Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

This is a list of recent commits to git.bioconductor.org, the master(development) branch of the Bioconductor GIT repository.

This list is also available as an RSS feed (master branch), and RSS feed (release branch)

Package: flowPloidy
Commit: 8fdf48467a0e50fda951ce57c87e17fbf1b4b4d8
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-17 21:52:28
Commit message:

 Namespace fixes

Because of course I broke them. Don't directly edit NAMESPACE, add the
import lines in the source files using the `#' @importFrom` syntax
 
Package: flowPloidy
Commit: 72c8411437f328c6ce426e5349b30cb3475e32a3
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-17 21:33:44
Commit message:

 Version bump, updated NEWS file
 
Package: flowPloidy
Commit: 5bbc88a91f9c4b78ae8a70404ae5a4b84c1f8296
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-17 21:33:23
Commit message:

 Removed obsolete encoding setting from vignettes
 
Package: flowPloidy
Commit: 7cfaf861acf6324fd94f431ed3ac63bb9a077c8a
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-17 21:09:29
Commit message:

 Set linearity limits to 1.5, 2.5

This is now controlled by the internal variables linL and linH, in case I
want to change the range again in future.
 
Package: flowPloidy
Commit: 033d2bcd804f3d6c51731f37bfd2316ca8268e1d
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-17 20:48:46
Commit message:

 Switched numericInput for selectInput for Sample Number

Tracey found a way to break the numericInput - the textbox is editable,
allowing the user to enter invalid values. Typically, she would select the
textbox, and delete the current value before entering the new one. As soon
as the old value was deleted, shiny would update the value to NULL, not
waiting for the new value to be entered. This caused the app to crash
completely and irrecoverably. Switching to selectInput, the user can only
pick between the valid options, they don't have an opportunity to enter
arbitrary values (or NULL), so they can't break things (as easily).
 
Package: Biostrings
Commit: 4b43c7de3ac053336f3096e4385e4172e4bf3511
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-17 21:03:53
Commit message:

 Fix bug in stringDist() where the pairwise alignment scores were
returned instead of their opposite when a substitution matrix was
used (i.e. when called with method="substitutionMatrix").
 
Package: RaggedExperiment
Commit: 26d6f24e39d8edc14ea0ba4258c5e3708cc29c49
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-01-17 20:39:10
Commit message:

 use html_document from BiocStyle
 
Package: flowPloidy
Commit: 32cab1bf76740590d42b0f3d802ed4b501311c49
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-17 20:31:25
Commit message:

 Refactor vignette images, collected pandoc config in a new dir

images now in separate directories, to make it easier to see how the
vignettes are structured.
 
Package: flowPloidy
Commit: 8578720ae5ca44040c299c4fc911486d566b67aa
Author: Tyler Smith <tyler@plantarum.ca>
Date: 2018-01-17 20:29:51
Commit message:

 deleted transient images, not actually used anywhere
 
Package: Biostrings
Commit: ce5846feb86d3f8a5d99e8d7d71e48f8cc87d89b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-17 19:51:58
Commit message:

 Make sure reverseComplement() also works properly on
QualityScaledRNAStringSet objects.
 
Package: Biostrings
Commit: a43fa1d13c8b263f842036ff4b28fde513151364
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-17 19:40:44
Commit message:

 fix reverse() and reverseComplement() on QualityScaledDNAStringSet objects
 
Package: Biostrings
Commit: f25eeb49bea4b7ab4180bd1dc16894eafa01a2a1
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-01-17 18:49:06
Commit message:

 - Make the 'quality' slot of QualityScaledXStringSet objects a
  parallel slot.
- Remove the "[" and "append" methods for these objects (they're not
  needed anymore).
 
Package: BiocFileCache
Commit: be3dc1c417735bb90686ac383e2cf49b68da1d65
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-01-17 18:26:12
Commit message:

 emit warning when schema not updated
 
Package: BiocFileCache
Commit: 75e5f57f656bb89ef7773dc9074d69b00e32c057
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-01-17 18:24:46
Commit message:

 .util_ask() provides own '(yes / no):'

- better handling of interactive session
- some testable functionality + unit test
 
Package: derfinder
Commit: d90f44a0c82ad398e6c5a1cdb20b7b7f52465349
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-17 18:27:41
Commit message:

 1.13.4 -- fix BamFile link for Windows, thanks to feedback from James MacDonald
 
Package: RnBeads
Commit: 8bd358ce1491b2dcf95912960c4bd6ca8f11b585
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2018-01-17 18:25:14
Commit message:

 Merge branch 'feature/RnBeads2.0'
 
Package: RnBeads
Commit: 27e7b0eefad8cddf74e17a1cb5199707c088eba8
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2018-01-17 18:24:56
Commit message:

 updated version and news
 
Package: RnBeads
Commit: 1db9580ab4deadc3757707e3370aaf3e073835c6
Author: lutsik <pavlo.lutsik@gmail.com>
Date: 2018-01-17 14:36:12
Commit message:

 Merge branch 'bsseq-loading-fix' into feature/RnBeads2.0 
Package: RnBeads
Commit: c44ebfb26ac3d732c15a4c47128abcae3404aab4
Author: lutsik <pavlo.lutsik@gmail.com>
Date: 2018-01-17 14:35:19
Commit message:

 set the mean.meth and coverage columns to NA during EPP loading to avoid
subsequent warnings 
Package: RnBeads
Commit: cf8a4f9d5bfe4796a05efd3c3d7fc157296f2ba4
Author: Michael Scherer <mscherer@lap-13-66>
Date: 2018-01-10 08:56:26
Commit message:

 Merge branch 'feature/RnBeads2.0' of github.com:epigen/RnBeads into feature/RnBeads2.0

Conflicts:
	R/differentialVariability.R
	R/main.R
 
Package: RnBeads
Commit: a95de26062c8ebd1aa3648914e1d60066b024728
Author: Michael Scherer <mscherer@lap-13-66>
Date: 2018-01-10 08:15:06
Commit message:

 Merge branch 'feature/imputation_fix' into feature/RnBeads2.0
 
Package: RnBeads
Commit: 2da48b39b92b1b764fa3ff7cbf589389bf5107b4
Author: Michael Scherer <mscherer@lap-13-66>
Date: 2018-01-10 08:14:11
Commit message:

 Improved running time of imputation
Added new method (updateMethylationSites) in RnBSet-class to update methylation levels of the object
 
Package: RnBeads
Commit: 1406f01028944360d3a9f733c2b5b1e307684c1a
Author: Michael Scherer <mscherer@lap-13-66>
Date: 2018-01-05 14:12:59
Commit message:

 Some cosmetics in the diffVar plots
 
Package: RnBeads
Commit: d47ee2da3b9d854665891e6f32247b3855741f50
Author: Michael Scherer <mscherer@lap-13-66>
Date: 2018-01-04 17:27:00
Commit message:

 Removed warnings produces by diffVar module
 
Package: RnBeads
Commit: 76b2caa97d06c2d4cf3a88afc2a24b167da8efeb
Author: Michael Scherer <mscherer@lap-13-66>
Date: 2018-01-04 15:45:46
Commit message:

 Optimized run time for the imputation
 
Package: RnBeads
Commit: 7aa22e38c473ab20945d80c959686049602c3d2d
Author: Michael Scherer <mscherer@lap-13-66>
Date: 2018-01-03 15:28:19
Commit message:

 Fixed bug in imputation: ff matrix was not correctly updated
Added new imputation methods: median.samples and median.cpg
 
Package: annotatr
Commit: 1dd067e08d5f95fda4bb64196a48f2ef37c82ae2
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-11-17 10:42:43
Commit message:

 endoapply() and mendoapply() are now regular functions instead of
generic functions.
 
Package: annotatr
Commit: 681ffa9b6f57a5701caf092e1c2abcdd5aa88704
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-10-30 16:54:22
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
 
Package: annotatr
Commit: 7ddd37fa5e578d1a94150ee2a0192dd797bfdf7e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-10-30 16:41:23
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
 
Package: annotatr
Commit: 1fbb61fc84522604f4363bd0c5beb1a72464ac06
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2017-10-26 21:39:21
Commit message:

 Require R >= 3.4.0

 
Package: annotatr
Commit: afe4e75a63d0219e36a9b1d04039f1d490f62277
Author: Raymond Cavalcante <cavalcante.raymond@gmail.com>
Date: 2017-10-26 21:38:55
Commit message:

 Bugfix: Errant space in test data

* This causes errors on the Bioc build system, but nowhere else... Odd. Thanks to Martin Morgan for finding the extra space. 
Package: qcmetrics
Commit: 76b090f4bcff75916997680e3e815ebc3645cf47
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 14:50:14
Commit message:

 update news
 
Package: qcmetrics
Commit: 933a256718e3a6da7fbef53c5ace11b31df12df1
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 14:35:07
Commit message:

 remove html_document2
 
Package: qcmetrics
Commit: 80584887cf0be74eaaeb561cac693a4e0b942227
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 14:33:16
Commit message:

 remove html_document2
 
Package: qcmetrics
Commit: 9f67902160d33c9cdfb25dcf0e80f91c75876ff6
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 14:32:25
Commit message:

 Merge branch 'devel'
 
Package: qcmetrics
Commit: 06f9c8eb3173013ef6c31f9eba588e51a3f95c7e
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 14:32:16
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/qcmetrics into devel
 
Package: qcmetrics
Commit: 3a2eac43000caa04fe7b93c1bd39a2a35bb52224
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-27 15:44:42
Commit message:

 update pkgdown site
 
Package: qcmetrics
Commit: 5e243148bd0994128e83c1d9bbe923b29d197742
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-27 15:43:17
Commit message:

 Merge branch 'master' into devel
 
Package: qcmetrics
Commit: 8a501f30b2fe1a42aa3f311ca174c43cb97a9fb2
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-27 15:42:31
Commit message:

 Merge branch 'master' into devel
 
Package: qcmetrics
Commit: 9b7936f3e4399e4d4cf9273e9f5af091088b12d2
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-27 15:40:48
Commit message:

 merged fix to use BiocStyle
 
Package: qcmetrics
Commit: d0c53063b00c7d2318680f47ada05635f53f1c2e
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-27 15:40:13
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/qcmetrics into devel
 
Package: qcmetrics
Commit: 62efe970d9ab46727826353bc0fd3176462b62b2
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-25 12:16:23
Commit message:

 Merge branch 'master' into devel
 
Package: qcmetrics
Commit: 3e7ae7d07a8df07ee4d5f8891ea82b7587c64b19
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-25 12:13:27
Commit message:

 Merge branch 'master' into devel
 
Package: qcmetrics
Commit: a6609cf90ed55d69ad4c7490c02bc7b26ebcebee
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-25 12:07:05
Commit message:

 Merge branch 'master' into devel
 
Package: BPRMeth
Commit: 3a84422bc0d935c6ae111d3a9030ec228bd950b9
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-17 17:19:58
Commit message:

 Bump version
 
Package: BPRMeth
Commit: 3b66c3f23160a218ff6dde7533f666098eef94fd
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-17 17:19:20
Commit message:

 Solve numerical issue for mu parameter in VB
 
Package: derfinder
Commit: e7bbb675eef4cd560440a0f0e6354853074cd2aa
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-17 16:26:44
Commit message:

 v1.13.3 -- fix many links for Windows
 
Package: derfinder
Commit: 2dee40434b8916a2e8acc717e3300c07ad5236b2
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-17 16:24:00
Commit message:

 v1.13.2 -- fix many links for Windows
 
Package: derfinderPlot
Commit: 32876a1c4f990c2ba7bbc7d5da4201420e4e6acb
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-17 16:06:48
Commit message:

 v1.13.1 -- fix many links for Windows
 
Package: regionReport
Commit: 92d02b0d83262b76859e7edaed719ae14eb973ba
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-17 15:55:02
Commit message:

 v1.13.1 -- fix a link to plotIdeogram
 
Package: recount
Commit: e1ff7766bc410e5435e789bc3f4e3b33e24453af
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-17 15:44:28
Commit message:

 v1.5.5 -- fix doc link for Windows build machines
 
Package: VariantFiltering
Commit: 464671bd7669bbcca29a1f18b269404f0cee9698
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-01-17 15:36:34
Commit message:

 Do not complain about input files without .vcf.bgz extension when they have .bgz extension.
 
