arora
Date: 2015-03-03T21:03:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeChEA.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makePazar.R
code update

- correct DispatchClass and Tag for Pazar Files
- correct LOcation_prefix for ChEA files
Revision: 100126
Author: venkatre
Date: 2015-03-03T20:39:52+00:00
Paths:
Modified  /trunk/madman/Rpacks/DNAcopy/DESCRIPTION
Modified  /trunk/madman/Rpacks/DNAcopy/R/segment.R
Modified  /trunk/madman/Rpacks/DNAcopy/inst/CHANGES
Midified segment to address "no visible binding for global variable"

Revision: 100122
Author: s.arora
Date: 2015-03-03T19:00:18+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
code update
- allow TaxId to have NA_integer_
Revision: 100121
Author: k.oneill
Date: 2015-03-03T18:52:27+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowType/vignettes/flowType.Rnw
Changed example to use kmeans instead of flowMeans due to bug in flowMeans.
Revision: 100120
Author: s.arora
Date: 2015-03-03T18:49:20+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/ahmToJson.R
code update

- move dispatchclass inside rdatapaths when creating JSON
Revision: 100119
Author: s.arora
Date: 2015-03-03T18:28:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/DESCRIPTION
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/AnnotationHubMetadata-class.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/helperFunctions.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeBioPaxImporter.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeChEA.R
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makePazar.R
code update

- make species, genome and taxId for ChEA and Pazar files NA
- change importBioPax to BioPax to remain consistent with other dispatchClass's
- correct bug in helper function .httrFileInfo()
-  correct code inside constructor
a) single call to helper function .httrFileInfo()
b) sourceSize is expecting integer so NA_real_ instead of NA
c) SourceLastModifiedDate is expecting POSIXct intead of NA
d) TaxId is expecting NA_integer_ instead of NA_character_


Revision: 100116
Author: s.arora
Date: 2015-03-03T17:58:39+00:00
Paths:
Modified  /trunk/madman/Rpacks/AnnotationHubData/R/makeChEA.R
code update

- file contains data from multiple organism
adjust species, genome and TaxonomyId

Revision: 100114
Author: c.panse
Date: 2015-03-03T17:14:16+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/vignettes/specL.Rnw
Modified  /trunk/madman/Rpacks/specL/vignettes/specL.bib
vignette bib update
Revision: 100113
Author: l.collado-torres
Date: 2015-03-03T15:34:38+00:00
Paths:
Modified  /trunk/madman/Rpacks/derfinder/DESCRIPTION
Modified  /trunk/madman/Rpacks/derfinder/NAMESPACE
Modified  /trunk/madman/Rpacks/derfinder/NEWS
Modified  /trunk/madman/Rpacks/derfinder/R/analyzeChr.R
Modified  /trunk/madman/Rpacks/derfinder/R/calculatePvalues.R
Modified  /trunk/madman/Rpacks/derfinder/R/derfinder-package.R
Modified  /trunk/madman/Rpacks/derfinder/R/findRegions.R
Modified  /trunk/madman/Rpacks/derfinder/R/mergeResults.R
Modified  /trunk/madman/Rpacks/derfinder/man/analyzeChr.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/calculatePvalues.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/derfinder-package.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/findRegions.Rd
Modified  /trunk/madman/Rpacks/derfinder/man/mergeResults.Rd
Modified  /trunk/madman/Rpacks/derfinder/vignettes/realVignettes/derfinder.Rmd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: df61459725658dc91b3a05973157e2cdd0d86567

    v1.1.16 -- attempts to work with bumphunter's recent changes in 1.7.3

    Note that it actually requires bumphunter 1.7.4 as available from https://github.com/ririzarr/bumphunter/pull/3 These changes are not
    compatible with the current BioC-release.