Package: DChIPRep
Commit: 869c4110999e7d039ecf914bf586f2aa6531ccd4
Author: Bernd Klaus <bernd.klaus@embl.de>
Date: 2018-01-17 15:12:13
Commit message:

 removed Python dependencies, added note on this to the vignette
 
Package: rtracklayer
Commit: 376a89184ec2d762aa449b8763397a93bcb81948
Author: larman <michafla@gene.com>
Date: 2018-01-17 15:05:12
Commit message:

 no longer upload regions to table browser for whole genome case

should help with #5
 
Package: GenomicScores
Commit: 6e4d31319cedf408f75b6213ec3447bba8963e35
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-01-17 14:53:54
Commit message:

 replaced html_document2 by html_document in vignette.
 
Package: rols
Commit: 84ce2183891a88b7efe5ab129036751f92152192
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-17 12:31:35
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/rols into devel
 
Package: rols
Commit: 1ee47f2a2bb5701bba89fb3a19a3c4c23c2d4f1b
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-11-27 20:33:47
Commit message:

 Merge branch 'master' into devel
 
Package: rols
Commit: a52ae0ae7aed12472241e1fb406469b99a1b4264
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-11-27 20:31:58
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/rols into devel
 
Package: biomaRt
Commit: 9e4bbc3d0507c582428af4372e187f6c65130d5b
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-17 10:41:49
Commit message:

 Patch issue using versions in useEnsembl()
 
Package: biomaRt
Commit: 7eb426ac5651ba86003465f5efbd5d64341fb47a
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-16 14:01:08
Commit message:

 Suppress message about 'no encoding supplied' when querying Ensembl
 
Package: RforProteomics
Commit: 08abe0f3648fff84c5815b5723b3816b2fa7028f
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-17 11:17:59
Commit message:

 test for duplicated commits in Bioc history
 
Package: BPRMeth
Commit: 507e868e74cfb310fcca03d9d00a2cf50931ad1f
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-17 09:39:44
Commit message:

 Bump version
 
Package: BPRMeth
Commit: fb4f7eb665852a4b6a50239c3a9e168e32575f2f
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-17 09:39:09
Commit message:

 Minor changes in Rd file
 
Package: SPLINTER
Commit: d459ccf807a0ef232f9afae71ce8d5aad5922d88
Author: Diana Low <lowdiana@gmail.com>
Date: 2018-01-17 02:24:11
Commit message:

 updated use of ranges to overlapsRanges (GenomicRanges package) in splitPCR function
 
Package: limma
Commit: 242229013be21a533e7730d94e677f4a6cf4e6fa
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2018-01-17 03:14:22
Commit message:

 Minor edit to alias2Symbol.Rd
 
Package: eiR
Commit: 367d8444355f47d1a9aaf25532d66fea00d652a9
Author: khoran <khoran@cs.ucr.edu>
Date: 2018-01-17 00:52:33
Commit message:

 fixed bug caused by using gzfile on non-gzipped files. Only affected R 3.5.x
 
Package: edgeR
Commit: 3fd6fe619a75826d661550399c6d55c5bb2fc57b
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2018-01-16 23:36:13
Commit message:

 Bug fix to filterByExpr.
 
Package: flowWorkspace
Commit: 6a7e283ead2063b48b188df23070601d16c1cc95
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-01-16 19:59:27
Commit message:

 Merge branch 'trunk' into devel
 
Package: flowWorkspace
Commit: 9e0b3d5156c1d73d4c9e7b4f05c968b116f22247
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-01-16 19:59:19
Commit message:

 bump
 
Package: flowWorkspace
Commit: e0fed8de0d49310c9432933a747094efa8a2c4d4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-01-16 19:58:50
Commit message:

 Merge branch 'trunk' of github.com:RGLab/flowWorkspace into trunk
 
Package: flowWorkspace
Commit: f8c665e32a23a81bc9c6e0e3df7e57c988e097d2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-01-16 19:24:33
Commit message:

 rm the svg code in plot function since it is not used and triggers the device issue sometime
 
Package: flowWorkspace
Commit: f749d01f2bd8a7150ba21d9c5d2d2fdebef76fe9
Author: Greg Finak <greg.finak@gmail.com>
Date: 2018-01-16 19:24:58
Commit message:

 Update .travis.yml

install cytolib from github 
Package: affycoretools
Commit: 4d77130aeb0e90f86ee3da928ed0ca3a887e7983
Author: Jim MacDonald <jmacdon@ogopogo.deohs.washington.edu>
Date: 2018-01-16 19:46:21
Commit message:

 Bugfix for getMainProbes for Gene ST arrays. The 2.0 versions have transcript_cluster_ids in the core_mps table, but the 1.0 versions do not (or at least not complete set). So I reverted back to using meta_fsetid.
 
Package: PSICQUIC
Commit: 18a46a7cdd17c2f5bfdfbb83637690bcda8699eb
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2018-01-16 19:38:56
Commit message:

 downrev'd biomaRt required version
 
Package: RforProteomics
Commit: 4cffc1a0ea6a968905f0b4131cef15cce79ca324
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 15:46:24
Commit message:

 remove biocprot from Bioc until biocpkgs becomes available in Bioc
 
Package: S4Vectors
Commit: 9c065df2f8620b28f6dfa3b0986102e6327621a2
Author: larman <michafla@gene.com>
Date: 2018-01-16 15:29:50
Commit message:

 mcol combination pushed down into DataFrame(), fixes #8
 
Package: recount
Commit: e09307a68a8f32bb03a349af4e9ef7b5d3c47096
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2018-01-16 15:42:40
Commit message:

 v1.5.4 -- fix a unit test for download_study() + 2 misc changes
 
Package: MSnbase
Commit: 15477bd8551299a1c31a40c8a886e718f026a397
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 14:16:23
Commit message:

 no docs on Bioc
 
Package: pRoloc
Commit: 4bbfe21ba193acb2ae3fdfa5465ae1cfc7fc61b6
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 14:15:44
Commit message:

 no docs on Bioc
 
Package: pRoloc
Commit: c0287fec7b09f1e203ee4f10ecfe5e7e3d789c88
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-16 13:38:39
Commit message:

 New nipals method in dimensionality reduction for plot2D - closes #103
 
Package: pRoloc
Commit: e3e6e40962aea1858764b27a1b9af8017bc6bb73
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-11-07 14:12:30
Commit message:

 update pkgdown site
 
Package: pRoloc
Commit: 400ad4ce7984ba413658724e8a1f40e6991b143b
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-11-07 12:51:50
Commit message:

 Fix bug in private dimred and set appropriate number of colnames
 
Package: pRoloc
Commit: c84dc7a68307efdbc33d9c02992eed3a369c9804
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-11-07 12:49:51
Commit message:

 update news with new versions
 
Package: pRoloc
Commit: 841290f4e025aadf3d0195d2a876e1a7378f02ac
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-11-07 12:47:32
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/pRoloc into devel
 
Package: pRoloc
Commit: 6f723cf6cda147b5c7ff913c0748fe0edca3a0da
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-15 19:56:19
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/pRoloc into devel
 
Package: pRoloc
Commit: 8fcad76166f92565492f36a639daa99a9c462835
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-15 19:36:59
Commit message:

 Merge branch 'master' into devel
 
Package: pRoloc
Commit: c8eb15c6b97596d6d35d9140361dc62b60923c09
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-15 19:29:48
Commit message:

 merged with master
 
Package: MSnbase
Commit: 64844885a64cbf366538473141be670e1eeeeff2
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2018-01-16 14:17:49
Commit message:

 Merge pull request #293 from lgatto/readChromData

Read chrom data 
Package: MSnbase
Commit: a3373d37646260fd867d511a1f679ea8f4245fd8
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-15 15:12:27
Commit message:

 Merge branch 'master' into readChromData
 
Package: MSnbase
Commit: 63b8af4b9607d5eabbda1b5c461a8016732d37ed
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2018-01-14 14:34:26
Commit message:

 Merge pull request #288 from lgatto/issue282-spectraHierarchy

Add filterPrecursorScan,MSnExp-method. 
Package: MSnbase
Commit: b0630d1231f032def963480ada6a10fab1d235df
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-12 10:33:39
Commit message:

 update pkg site
 
Package: MSnbase
Commit: af2aa2ea99af79f34358e3c76e080ea1bb823107
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-12 09:49:27
Commit message:

 move new combineFeatures' fcol after method for fix failing test
 
Package: MSnbase
Commit: ddde6968a44beb20403add66b5b0333f6e0b2e1b
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-12 08:59:43
Commit message:

 Add the missing comparison for the unit test
 
Package: MSnbase
Commit: 86bcc14d78139b4c7bdab36fdc09e147ab1a18b0
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-12 06:26:17
Commit message:

 Use @sgibb's .combine_data.frame function
 
Package: MSnbase
Commit: b411c6dd45d34e5efd115993e790baa19a54c391
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-11 19:11:45
Commit message:

 MSnSetList optimisations

- don't check the validity of individual MSnSets when running
  listOf, as it's done later.
- skip validation of the (possibly large) list of MSnSets when
  subsetting.
 
Package: MSnbase
Commit: 4a8b9125972211b34666a2936fc0a669738b2841
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-11 15:06:54
Commit message:

 Add .combine_data.frame2
 
Package: MSnbase
Commit: 9acc0b4a4457b5c84489f654e4a6eae75cc92e09
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-11 11:23:32
Commit message:

 update news with link
 
Package: MSnbase
Commit: 9c902c5ef8ff7e775affb23ddc5156c12d46a47c
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-11 11:23:10
Commit message:

 combineFeatures now has fcol - close #195
 
Package: MSnbase
Commit: 6be697da3ce481437bd716d91492b7a786a5e9b5
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-11 09:50:58
Commit message:

 MSnSelList@featureData is now a DataFrame (was data.frame)
 
Package: MSnbase
Commit: 824766ee268a70fb5c3b2a848ae76be8207916e0
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-11 08:52:04
Commit message:

 Add unit test for .polarity_char
 
Package: MSnbase
Commit: 70b12494e293ece3f9faf83924dc4c342eeb69dc
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2018-01-10 22:22:18
Commit message:

 Merge branch 'master' into readChromData 
Package: MSnbase
Commit: 508e937d4bd2f25b207466b4c97e51279a819d7a
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-10 21:28:23
Commit message:

 MSnSetList updates - closes #295
 
Package: MSnbase
Commit: 8418bf3fa75aa4947e0c9921dc50f892841961c5
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-10 20:52:38
Commit message:

 use requireNamespace to remove note (bis)
 
Package: MSnbase
Commit: 085e1e4aaac92bd482488dc8d38b7b1a134465fa
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-10 20:41:30
Commit message:

 use requireNamespace to remove note
 
Package: MSnbase
Commit: b37f5ee10b6232eb01edf984f09faeb926fc8193
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-10 10:20:00
Commit message:

 Add missing Rd file.
 
Package: MSnbase
Commit: cf406b7dd27969b25803a861372bb9c923019720
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-10 06:28:30
Commit message:

 Update help and add readSRMData to the vignette(s)
 
Package: MSnbase
Commit: 362bc79c8b6cff8387d59424ca9864938e2b2625
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-09 15:15:48
Commit message:

 Add unit test for readSRMData

- Add readSRMData unit test.
- Finalize documentation for readSRMData.
 
Package: MSnbase
Commit: 6c22013353ed39cac78b08afd27ab0d24b932226
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-09 06:32:35
Commit message:

 Add polarity,Chromatograms method

- Add polarity,Chromatograms method.
- Add related unit tests and documentation.
 
Package: MSnbase
Commit: 08c1e7ca730477d6c9f70f39f4938154d754fbcd
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-01-08 10:04:51
Commit message:

 Intermediate (unstable) commit
 
Package: MSnbase
Commit: 180827a43fe5dc648e2a4be897df1e2cf24438d8
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-12-22 12:08:05
Commit message:

 Merge branch 'master' into readChromData
 
Package: MSnbase
Commit: 6d6cf272c606e058ff7f39db6d5d3e704ec65f00
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-12-22 08:20:30
Commit message:

 Merge branch 'master' of github.com:lgatto/MSnbase
 
Package: MSnbase
Commit: 3bfb015475cc8085e31852d4fd91d464c96002e1
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-12-22 08:20:21
Commit message:

 update MSnSet man with more coercion details
 
Package: MSnbase
Commit: 8a73f0626d36186c546fdc142b077fca7dc9792f
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-12-20 05:45:44
Commit message:

 Address comments from @sgibb in pull request #290
 
Package: MSnbase
Commit: fa9a98934d5de2c108df2dcae7d3ca5bc4d5ceee
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-19 16:57:14
Commit message:

 Merge branch 'issue282-spectraHierarchy' of github.com:lgatto/MSnbase into issue282-spectraHierarchy
 
Package: MSnbase
Commit: d6daeca90002812a05b681ef728268b7140de9d4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-19 16:55:51
Commit message:

 Rename argument scanIndex into acquisitionNum
 
Package: MSnbase
Commit: d19f3698e41f859e6ef3f4cba340d0fd0d29081d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-19 16:47:30
Commit message:

 Change dist to trusty in .travis.yml
 
Package: MSnbase
Commit: 045adf78358c5cb793089983a5f3e084a4374c4f
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-12-19 15:51:52
Commit message:

 update news
 
Package: MSnbase
Commit: f6200448c1f003e8e51526705d149b2411d2ea59
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2017-12-19 15:57:51
Commit message:

 Merge pull request #290 from lgatto/chromatogram_fdata

Chromatogram fdata 
Package: MSnbase
Commit: 588a1e2487e977d490f9b9c3f1b92bbc9e6ba768
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2017-12-19 15:57:36
Commit message:

 Merge branch 'master' into chromatogram_fdata 
Package: MSnbase
Commit: 6fc919f2300a7c0e46d096508c5b611ebff65a77
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-19 15:33:34
Commit message:

 Add libhdf5-dev to .travis.yml
 
Package: MSnbase
Commit: d89ef10379ec322a06d58aa5cc16be830a390520
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-12-19 15:24:00
Commit message:

 new gh devel version
 
Package: MSnbase
Commit: ec7873b2a98ec16b7ddaeb48a5aa0116e7862565
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2017-12-18 19:41:59
Commit message:

 Merge branch 'master' into issue282-spectraHierarchy 
Package: MSnbase
Commit: 2a8200e78152fdd66cb4c28ed5edbbf39e93ae3f
Author: Laurent Gatto <lg390@cam.ac.uk>
Date: 2017-12-18 19:40:24
Commit message:

 Add space between while and ( 
Package: MSnbase
Commit: 50c281cea9186320dd43877d9283e248bc499596
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-12-18 10:27:55
Commit message:

 Update NEWS
 
Package: MSnbase
Commit: fb101c167e182be73189a62d420d9b47c1201b75
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-12-18 10:24:47
Commit message:

 Merge branch 'master' into chromatogram_fdata
 
Package: MSnbase
Commit: 3526729cc2df95f5d04b9ce52a6e5bdfc49e2108
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-12-18 10:09:22
Commit message:

 Add featureData slot to Chromatograms class (issue #289)

- Add featureData slot to Chromatograms class.
- Add getter/setter method for featureData.
- Add precursorMz, productMz and mz,Chromatograms method.
- Add related unit tests and documentation.
 
Package: MSnbase
Commit: 1be509b9cd7ea3ada4aa5f40e63d58ab3ae02b81
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-16 20:48:35
Commit message:

 Fix filterPrecursorScan,MSnExp-method unit tests
 
Package: MSnbase
Commit: d43fb2e555d40aa07128ae2d0c9216407d11c7ba
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-16 20:00:36
Commit message:

 Add alias entry for filterPrecursorScan generic
 
Package: MSnbase
Commit: 6c4164b29dbb3174772c93691e3051c758b13cb5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-16 19:48:59
Commit message:

 Add NEWS.md entry
 
Package: MSnbase
Commit: bdf506005ca4a4a6cc8e1685c6ee12caa86513eb
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-16 19:44:21
Commit message:

 Merge branch 'master' into issue282-spectraHierarchy
 
Package: MSnbase
Commit: 0e396ad9c3896ad333f86fbb5a4dce98a2b40bef
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-16 19:43:38
Commit message:

 Allow multiple scanIndices
 
Package: MSnbase
Commit: 09407b9a2a41e83420a296fbfea44562436a9322
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-16 19:43:09
Commit message:

 Add filterPrecursorScan,MSnExp-method
 
Package: MSnbase
Commit: 5bd2005fa594d70d3315c26a18fd4baeeaf19f60
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-15 20:38:58
Commit message:

 First implementation of .filterSpectraHierarchy
 
Package: MSnbase
Commit: e5eeb5b82454b4613db3b212693657dacbd825f6
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-15 19:26:59
Commit message:

 Add unit test for spectra hierarchy
 
Package: MSnbase
Commit: 6994dec87e9ef8c4083623b125ded18eb8022ef5
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-12-15 10:20:19
Commit message:

 Add featureData slot to Chromatograms class
 
Package: MSnbase
Commit: d760947d1fed2fbb2975813991e7028c27b6b08c
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2017-12-15 07:09:13
Commit message:

 Add first readSRMData code
 
Package: biocViews
Commit: efb19139a09c722bd36b24be97cdb535cf444aac
Author: lshep <shepherl@gmail.com>
Date: 2018-01-16 13:12:50
Commit message:

 Add requested biocViews term

  - ExperimentData -> TechnologyData -> SequencinData -> SingleCellData
 
Package: brgedata
Commit: 8f79a955781122c0ccde2d163620df249a5be700
Author: Carlos Ruiz <yocra3@gmail.com>
Date: 2018-01-16 13:13:33
Commit message:

 Remove rexposome from dependencies
 
Package: brgedata
Commit: be2c05f564517bdb2ba8936b3caeab24f9bc08b0
Author: Bioinformatic Research Group in Epidemiology (BRGE) <juanr.gonzalez@isglobal.org>
Date: 2018-01-12 13:03:02
Commit message:

 MAD data added
 
Package: M3C
Commit: 7a2dd61dab9fbfac764be686c613f9af16efe04f
Author: crj32 <chris.r.john86@gmail.com>
Date: 2018-01-16 11:22:06
Commit message:

 small fix to annotation code
 
Package: MultiDataSet
Commit: 5f1f6a58a1eec7eba11543496a47245bbf4d649e
Author: yocra3 <carlos.ruiz@isglobal.org>
Date: 2018-01-16 11:20:39
Commit message:

 Include again vignettes depending on brgedata.
 