    However, this version does not pass R CMD check due to a current bug in
    bumphunter 1.7.4

Revision: 100112
Author: c.panse
Date: 2015-03-03T14:27:37+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/NAMESPACE
Modified  /trunk/madman/Rpacks/specL/src/lower_bound.cpp
fixed Rcpp import;
Revision: 100111
Author: c.beauparlant
Date: 2015-03-03T14:17:12+00:00
Paths:
Modified  /trunk/madman/Rpacks/metagene/DESCRIPTION
Modified  /trunk/madman/Rpacks/metagene/NAMESPACE
Modified  /trunk/madman/Rpacks/metagene/R/Utilities.R
Modified  /trunk/madman/Rpacks/metagene/R/bam_handler.R
Modified  /trunk/madman/Rpacks/metagene/R/demo.R
Modified  /trunk/madman/Rpacks/metagene/R/metagene.R
Modified  /trunk/madman/Rpacks/metagene/inst/unitTests/test_bam_handler.R
Modified  /trunk/madman/Rpacks/metagene/inst/unitTests/test_metagene.R
Added  /trunk/madman/Rpacks/metagene/man/Bam_Handler.Rd
Modified  /trunk/madman/Rpacks/metagene/man/metagene.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 149370c8f8412ae7114bb88190c930f5cafe6c07

    Merge pull request #35 from adeschen/master

    metagene$plot parameter check and unit tests

Commit id: 268dffa43e856fa614f0e6f3cc3e668e73047296

    Changing gplots library from depends section to imports section.


Commit id: d5251aff1529584e13b006ff4b12a38aa5ed6287

    Merge branch 'master' of https://github.com/CharlesJB/metagene


Commit id: 81eba472de29a571818372fbb3b7b1c316a85954

    Update version

    Update version to 1.99.6

Commit id: 7679b4d5eddaed2564f9fdd0f0b1326060bbcfa5

    Changing rtracklayer library from depends to imports section.


Commit id: 9b663d74981c93e47d3952017aafc488c01099cd

    Closing parenthisis in method section. Updating manual.


Commit id: 4bbfe442fa2a34e95479aaeab25e7d9efcc0a051

    Change indent to by a multiple of 4 spaces


Commit id: 865c883a7529a43e8b629ccc03d1497802b53b9f

    Adding parameter check in metagene() method. Adding unit tests. Updating method description and manual. Adding Bam_Handler class manual.


Commit id: 1f6697c149b7cfbb5fb871fafb7847be37fe799c

    Merge branch 'master' of https://github.com/CharlesJB/metagene

Revision: 100110
Author: c.panse
Date: 2015-03-03T14:08:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/specL/src/Makevars
Modified  /trunk/madman/Rpacks/specL/src/lower_bound.cpp
svn propset svn:keywords HeadURL Id *.cpp
Revision: 100109
Author: c.fletez-brant
Date: 2015-03-03T14:06:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/flowClean/R/flowClean.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 7d7548d58328c7b4e3e8b3ec460536d8475907fd

    revert to no #cell

Revision: 100106
Author: j.leek
Date: 2015-03-03T13:43:25+00:00
Paths:
Modified  /trunk/madman/Rpacks/sva/DESCRIPTION
Modified  /trunk/madman/Rpacks/sva/R/ComBat.R
Added  /trunk/madman/Rpacks/sva/tests
Added  /trunk/madman/Rpacks/sva/tests/testthat
Added  /trunk/madman/Rpacks/sva/tests/testthat/test_combat_bladderbatch.R
Added  /trunk/madman/Rpacks/sva/tests/testthat/test_combat_errors.R
Added  /trunk/madman/Rpacks/sva/tests/testthat/test_combat_sim.R
Added  /trunk/madman/Rpacks/sva/tests/testthat.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: a7cb4b2861e059ea0fea31fa6c771b6445aa047c

    Merge pull request #5 from wevanjohnson/master

    Added unit tests for ComBat

Commit id: 7632f0c7a484ded48cd40ca0bb48ad96e80961e7

    Made the following changes: 1) added unit tests for ComBat to check ComBat errors for confounded designs and for the output on simulated and the bladder cancer data. 2) Streamlined some of the ComBat errors (just shortened the text). 3) Added myself as a maintainer of the package since I am the only one updating/maintaining the ComBat part of the package.