Package: BiocStyle
Commit: 8716570c8e2e252f0566a361aee604c393a4af6c
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-16 10:53:07
Commit message:

 version 2.7.5
- code refactorization after transition to updated style
 
Package: topdownr
Commit: 4fe54ab7383e0014a809c38ccf24f9d2e439aa9d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-15 18:56:51
Commit message:

 Rerun pkgdown
 
Package: topdownr
Commit: ee89ad161d5d48c458d38ebb9e2376e04af3c303
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-15 18:47:05
Commit message:

 Add plotting example to the analysis vignette
 
Package: topdownr
Commit: f3af26e23a43d463a5bdab08b02391095bdb920b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-15 18:46:51
Commit message:

 Add maximise argument to bestConditions; see #52
 
Package: topdownr
Commit: abb63c1c5d08a7a29ad9e158509f9d96df537bd9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-15 17:30:34
Commit message:

 Fix file selection error for filenames with special characters
 
Package: topdownr
Commit: e7f1e18a592ca2b6e8b4dbc69263d5b8cb4a8837
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-15 09:10:27
Commit message:

 .highestNcbCoverage gains a maximise argument; see #52
 
Package: topdownr
Commit: e195ad94a5bb02e19bf4676ae3af760b7fc1b849
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-15 08:50:32
Commit message:

 Use aes_string to avoid warning about undefined global variables
 
Package: topdownr
Commit: 8c5b501e909e24f5fd8dc5fba49f9ac8e0ace323
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-14 19:46:21
Commit message:

 Finalize plot,TopDownSet-method
 
Package: topdownr
Commit: 58a14db651236f90aec676595e8204eb5b684d5b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-14 12:19:24
Commit message:

 Fix colnames call in .readMzMl
 
Package: topdownr
Commit: 020638033865678aa9d00f40626f667ed50f0f27
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-14 12:06:16
Commit message:

 Create separate .condition2data.frame function
 
Package: topdownr
Commit: 28c4a81cfe8c6e3025a8cd28e00894a51199185c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2018-01-14 12:05:39
Commit message:

 Keep SpectrumIndex to find correct spectrum in mzML files
 
Package: topdownr
Commit: 476db56f8e4152b9902eccbb7c12053c3049cbd5
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-29 20:22:40
Commit message:

 Add basic plot,TopDownSet-method
 
Package: topdownr
Commit: 31c178aa18f887fbfaefe66dd90358ea7fadcbfa
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-29 20:22:23
Commit message:

 Fix tds documentation format
 
Package: topdownr
Commit: 8c7921602f121f3589df01ab6c9da4724d4f8557
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-28 17:04:55
Commit message:

 Keep full filenames
 
Package: topdownr
Commit: 489cebc02d984a758473a2bb7e126afa406e7950
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-28 17:03:44
Commit message:

 Add .readSpectrum
 
Package: topdownr
Commit: af8765b653cbc48f9933a448c5ba90505a2eaf53
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-28 16:41:01
Commit message:

 Remove useless .fileExists
 
Package: topdownr
Commit: afa9e2f8e14eab718bc3b09fd301e3ca9ca8fee3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2017-12-28 15:54:16
Commit message:

 Bump github devel version
 
Package: PureCN
Commit: 2318d4888755698bb9717450587764f2f79bba92
Author: lima1 <mriester@gmx.de>
Date: 2018-01-14 16:18:54
Commit message:

 Added line break in vignette.
 
Package: PureCN
Commit: 0c04de9d9b31a22770dc2f9ad9a062e18998ef18
Author: lima1 <mriester@gmx.de>
Date: 2018-01-14 16:11:55
Commit message:

 Added genome argument to new calculateMappingBias.
 
Package: VariantFiltering
Commit: 44f8f8a4a138636faceeaf131f4b680f62714892
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-01-15 15:45:09
Commit message:

 Added functionality on selecting SO terms with shinyTree, although still needs to be activated.
 
Package: VariantFiltering
Commit: cb20a3024080fbf6ceda02ad08f4f1f61ee586e3
Author: JoanFernandez <joanfernandez1331@gmail.com>
Date: 2018-01-15 14:00:04
Commit message:

 Fixed errors
 
Package: VariantFiltering
Commit: 9d514e0c14851eb0710758f8cf5e462945dec2fc
Author: JoanFernandez <joanfernandez1331@gmail.com>
Date: 2018-01-09 17:08:01
Commit message:

 Fixed namespace
 
Package: VariantFiltering
Commit: 4aef14a07873e0ef7df09c10f981e3ceb1cd1f71
Author: JoanFernandez <joanfernandez1331@gmail.com>
Date: 2018-01-09 13:52:37
Commit message:

 SOterms tree generation and translation
 
Package: BPRMeth
Commit: 3539fecdf6715e27bf2d45ed5a67162a0639100f
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-15 15:08:08
Commit message:

 Minor update on vignette
 
Package: BiocStyle
Commit: 0baf135379fc71b71b681ea50094488495974fb6
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-15 14:43:55
Commit message:

 version 2.7.4
- add argument 'titlecaps' to 'html_document' (closes https://github.com/Bioconductor/BiocStyle/issues/40)
 
Package: InteractionSet
Commit: fdf55e29f989f0bb137c46798a45dc0826f6c04c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-15 14:18:38
Commit message:

 Cleaned up boundingBox C++ code for simplicity.
Fleshed out the tests for more scenarios.
 
Package: BiocStyle
Commit: ca0f7f5073ba622a8fd64c214cdc0e64abd89306
Author: aoles <andrzej.oles@gmail.com>
Date: 2018-01-15 14:28:01
Commit message:

 version 2.7.3
- make defunct functions depracated in last release
 
Package: BPRMeth
Commit: be8635ee5c907da161602bd47074a7743be61fa2
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-15 13:29:57
Commit message:

 Update version
 
Package: BPRMeth
Commit: ffd4ff7a4e411d42d89da8bcc2c786f06d587608
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-15 13:23:27
Commit message:

 Update gitignore file
 
Package: InteractionSet
Commit: e7ba514bb0e2b54a9f93fe54ca69f958f674671d
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-15 13:09:31
Commit message:

 Added name checks upon concatenation.
 
Package: InteractionSet
Commit: a9ee9e6ebb43866d1a085a61de096cc85db41870
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-15 13:06:52
Commit message:

 Fixed as() so that it calls validObject() without disableValidity.
Modified concatenateObjects() to disableValidity for check=FALSE.
 
Package: InteractionSet
Commit: 51475f4e8a89fd5b067dc8459e61accabd3459bb
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-15 12:58:55
Commit message:

 Streamlined concatenateObjects for GInteractions.
 
Package: BPRMeth
Commit: 5f6d77956b1a26311707f1fe7d70bbbfe083a737
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-15 13:17:52
Commit message:

 Update gitignore file
 
Package: BPRMeth
Commit: a4244d07b14f1e1ffcd5f09ee8b9c8360236bc8b
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-15 13:14:01
Commit message:

 Remove project file
 
Package: BPRMeth
Commit: 40a422eba1a3fd54d8feea17008cb01e57c8943a
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2018-01-15 12:31:46
Commit message:

 Minor changes in examples
 
Package: biomaRt
Commit: 9fcbc15584d9930872ac0b4cfa600dfb24a7742b
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-15 10:05:30
Commit message:

 Fixed logic error
 
Package: biomaRt
Commit: cde0789eb90243a10ab07caa8ed53887c308ff5b
Author: Mike Smith <grimbough@gmail.com>
Date: 2018-01-15 09:32:57
Commit message:

 Added support for omitting the subdomain to ensembl i.e. host = "ensembl.org"
 
Package: RforProteomics
Commit: 93db2d64fce3560b8c84d1366cf7b99366eb2827
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-15 05:59:52
Commit message:

 no docs on Bioc
 
Package: RforProteomics
Commit: f0573aa9afbcc5e1db14faab8ccbe91499ea561e
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-15 05:50:10
Commit message:

 build pkgdown with biocprot vignette
 
Package: RforProteomics
Commit: 0a63077e48ba35ce7539f19c62b6a429e676c029
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-13 21:44:17
Commit message:

 add pkg down dir
 
Package: GOSemSim
Commit: 0b5874d58224aaf4e94321bf49210cef71b8c062
Author: guangchuang yu <guangchuangyu@gamil.com>
Date: 2018-01-15 03:21:36
Commit message:

 update citation
 
Package: ELMER
Commit: c297ceee334959e4bd5a9e7ce2143add4da2d5d6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-14 19:29:06
Commit message:

 There was a change in DNA methylation which added the strand to the probe. But we  will ignore the strand while searching for distal/promoter probes.
 
Package: TCGAbiolinks
Commit: 17d45de7deea7bb1a8920fa3b931bc605931bbf3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-14 14:35:22
Commit message:

 Fix enconding
 
Package: TCGAbiolinks
Commit: d06acab14ea85464ea120b8b3c41633b2aa37f5b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-13 02:33:22
Commit message:

 fix travis
 
Package: TCGAbiolinks
Commit: 269b0747af4dcf8ef69906f666a973b09c7c3916
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-12 21:40:00
Commit message:

 Fix numbering
 
Package: ELMER
Commit: bf0c2603f54e83d173cd5c334a63658ecaa34025
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-14 14:32:30
Commit message:

 Fix man
 
Package: ELMER
Commit: 4c441d2c055a2ef5f1a593f7688be4aa22aa809c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-01-13 03:04:53
Commit message:

 Fix travis
 
Package: InteractionSet
Commit: 8b5384097c06b12fde946864909a6d7574e8833a
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-14 12:32:19
Commit message:

 Removed comment from HP after fix.
 
Package: InteractionSet
Commit: eb8ae61de875fae30abe80a949f1ff359ad59fa9
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-14 12:28:47
Commit message:

 Forced mcols for GI objects to be a DataFrame.
 
Package: InteractionSet
Commit: a0054713839570e9424d7a251e2efdf2a52c889f
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-01-14 12:16:45
Commit message:

 Fleshed out tests for mcols subsetting.
 
Package: PureCN
Commit: d4ef49f8af4ed454944ddd055396763585dfca57
Author: Markus Riester <markus.riester@novartis.com>
Date: 2018-01-14 03:43:15
Commit message:

 Fixed typo in vignette.
 
Package: PureCN
Commit: de6f40117f01a71179c3c3e979fbbfb83bf3e761
Author: Markus Riester <markus.riester@novartis.com>
Date: 2018-01-14 03:28:05
Commit message:

 Forgot to add new files.
 
Package: PureCN
Commit: c21b35de96366203f78b6f31e71c481b98299af8
Author: Markus Riester <markus.riester@novartis.com>
Date: 2018-01-14 03:23:23
Commit message:

 Major rework of mapping bias database. Make it possible to pre-compute and avoid parsing of large VCF (https://github.com/lima1/PureCN/issues/4). Undo the speedup heuristics from the previous commit.
 
Package: PureCN
Commit: 5cf81e5d7b361521767f6988ae85a7dbf934c23d
Author: lima1 <mriester@gmx.de>
Date: 2018-01-11 03:44:09
Commit message:

 First attempt in removing optima with poor SCNA-fit (https://github.com/lima1/PureCN/issues/5).
 
Package: PureCN
Commit: 8708a1d33716c763c4133a68731985a0d3f85118
Author: Markus Riester <markus.riester@novartis.com>
Date: 2018-01-11 01:20:06
Commit message:

 Skip high ploidy solutions of samples with dominant copy number state (https://github.com/lima1/PureCN/issues/5); add bootstrapping option to PureCN.R
 
Package: RforProteomics
Commit: c46c5dc2417261c7d09c6d3631c5377a2e6deb89
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-13 21:04:55
Commit message:

 no docs on Bioc
 
Package: RforProteomics
Commit: 7c819e4917f0e51927527da641b255a6005bff0a
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-13 21:04:35
Commit message:

 Merge branch 'master' into devel
 
Package: RforProteomics
Commit: bdc8b0998aa003b6e285f32f252bc100246539f5
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-13 21:04:13
Commit message:

 adjust version
 
Package: RforProteomics
Commit: 7594229b8d44d1aecb3585151a5eee8712ce5e6f
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-13 14:48:15
Commit message:

 update news
 
Package: RforProteomics
Commit: 80fbe90210ace7ff2e0d61407e7963953927e84a
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-13 14:47:21
Commit message:

 add note about isobar section
 
Package: RforProteomics
Commit: d2533952691e153fc2e3aebbb99fdcf285581969
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-01-13 14:43:55
Commit message:

 Fix failing vignette and add mention of DEP package

The isobar section was failing for an unknown reason - the code
could be executed interactively. For now, I have just don't
evaluate the isobar code chunks but kept the resulting figure.
 
Package: RforProteomics
Commit: a40a2d743653e2086fcbae386ef3a76f06f4b1e2
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-12-03 21:15:03
Commit message:

 udpate pkgdown site
 
Package: RforProteomics
Commit: 53acdb79f58319155856ac5ba37313d64dc14698
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-20 03:57:21
Commit message:

 update pkgdown
 
Package: RforProteomics
Commit: ac29bd8795e8e7eb1bf6c5ee4d4b4418277e8604
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-19 21:34:15
Commit message:

 rephrasing in vign re on-disk
 
Package: RforProteomics
Commit: bf370a985c44ba4937c3cd5f29ce2041b788544b
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-19 20:31:13
Commit message:

 bump version
 
Package: RforProteomics
Commit: 3b03bf95d5cf2d7a02ee555b2e17cf6f8f743635
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-10-19 20:17:42
Commit message:

 update pkgdown
 
Package: RforProteomics
Commit: 9c8925bac397cf4933b72593b11a61443759e94f
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-07-01 10:29:37
Commit message:

 fix N15 figures
 
Package: RforProteomics
Commit: 2653f53d763eaf354ade9b269087bfb44bc10924
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-07-01 10:21:11
Commit message:

 fix funny todo
 
Package: RforProteomics
Commit: a88e33037a36a8d0370f7bb9554684dfcebe1649
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-07-01 10:06:29
Commit message:

 new vignettes
 
Package: RforProteomics
Commit: 212a9f58497c933079b70b06d18dae27bc38e285
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-07-01 09:47:09
Commit message:

 pkgdown with new vignettes
 
Package: RforProteomics
Commit: 44cc692929b72f1947ea6052e075dccd10b4b577
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-30 09:12:36
Commit message:

 regenerate web page with 3 vignettes
 
Package: RforProteomics
Commit: eef2619d81e7a5cb7b773e72c630e39724d7ca0d
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-29 16:08:25
Commit message:

 update news
 
Package: RforProteomics
Commit: 1f34df283efc617f8096deb349f992c6ba674496
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-29 15:19:45
Commit message:

 proteomics downloads vignette
 
Package: RforProteomics
Commit: e895467b7eda122394f7ac76943e2bbdebd284a3
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-29 08:22:10
Commit message:

 Bioc proteomics package downloads vignette
 
Package: RforProteomics
Commit: 442b4b5abab69a439f441decdb00763b549db58c
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 15:45:27
Commit message:

 update links to online html vignettes
 
Package: RforProteomics
Commit: 6e9fc2acf075056be31d6ae5ec7fb5340a9a852f
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 14:26:13
Commit message:

 update news
 
Package: RforProteomics
Commit: 5ba6e668e257613f4a1582274f5afb0ac4e0e4f5
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 14:24:23
Commit message:

 update news in docs
 
Package: RforProteomics
Commit: 802ae838a6066e388357f18ec6f829b004ef4c57
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 14:17:38
Commit message:

 update news
 
Package: RforProteomics
Commit: 22883961148ab5a50ca546a025dc836e226fe239
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 13:51:03
Commit message:

 add pkgdown site
 
Package: RforProteomics
Commit: 7c3d29c81e23de6b6f0cd07c72e934aab48c7121
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 13:50:38
Commit message:

 last changes
 
Package: RforProteomics
Commit: 08b2dd48f62da6f8f4118403b03b8e34e27b7adf
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 13:04:03
Commit message:

 update vignettes
 
Package: RforProteomics
Commit: 04155c659ca4d6eea6a8ca270dbf40c4fe9411f1
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 11:20:23
Commit message:

 fixing vig
 
Package: RforProteomics
Commit: ee69e5d76004b10258805cd626f166f978546aca
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 11:06:13
Commit message:

 move vignettes the rmd, no vigsrc
 
Package: RforProteomics
Commit: 8ed6ec655315cba8f3f2183188307f468174754d
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-06-27 06:10:35
Commit message:

 add mstut functions
 
Package: RforProteomics
Commit: d902b441669d2ab54e40b8298687c55909814bb0
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-18 21:05:58
Commit message:

 fix and update vignettes
 
Package: RforProteomics
Commit: 6a86f74af2d6d9fbe23387cb7817718b0de25557
Author: Laurent <lg390@cam.ac.uk>
Date: 2017-04-18 20:20:53
Commit message:

 update version
 
Package: RforProteomics
Commit: c59b318c44fd79e62bc357a785d5d1817d2a62b5
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-10-15 10:22:37
Commit message:

 suggest genefilter
 
Package: RforProteomics
Commit: fefaa72c6ec09d29a74a8e437db1c56585dbeb4c
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-10-12 21:28:00
Commit message:

 fix wrong/outdated version
 
Package: RforProteomics
Commit: bae314b65a796823a986829062d1e1491203fe2e
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-10-09 16:32:42
Commit message:

 Update/compile static vignette for new release
 
Package: RforProteomics
Commit: d4362e57a44390b216a98cf1defc9c10a27809a2
Author: Laurent <lg390@cam.ac.uk>
Date: 2016-03-01 09:57:23
Commit message:

 fix typo
 
Package: RforProteomics
Commit: 7bb281478a63d648c9b2e65e2ac7ce3355c6abb8
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-05 09:07:02
Commit message:

 new devel version
 
Package: RforProteomics
Commit: 476ddcf75c44f575c1ac2e1a5647d2eacec0ac9e
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-05 09:03:12
Commit message:

 update msdatatab
 
Package: RforProteomics
Commit: ab5fa3de5399998305999400c07dd56d33590094
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-12-05 06:35:05
Commit message:

 split imaging data in two rows; see #12
 
Package: RforProteomics
Commit: 8d9cc41c0f730f87dad9cddd9b7dacca01ca0714
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-05 02:34:06
Commit message:

 new devel version
 
Package: RforProteomics
Commit: 640fb1658899ab5baea09b34cad89db189b83cb2
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-05 02:25:46
Commit message:

 update msDataTab
 
Package: RforProteomics
Commit: 438d6959174c697b3d1be52b73a116fadfd9f192
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-05 02:22:17
Commit message:

 fix conflict
 
Package: RforProteomics
Commit: 557dfbe28dcbe80a4b6909530dac307a72cf01ad
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-05 02:21:30
Commit message:

 udpated vignette
 
Package: RforProteomics
Commit: 3f11b9b904e147102f6a59aa379e9ddc16414449
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-04 15:56:02
Commit message:

 update msDataTab
 
Package: RforProteomics
Commit: 24cc5403c92be0df76889c195dda521a4ff68941
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-04 15:55:19
Commit message:

 adding comprehensive MSnID/msmsEDA/msmsTests example
 
Package: RforProteomics
Commit: 42958265abe6d2437ee8c785094da34344d394cd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2015-12-01 18:33:26
Commit message:

 add Imaging formats and Cardinal/MALDIquantForeign
 
Package: RforProteomics
Commit: 550424623331368b8dda800cc382731abc9e9a9b
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-01 00:45:05
Commit message:

 new devel version
 
Package: RforProteomics
Commit: 62ed09b3fc27b4c3c8b246d894530855edbde4ed
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-12-01 00:41:42
Commit message:

 link to MSnbase-io vignette
 
Package: RforProteomics
Commit: 876e620b8c554c6cdebbe005bf101bb0b771e54d
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-11-30 13:23:38
Commit message:

 update vignette and msDataTab fun
 
Package: RforProteomics
Commit: fae9a5d09cc46154d87d05c64de97f7117c2777c
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-09-30 10:22:27
Commit message:

 Fix vignette for mzTab v0.9
 
Package: RforProteomics
Commit: aae04a14e5937350625ab779ff68ed4ae69012e2
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-06-11 23:16:23
Commit message:

 document news
 
Package: RforProteomics
Commit: e54d2d0a427ac031f67acd75a8424a2a16972e26
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-06-11 23:15:18
Commit message:

 rename ims fig
 
Package: RforProteomics
Commit: ec906d6b3495984b981bec6ec9a272767bc862b5
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-06-11 22:14:00
Commit message:

 merged @sgibb's PR for MALDIQuant 1.12
 
Package: RforProteomics
Commit: d1eae1d0a4acd988ed4664b992ecd1bf78fc39ab
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-06-08 22:26:13
Commit message:

 vis vig is build with package, fix section numbering and url
 
Package: RforProteomics
Commit: cffadbf1020fd1dc2f09e9d3a6027f33b73f874d
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-06-08 17:39:17
Commit message:

 update r4p vignette
 
Package: RforProteomics
Commit: bae71212ac5a79c4e12d2be0129fe371c85a1670
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-06-08 17:39:08
Commit message:

 add RR biocview
 
Package: RforProteomics
Commit: 738df0c6d42e7d98cdbe243b61b94cde22168373
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-03-24 01:15:21
Commit message:

 fix vis vig building
 
Package: RforProteomics
Commit: 384b007f8ac955b73bee44600a698f84a7c80b1d
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-03-24 00:55:14
Commit message:

 vis ref and vis static
 
Package: RforProteomics
Commit: 56d9dfc23da25fe6bbe2cd894c433487f8482fbc
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-02-22 18:15:30
Commit message:

 update vignette and makefile!
 