Revision: 100105
Author: g.yu
Date: 2015-03-03T13:36:29+00:00
Paths:
Added  /trunk/madman/Rpacks/ChIPseeker/.gitignore
Modified  /trunk/madman/Rpacks/ChIPseeker/DESCRIPTION
Modified  /trunk/madman/Rpacks/ChIPseeker/NEWS
Modified  /trunk/madman/Rpacks/ChIPseeker/R/GEO.R
Modified  /trunk/madman/Rpacks/ChIPseeker/data/gsminfo.rda
Modified  /trunk/madman/Rpacks/ChIPseeker/inst/extdata/processedGSM.rda
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 1cb074ebaba33d448d723664251d27646c0ded37

    update GEO data

Revision: 100100
Author: g.yu
Date: 2015-03-03T12:01:24+00:00
Paths:
Modified  /trunk/madman/Rpacks/clusterProfiler/NEWS
Modified  /trunk/madman/Rpacks/clusterProfiler/R/compareCluster.R
Modified  /trunk/madman/Rpacks/clusterProfiler/man/plot-methods.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: 0721ed6ae5922c09b0c17b6a516974df8c96c2df

    set includeAll=T by default

Revision: 100099
Author: g.yu
Date: 2015-03-03T11:55:23+00:00
Paths:
Modified  /trunk/madman/Rpacks/ggtree/DESCRIPTION
Modified  /trunk/madman/Rpacks/ggtree/NEWS
Modified  /trunk/madman/Rpacks/ggtree/R/phylopic.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: da1e9c85367cf00f37ee72a3a5e938f03db5b164

    fixed windows compile issue

Revision: 100098
Author: t.hardcastle
Date: 2015-03-03T11:26:58+00:00
Paths:
Modified  /trunk/madman/Rpacks/riboSeqR/DESCRIPTION
Modified  /trunk/madman/Rpacks/riboSeqR/R/sliceCounts.R
1.1.2. bugfix in sliceCounts using more than two lengths
Revision: 100096
Author: s.neumann
Date: 2015-03-03T11:10:46+00:00
Paths:
Modified  /trunk/madman/Rpacks/xcms/DESCRIPTION
Modified  /trunk/madman/Rpacks/xcms/NAMESPACE
Modified  /trunk/madman/Rpacks/xcms/R/xcmsSet.R
Modified  /trunk/madman/Rpacks/xcms/inst/NEWS
Modified  /trunk/madman/Rpacks/xcms/man/xcmsSet-class.Rd
Commit made by the Bioconductor Git-SVN bridge.

Commit id: e890a0edd57ff2dbf57e2f73bceae09a387c8be1

    Use ProtGenerics, adapted xcms peaks()

Revision: 100095
Author: l.hedjazi
Date: 2015-03-03T10:04:48+00:00
Paths:
Modified  /trunk/madman/Rpacks/mQTL.NMR/R/process_mGWA.R
Commit made by the Bioconductor Git-SVN bridge.

Commit id: cade77ef0e38621e2b7a77dbb57ffd6043e294a6

    Update process_mGWA.R

Revision: 100094
Author: l.gatto
Date: 2015-03-03T09:54:53+00:00
Paths:
Modified  /trunk/madman/Rpacks/ProtGenerics/DESCRIPTION
add NeedsCompilation back
Revision: 100093
Author: l.gatto
Date: 2015-03-03T09:54:50+00:00
Paths:
Modified  /trunk/madman/Rpacks/ProtGenerics/DESCRIPTION
Modified  /trunk/madman/Rpacks/ProtGenerics/NEWS
fix conflicts
Revision: 100092
Author: r.castelo
Date: 2015-03-03T09:06:19+00:00
Paths:
Modified  /trunk/madman/Rpacks/VariantFiltering/DESCRIPTION
Modified  /trunk/madman/Rpacks/VariantFiltering/R/annotationEngine.R
Modified  /trunk/madman/Rpacks/VariantFiltering/R/commonFunctions.R
Fixed bug that was mixing sequence level styles on the resulting object.
Revision: 100091
Author: d.strbenac
Date: 2015-03-03T05:00:55+00:00
Paths:
Modified  /trunk/madman/Rpacks/ClassifyR/DESCRIPTION
Modified  /trunk/madman/Rpacks/ClassifyR/man/KullbackLeiblerSelection.Rd
No longer relevant description removed from documentation of KullbackLeiblerSelection.

Source Code & Build Reports »

Source code is stored in svn (user: readonly, pass: readonly).

Software packages are built and checked nightly. Build reports:

 

Development Version »

Bioconductor packages under development:


Developer Resources:

Fred Hutchinson Cancer Research Center