Package: RforProteomics
Commit: 7f13e059d609c040de720ff65a1ba0b6b08a9a57
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-02-21 22:25:34
Commit message:

 vis vig updates
 
Package: RforProteomics
Commit: 88e484f296d8dc5e30e4b36fc7ff2837cc505b06
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-02-12 01:17:50
Commit message:

 new devel version
 
Package: RforProteomics
Commit: 1232ae7b99f2aa83ea6c929271c694c862854da0
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-02-12 01:15:03
Commit message:

 suggest rmarkdown
 
Package: RforProteomics
Commit: 880430e8491c7a09b0d764cf81cbda90ad7a0b8d
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-02-11 00:10:06
Commit message:

 new dev version
 
Package: RforProteomics
Commit: e4ab55c69666849940886dc24f5de3efa2dd685e
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-02-11 00:08:58
Commit message:

 don't require GNU make
 
Package: RforProteomics
Commit: b0dec53c2e9d56201145a6c1dfdd950aa3ad5c04
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 15:21:17
Commit message:

 dev version
 
Package: RforProteomics
Commit: 8428ddcc581cae60bf9e9d6ce5c50665c71b097d
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 15:18:11
Commit message:

 update vig for startup msg
 
Package: RforProteomics
Commit: 18b3e9652983f35217455997f574bb63e4e71c88
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 14:20:54
Commit message:

 revert to previous version to fix startup msg
 
Package: RforProteomics
Commit: 6cc6ceeacc1c4cae3033f53e405a22a9aee551e4
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 14:20:09
Commit message:

 Merge branch 'master' of github.com:lgatto/RforProteomics
 
Package: RforProteomics
Commit: 416b4550cbcf28608aa3848cb5c45d35f4d1ce3e
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 14:19:55
Commit message:

 fix startup msg
 
Package: RforProteomics
Commit: 6b77578f3690e27e4f5843463608574d1ebb0142
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 14:16:38
Commit message:

 new devel version
 
Package: RforProteomics
Commit: d00b9c15815605350c09285c018668924f932955
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 12:10:05
Commit message:

 update news
 
Package: RforProteomics
Commit: fd7be904154b54bd8b2ab52ce5d8dcefbc0ea9fe
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 12:09:36
Commit message:

 document workflows
 
Package: RforProteomics
Commit: 307bd30237babb850e8e2a0359f48d887f59f925
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 09:35:04
Commit message:

 mention plot's types
 
Package: RforProteomics
Commit: 3a3d4d1ac6264b6273d8a153150f5d807801dc8c
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-30 00:09:11
Commit message:

 animations
 
Package: RforProteomics
Commit: 816ca4358d3f272d3eb0b869c4b02fc1794cc0dc
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-29 22:06:18
Commit message:

 MS animation
 
Package: RforProteomics
Commit: 204204e5fc16628d32777e04c38203dfe826c2fc
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-28 18:05:06
Commit message:

 new devel version
 
Package: RforProteomics
Commit: 1601d8d21cb57fd44946481bb235a2d84c949ef3
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-28 18:02:32
Commit message:

 remove figs
 
Package: RforProteomics
Commit: 94921537d4188cf5206b801bbe85d8eb47269a68
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-28 17:59:14
Commit message:

 remove workflow
 
Package: RforProteomics
Commit: 20c7e13bec13f48482d25a14175b9e8bd71dab85
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-28 17:56:52
Commit message:

 update biocviews
 
Package: RforProteomics
Commit: 034aa69e269a50cdb0b58ea1bc6f1cccf3d9e626
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-28 17:47:05
Commit message:

 bump version
 
Package: RforProteomics
Commit: 8dbe86ccc824a9b72511280f3aa032c24234ed1d
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-28 17:45:59
Commit message:

 upate cleaning
 
Package: RforProteomics
Commit: 77b296299ecd04e4d6a8c930305dd659803714c1
Author: Laurent <lg390@cam.ac.uk>
Date: 2015-01-28 17:34:21
Commit message:

 vis vig updated
 
Package: RforProteomics
Commit: 6c2b4f98a7e612d06b775f01db94c217646ec6a0
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-16 08:47:59
Commit message:

 keep rmd
 
Package: RforProteomics
Commit: ecdc30f87c1d04864d5b7ef75e0084544736cace
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-16 08:40:46
Commit message:

 remove workflow rmd
 
Package: RforProteomics
Commit: 2d831a6d393343691c607f47998c2892d1c17f7f
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-16 08:40:24
Commit message:

 remove workflow
 
Package: RforProteomics
Commit: 71243f2249f6b3a289aa1d80377c62cbe617d277
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-16 03:00:50
Commit message:

 fix syntax
 
Package: RforProteomics
Commit: 1f8aa9789572926b63426f1827d4cd355bec9586
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-16 02:59:33
Commit message:

 add mzr for id
 
Package: RforProteomics
Commit: 72e6637fd292f4365a39126db9b91cb6f3d157cf
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-16 02:56:25
Commit message:

 workflow and figs
 
Package: RforProteomics
Commit: ad043f3a1b971d9799beef7f30f0aa7331644416
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-16 02:50:53
Commit message:

 workflow cleanup and sections
 
Package: RforProteomics
Commit: 580be536041319ee6c380bab684efe42b25e1206
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-15 23:46:54
Commit message:

 cache package info
 
Package: RforProteomics
Commit: 646927b224746d540623d8902adc08df870703af
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-11-14 11:19:38
Commit message:

 update readme to point to release and support site
 
Package: RforProteomics
Commit: 220d69a9ba9d86b90d8a91fc2b9880193d7a0990
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-31 17:05:12
Commit message:

 fix vignette launcher fun
 
Package: RforProteomics
Commit: 2f42aa9b3a3d7d49d0a9afea432b6d071ec693e9
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-31 17:02:29
Commit message:

 more fixing and tidying up
 
Package: RforProteomics
Commit: a81b574e931e4d5b2aa6dcb49d45e4dd82ae223a
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-31 15:00:24
Commit message:

 fixing errors
 
Package: RforProteomics
Commit: 4d15813abd85fe245e04a4d783202c6bc23ea7fe
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-31 10:27:46
Commit message:

 rename without _ to fix errors
 
Package: RforProteomics
Commit: c62ea6927cf6ae256baab0e50df7321783c13695
Author: d.tenenbaum <d.tenenbaum@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-10-30 18:32:00
Commit message:

 Belatedly bump y to the next odd number. This should have been done
right before release. Not bumping in the release branch because we 
don't want to trigger a lot of downloading, but in the next release we will
definitely bump both release and devel the way we normally do for software
packages.


git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@3084 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 238eb02094b62b6de168622d45cbd4ecccf0036d
Author: d.tenenbaum <d.tenenbaum@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-10-13 21:57:01
Commit message:

 Bump version numbers after creating 3.0 release branch for experiment data packages.


git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@3077 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: d4b0280143fdbfeaa4c3567b281850f505f1a96f
Author: d.tenenbaum <d.tenenbaum@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-10-13 21:52:40
Commit message:

 Bump package versions prior to creating 3.0 release branch for experiment packages.


git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@3075 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 1e925b71f8f2936a1df90182057e6504bb9596f3
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-10-04 08:02:11
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@3055 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 2fb47c64e6fa5f6858e25e9382c7ff166e556062
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-04 08:01:03
Commit message:

 msnid section
 
Package: RforProteomics
Commit: 667a00edcc96ff2fe617e105ddfda8e38d5ec816
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-04 07:50:35
Commit message:

 Merge branch 'master' of https://github.com/vladpetyuk/RforProteomics
 
Package: RforProteomics
Commit: 28438aee53c996a27794507e3bbb360495b5d5aa
Author: Vlad Petyuk <petyuk@gmail.com>
Date: 2014-10-04 07:22:53
Commit message:

 added piece on MSnID
 
Package: RforProteomics
Commit: c3355bb884f0d704ba12032416935eb97c285f48
Author: Vlad Petyuk <petyuk@gmail.com>
Date: 2014-10-04 07:08:01
Commit message:

 added citation of the STEPS approach
 
Package: RforProteomics
Commit: e414967030f655819be2f71ea73dae2b168d17ad
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-03 12:42:05
Commit message:

 update re msgfgui acceptance
 
Package: RforProteomics
Commit: 623cb1420d1af0b57027f0a6ea998190855418cd
Author: Vlad Petyuk <petyuk@gmail.com>
Date: 2014-10-02 17:11:28
Commit message:

 Merge pull request #1 from lgatto/master

catching up 
Package: RforProteomics
Commit: 7ddba6bab12f72b211e2f2b6d7dc28d959fb6476
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-10-02 09:37:17
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@3047 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: f95f5b97ca7e032cfbb934bc9a64076053577040
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-02 09:28:43
Commit message:

 added HUPO 2014 poster
 
Package: RforProteomics
Commit: b6f684b78e6ef1590e652a40a2b8e408e29f8825
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-01 19:16:31
Commit message:

 mzr ident section
 
Package: RforProteomics
Commit: 54e36d8ac78f9f4386b802ce037257de7a1a8189
Author: Thomas Lin Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 18:50:25
Commit message:

 Corrected cross-ref 
Package: RforProteomics
Commit: 5e6f55f029ad9dcee097ac5481411446773878fa
Author: Thomas Lin Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 17:41:45
Commit message:

 Fixed spelling 
Package: RforProteomics
Commit: da707a268f99e21f848dff338aa4af4197842231
Author: Thomas Lin Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 17:40:52
Commit message:

 Fixed spelling 
Package: RforProteomics
Commit: bbc78e2435e2a774c002dde571340806fc4b9fa0
Author: Thomas Lin Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 17:39:25
Commit message:

 Merge pull request #2 from lgatto/master

merging the new MSGF sections 
Package: RforProteomics
Commit: 2da8c630640d99b427a6674f3c53dd68c33a0120
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-10-01 17:04:01
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@3044 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 8758a91eddab878c4def4165263a28436422f5c6
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-01 17:02:07
Commit message:

 merging the new MSGF sections
 
Package: RforProteomics
Commit: 8d5750631e2cffb33515143560e70a33457a5ecb
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:23:44
Commit message:

 Add subsection on MSGFplus and MSGFgui
 
Package: RforProteomics
Commit: 358384ce3380b056de8fc6f16f6c5514c2ecc100
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:23:30
Commit message:

 Move rTANDEM to subsection
 
Package: RforProteomics
Commit: da8a35fe810cfa10968329d4165b3789452afc9e
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:22:55
Commit message:

 Update mzID description
 
Package: RforProteomics
Commit: 49e052f98e6a4bc1cdbad38e7b88c532d59a8111
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:22:43
Commit message:

 Add MSGFplus on list of packages needing additional software
 
Package: RforProteomics
Commit: 45d1daca2ca31e1fe91caa43f8c8f2ebd36633cf
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:22:17
Commit message:

 Added loading of MSGFplus and MSGFgui
 
Package: RforProteomics
Commit: 295fb4566ed0678efd3f0b1c34455e8064b06761
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:21:28
Commit message:

 Add MS-GF+ references
 
Package: RforProteomics
Commit: 8a40688443c34c0fb1e385f2217780050aeede7a
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:21:16
Commit message:

 Add Thomas as author and suggest MSGFplus and MSGFgui
 
Package: RforProteomics
Commit: 6e20f4ece3098e38e2023c15c0389b8de83c7423
Author: Thomas Lin Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:03:02
Commit message:

 Merge pull request #1 from lgatto/master

Update local fork to match current 
Package: RforProteomics
Commit: 96f5c93ef505ddb479314b0ae47e2c1df0411e6f
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 14:02:30
Commit message:

 Revert 8a24aa7..078ad90

This rolls back to commit 8a24aa737d61b83a745b8bc65e90d82700d36da0.
 
Package: RforProteomics
Commit: 078ad904beae5b5b959c42d375b52a61d56f5aea
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 13:32:15
Commit message:

 change cols to columns because cols is deprecated
 
Package: RforProteomics
Commit: 9712033126bc87b9c6df1c5dfb6750a731cc9be9
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 13:31:53
Commit message:

 Added subsection on mzID
 
Package: RforProteomics
Commit: 45c01cfdea091418abd71b8e80405d8b423363ea
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 13:31:27
Commit message:

 Added subsection on MSGFplus and MSGFgui
 
Package: RforProteomics
Commit: 75242e8d084a42f16368db6c67b336ca8f196613
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 13:30:55
Commit message:

 Move rTANDEM to own subsubsection
 
Package: RforProteomics
Commit: fd5e1e2b5cb8801158cc6f0b5061d957a968d4e0
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 13:30:06
Commit message:

 Added MSGFplus as package needing external libraries
 
Package: RforProteomics
Commit: 2ed9f9fa9423b18e62a1bf3814d2257e7d47a62f
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-10-01 12:44:50
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@3043 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 8bacc71014bbe6134433a054699aadd53e6e8b37
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 12:29:43
Commit message:

 Add loading of mzID, MSGFplus and MSGFgui
 
Package: RforProteomics
Commit: 2b0b8e219480d8d291938290d79e02945c057431
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 12:29:06
Commit message:

 Added MS-GF+ refs
 
Package: RforProteomics
Commit: a671bb8dadf4b3967c23ecd8a7737a2742ff49d2
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 12:28:49
Commit message:

 Add mzID, MSGFplus and MSGFgui to suggest
 
Package: RforProteomics
Commit: 01f7371ed728be3b92b0839b42fa3aac0bbb20cc
Author: Thomas Dybdal Pedersen <thomasp85@gmail.com>
Date: 2014-10-01 12:28:26
Commit message:

 Add Thomas Lin Pedersen as author
 
Package: RforProteomics
Commit: 554b45b75299851ce89b3735b495732b8a7b8503
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-01 09:59:15
Commit message:

 compiled new vig with qc section
 
Package: RforProteomics
Commit: d10ff25de2a360314794eaa0efd93823b70ccd5c
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-01 09:34:51
Commit message:

 QC section
 
Package: RforProteomics
Commit: aa515713319f72eca86aaddd36ba9b446b6af73d
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-10-01 08:43:27
Commit message:

 add collaborative editing section
 
Package: RforProteomics
Commit: 62db1269171fbd76460a9c2bd34360edf06f0f71
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-09-04 16:39:45
Commit message:

 readme and news
 
Package: RforProteomics
Commit: 3d28b0fac2039049a09edbfbd4af4a91fb278ef3
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-09-04 16:39:35
Commit message:

 bioc workshop material
 
Package: RforProteomics
Commit: d0f3e43a14c6a1c760f31ef8d94131698f2024eb
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-27 15:41:02
Commit message:

 minor text update 2
 
Package: RforProteomics
Commit: f1e2da00b96bb964ab324b31d68b538b6199460a
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-27 15:40:18
Commit message:

 minor text update
 
Package: RforProteomics
Commit: 4d325e902b3b8a36474a8d6d0816df6273589058
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-27 15:38:48
Commit message:

 link to online viz vig
 
Package: RforProteomics
Commit: 15235e883aef4dddf9fbaa9ac03d8379a8f0c0ac
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-17 22:47:08
Commit message:

 workflow, from bioc2014 workshop
 
Package: RforProteomics
Commit: e20671c35be9da8d423a5295c052ee9df80ddc67
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-16 22:00:44
Commit message:

 new dev version
 
Package: RforProteomics
Commit: d70b074f09d5b39ee262e5158ccb991269d0931c
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-08-16 21:59:58
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2977 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: a4f4c18537f3ba5a9e7b83fe634471d7f3e35d7b
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-16 21:59:04
Commit message:

 Merge branch 'master' of github.com:lgatto/RforProteomics
 
Package: RforProteomics
Commit: c4d661bdcf0faf9323b3ca1ff90b5fb648b60b15
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-16 21:58:54
Commit message:

 use BiocStyle
 
Package: RforProteomics
Commit: 9ce779de05abc656592ed1d65b2c4745b59e633a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-14 15:22:15
Commit message:

 add hint to createFigure1_color.R
 
Package: RforProteomics
Commit: e9f22b5b89cf7899215f7c9bd31f9a8a214e2f55
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-13 20:09:01
Commit message:

 new dev
 
Package: RforProteomics
Commit: a9a62c71780925e21ccff24bd1afed28b85998ea
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-08-13 20:08:21
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2974 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 9fd85042c518f82a7cec57040341234220704ae3
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-13 19:37:16
Commit message:

 suggest additional parameters
 
Package: RforProteomics
Commit: 6a815264aa5f939fe660d77505a635f0da6a9ea4
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-13 19:37:01
Commit message:

 remove non-ascii character
 
Package: RforProteomics
Commit: f4528bcc59a0021340bd845fd2f7aa17e44fdc27
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-13 19:16:49
Commit message:

 spatprot section
 
Package: RforProteomics
Commit: 67e8922d8473312b27edcbd6257ec98f6afcf11d
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-13 16:00:41
Commit message:

 replace m/z by *M/Z*
 
Package: RforProteomics
Commit: 14d6db886109566d60a1bf56fa5d9690861d63a4
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-13 15:50:18
Commit message:

 IMS figure in pdf
 
Package: RforProteomics
Commit: dc63dba88301b4e18c0608357d4e8ed81c8e5b85
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-12 19:50:11
Commit message:

 msnbase figs in pdf
 
Package: RforProteomics
Commit: d6803d4cab08ffb2458121219de7098c3fcc6668
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-12 18:53:31
Commit message:

 vig updates
 
Package: RforProteomics
Commit: 12860e6b2fd48869bd951be8b4ffa3cb51bcbca6
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-12 10:49:27
Commit message:

 purl vig2
 
Package: RforProteomics
Commit: 81d0fe8bf0e38bd2190ee118b66c0ec36ba67a68
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-08-12 10:48:15
Commit message:

 re-fix Makefile

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2973 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 36f41ca05b571784019e51646be469db5eb1c4a3
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-12 10:45:01
Commit message:

 re-fix makefile
 
Package: RforProteomics
Commit: 3ccb67ee2355c3692c387b3e3a34516f91771a30
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-12 08:42:56
Commit message:

 bump v
 
Package: RforProteomics
Commit: 1f1ba47caa92c96fe4b09abf9bce57dc07d01e13
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-08-12 08:41:42
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2972 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: ca8bff0da7dfd44cc22b98c9c11f78fa82100375
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-12 08:38:10
Commit message:

 fix makefile, more viz vig
 
Package: RforProteomics
Commit: e8ea8cee2adbb5edeaa96fabdd6d8280a8325c46
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-11 19:51:15
Commit message:

 update link of MALDIquant vignette
 
Package: RforProteomics
Commit: cdcb2ebcad9bc2aec141923da24b636e22c73cb9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-11 18:35:08
Commit message:

 adapt to MALDIquant 1.11

The RProtVis vignette uses MALDIquant::plotImsSlice now. That's why MALDIquant
>= 1.11 is needed.
 
Package: RforProteomics
Commit: 276b43f7a948068e5e3ff9426775148603c271fd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-11 17:30:25
Commit message:

 add link to my webpage
 
Package: RforProteomics
Commit: 1dc435a12e0fb46cb7ad369f266dae199d1b5bd3
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-11 17:25:33
Commit message:

 fix mqwarp chunk
 
Package: RforProteomics
Commit: 6de2b0ea7c6f67541952521d73f1218873ef6262
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-11 17:25:12
Commit message:

 fix mqlabelpeaks chunk
 
Package: RforProteomics
Commit: 8d1094870277100ab004c00949997813c3b3aea2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-11 17:24:35
Commit message:

 fix screen shot path
 
Package: RforProteomics
Commit: 1fec6a1b99bead3ceff7784a174b40374dd80963
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-11 14:31:41
Commit message:

 don't show warnings
 
Package: RforProteomics
Commit: f7a41f127b8ca22079eefc63dad14fe649fce4b8
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-11 14:23:31
Commit message:

 Merge branch 'master' of github.com:lgatto/RforProteomics
 
Package: RforProteomics
Commit: a76949b170b1a5b5d9826585ead22220d8611229
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-10 19:07:33
Commit message:

 add ims-shiny screenshot
 
Package: RforProteomics
Commit: 3c156b00592fd8755609d83ef83099288bdd1175
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-10 18:45:08
Commit message:

 add links to Mq vignette and IMS shiny app
 
Package: RforProteomics
Commit: a418f564b76462b1cb8ae8c46f5dd8d8a449e84b
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-10 11:10:39
Commit message:

 fix margins
 
Package: RforProteomics
Commit: ea23b214a5e77ef8457e2e0849bb3cb96426ad5d
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-10 10:55:27
Commit message:

 MS barcode
 
Package: RforProteomics
Commit: ee0c74f6f840b339c96da2fa846ea4c67e27b460
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-10 09:42:52
Commit message:

 add spaces around =
 
Package: RforProteomics
Commit: 3c7785d018467123acf679de87bddb042ca2ecd3
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-09 23:07:52
Commit message:

 update readme, mention new viz vig in progress
 
Package: RforProteomics
Commit: ef9bb269759af6bc665d7b77069f405de4e3342f
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-09 23:07:31
Commit message:

 cache and link to pRoloc vig
 
Package: RforProteomics
Commit: 3bbf58ebc8718da2af7bd4fcd70e7a56dd30f01c
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-09 22:47:26
Commit message:

 merge viz conflict
 
Package: RforProteomics
Commit: bf2458d2286cf9e1131f02832090ea43160be122
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-09 22:42:44
Commit message:

 ms viz code and figures
 
Package: RforProteomics
Commit: 0f0065d89450b7b4f0b249a23cb52c16b34bcf66
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-09 11:47:11
Commit message:

 Merge branch 'master' of github.com:lgatto/RforProteomics

Conflicts:
	vignettes/RProtVis.Rmd
 
Package: RforProteomics
Commit: 496edbc1040cb62327748d26c15a8c52c8e6af6c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-09 11:44:32
Commit message:

 add IMS example
 
Package: RforProteomics
Commit: 2b378ce8e403cfe5b6c597d80ee4705c3c770406
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-09 11:44:23
Commit message:

 fix warping example
 
Package: RforProteomics
Commit: 61c21715dd98553424d27829b66bc3d36bd6f3db
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-09 02:15:08
Commit message:

 relevant packages and SI
 
Package: RforProteomics
Commit: b53b2d0944a09b47b9db64a9f61e6d0f54d864a6
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-09 02:14:51
Commit message:

 added protViz package
 
Package: RforProteomics
Commit: ec660e579785b48b37aa33c4fd241617f5f6002e
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-09 01:58:15
Commit message:

 rename viz vig
 
Package: RforProteomics
Commit: 94a46cc25e793a0285e7032fea71e4a985028061
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-09 01:29:05
Commit message:

 anscrombe's quartet
 
Package: RforProteomics
Commit: 7d043d49eeade32f61a8d9cba10d7881733c5c56
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-08 23:12:45
Commit message:

 customized MA plot
 
Package: RforProteomics
Commit: 44c98f18c9da883d52e85fa0644f08e872a4fb0f
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-08 23:12:28
Commit message:

 fix PXD000001 PRIDE urls
 
Package: RforProteomics
Commit: 087d699763fc9df04322a9ae99a25bf213b74cbd
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-08-08 17:31:35
Commit message:

 add MALDIquant preprocessing example
 
Package: RforProteomics
Commit: e522f6c16a8d946afe37090da72f2f320f8e4aee
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-07 20:22:10
Commit message:

 general viz links and refs
 
Package: RforProteomics
Commit: 4616828dc9776c4afc81b7c4457b3d9af12e7a15
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-07 18:04:59
Commit message:

 link in vig
 
Package: RforProteomics
Commit: 457da07adbc9c10db06a9f694cf81499e1708752
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-07 17:50:59
Commit message:

 url link to Mike's shinyMA repo
 
Package: RforProteomics
Commit: abc8c36d998b574f8e3414d068960edd3d8fe77c
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-07 17:30:30
Commit message:

 type in shinyMA man
 
Package: RforProteomics
Commit: 41e6ac76ae23a4ab4f3708978aaf2acb63d8995b
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-07 17:24:29
Commit message:

 shinyMA function
 
Package: RforProteomics
Commit: 298ed8068bc537a69e985db8808d179be1fac02a
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-07 13:37:28
Commit message:

 shinyMA app
 
Package: RforProteomics
Commit: c07d011e76619981b66a91d6ac371d9e9e894ae8
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-06 22:13:08
Commit message:

 first commit of ProtViz vignette
 
Package: RforProteomics
Commit: 0e0e32bb676e1bd8d3ec6bcf5c4c82d87a457020
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-08-02 15:24:58
Commit message:

 link to wiki
 
Package: RforProteomics
Commit: 5f357ad39ee86e065385d1bc29133031606ae977
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-28 02:00:01
Commit message:

 no need to ignore bioc2014 workshop as in own package now
 
Package: RforProteomics
Commit: fffff4d71f1533af941d3cfd528bb6c5955b4ecc
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-26 23:18:31
Commit message:

 fix vig make rule
 
Package: RforProteomics
Commit: 8d7a7436e58a523b150648fac8741a811f567a88
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 17:16:26
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2956 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 0271df0d408a32970342556d61734cbcf24f90b6
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 17:14:10
Commit message:

 updated vig.pdf
 
Package: RforProteomics
Commit: 1fdcdeb36e344299ad1ebe7a1a1bbb88168b923d
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 17:03:26
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2955 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 2ded9cc25ffb5603dd3d4e361254c0b949eba4b7
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 17:02:14
Commit message:

 add package when loading data
 
Package: RforProteomics
Commit: f48872029f14470e4f21fd2a1b38048c90cade6a
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 16:50:49
Commit message:

 fix conflict

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2953 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: ef06477396f368090c963a6004fba3adb5bc03b7
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 16:49:22
Commit message:

 no require
 
Package: RforProteomics
Commit: 76c267e963f59d6de8fc989d9c450537bf42b3bf
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 16:42:58
Commit message:

 check notest and warnings

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2951 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 8a7e8d53d24a8985d024e4a9c0530bfc7051325a
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 16:42:48
Commit message:

 get back to official devel v

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2950 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: fa2f7b74fde191cfd966c681b42ebeae62e4805c
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 16:42:45
Commit message:

 bump v

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2949 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 0661877c02850349b785e7fec33189ded421f86b
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 16:42:42
Commit message:

 get back to official devel v

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2948 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 6ebd4a27153656edb2fb59a1a27b2b2da68b0a6f
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 16:42:38
Commit message:

 bump v

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2947 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 654cf4f5675956c55b55a0793d01364f72542fcb
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 16:40:53
Commit message:

 check notest and warnings
 
Package: RforProteomics
Commit: 4b64dcecf2c55a1b279e0ae4e2311d24424e8658
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 13:46:56
Commit message:

 Merge branch 'local-hedgehog'
 
Package: RforProteomics
Commit: 671baac457dd196e3377c8f48526a7f0a98e67ec
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 11:33:49
Commit message:

 get back to official devel v
 
Package: RforProteomics
Commit: 4b42f2ca35fc2c33ac171b19d0cdd33c03cc4071
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 08:42:57
Commit message:

 bump v
 
Package: RforProteomics
Commit: d4faa0537432eb64b041fe57b1916f8f63fce0f7
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 11:44:48
Commit message:

 fix v

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2942 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 7b4b4dffdada26d3250d15ef721704a0e66b147b
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 11:33:49
Commit message:

 get back to official devel v
 
Package: RforProteomics
Commit: bbb3b76364fc4455d13334d5935195be11dde1ec
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 11:32:45
Commit message:

 release version

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2941 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: f7fa7a4c08df6c110d751cf644de19c122f3f43e
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 11:32:41
Commit message:

 bump v

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2940 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: f9be5c5b05941d2871613b7ae837c39da04bc825
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 08:42:57
Commit message:

 bump v
 
Package: RforProteomics
Commit: 4fdb7f697947150210c13bafef26b52c2543beb3
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 03:06:54
Commit message:

 ignore

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2939 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 933e9193d47a9deca975a9229aabc2eae798b86b
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 03:05:12
Commit message:

 gitignore
 
Package: RforProteomics
Commit: 12047ad02fa36fa5d8b5e1aa4c7d2beb1c73fefd
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 03:02:33
Commit message:

 prebuild pdf

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2938 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 11909ba8d1d8bb67c548b8918e89ade25e599ff7
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 03:01:45
Commit message:

 removed dup vig files

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2937 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 37183c7262bce08e37cd0468272d73328dc00b0d
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 03:01:30
Commit message:

 new funs and vignette updates

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2936 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: d3091d836cb8a2eaf75c8f9cf7731ef3c9ce4da4
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 02:57:26
Commit message:

 remove .gitignore

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2935 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 26c5320d6d20dfd8d7f9f9fe3c12aa78544556e6
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-07-24 02:57:22
Commit message:

 remove twitter

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2934 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: d2e1c88f07c34b7ac8e4411b02740c983a981ee5
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 02:53:32
Commit message:

 prebuild pdf
 
Package: RforProteomics
Commit: a312ffe5ed3e976b27622272bfb1fa953bc5b2bd
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 02:02:24
Commit message:

 removed dup vig files
 
Package: RforProteomics
Commit: 59dbc1369d31210de55e96230d03a0a646dfe415
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-24 02:00:05
Commit message:

 new funs and vignette updates
 
Package: RforProteomics
Commit: 5fae9168f6a77a8d9020622cf542a4cc5deb57a8
Author: Laurent <lg390@cam.ac.uk>
Date: 2014-07-23 14:21:33
Commit message:

 Merge branch 'local-hedgehog'
 
Package: RforProteomics
Commit: 9c622af546cab7f45cdaf79b1d4f8d8643e7c2cf
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-05-08 12:46:33
Commit message:

 remove .gitignore
 
Package: RforProteomics
Commit: 95934f9fc8e3fa787905884bd7ed9423c8b07bf6
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-04-29 22:01:56
Commit message:

 remove twitter
 
Package: RforProteomics
Commit: 39666e67308a3f7fac77e93c4b2b217dc35d9219
Author: d.tenenbaum <d.tenenbaum@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-04-11 21:30:17
Commit message:

 Second version bump after creating 2.14 data/experiment release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2801 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: d5de86fc264250c32888a3d13578aaf14c1290b2
Author: d.tenenbaum <d.tenenbaum@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-04-11 21:27:08
Commit message:

 First version bump of data/experiment packages prior to creating 2.14
release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2799 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 8fd0b9351c4a124a018972dab92b483da12d5eb4
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-03-28 22:24:41
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2758 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 0364c017daa72fbf44d987de5627fa91b53dbf08
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-03-28 22:24:07
Commit message:

 pxr renamed rpx
 
Package: RforProteomics
Commit: 239742c2006c20abc0880a28f03c76d20b63dc76
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2014-03-24 18:51:30
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2744 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 94ed5900e4233b6e7dab29dfac599a91bdf766a7
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-03-24 18:46:51
Commit message:

 import pxr
 
Package: RforProteomics
Commit: 21f13113aa9f695fc445fb983b1e8c02052f1cd8
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-03-24 18:44:43
Commit message:

 updated vignette
 
Package: RforProteomics
Commit: 9648bc5dd4a3a9cc5896fa898445cc4f44e058c3
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-03-24 17:06:50
Commit message:

 add PX ref
 
Package: RforProteomics
Commit: d3593a1cc04e33b49fdd1840b3fd8ae81cd0a304
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-03-24 16:35:30
Commit message:

 type in comment
 
Package: RforProteomics
Commit: ca664ec02f22036dff8602a4c62bb516b33b78ce
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-03-24 16:35:07
Commit message:

 .Deprecated getPXD000001* functions in favour of pxr
 
Package: RforProteomics
Commit: 56670d99f7aceb5b40e333e84f85dd24bce94841
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2014-03-17 19:45:05
Commit message:

 biocVersion has to be of type character
 
Package: RforProteomics
Commit: 3359139546aea6564c5c007b228136cb0784abfc
Author: Laurent <laurent.gatto@gmail.com>
Date: 2014-01-11 21:37:31
Commit message:

 updated REAMDE
 
Package: RforProteomics
Commit: dfbf0b5df5defc16bf7320c8f541d1022c67d0a2
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-12-14 11:54:44
Commit message:

 downloadData and getThermoHelaPRTC from prot-main

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2647 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 49dbfc89e3bd0b12c09fa15e367a1204a070f4bb
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-12-14 11:45:52
Commit message:

 seealso downloadData
 
Package: RforProteomics
Commit: 8ce83325fc87c1fd3603be2e1048680598cc58e0
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-12-14 02:09:30
Commit message:

 new getThermoHelaPRTC fun
 
Package: RforProteomics
Commit: d1c3062bf8158d9ec9b216dd71b10a2e505e73f9
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-12-14 01:18:01
Commit message:

 fix typo
 
Package: RforProteomics
Commit: 90064d4a185be5789a19d326eff6ae347e8280e7
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-12-14 00:54:44
Commit message:

 downloadData man
 
Package: RforProteomics
Commit: 981c3de3b72775556cb4d9b6a7aba1ee7634f11c
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-12-14 00:54:23
Commit message:

 new downloadData function
 
Package: RforProteomics
Commit: e48ff89914beee77f84f74edda9be1567e825cad
Author: hpages@fhcrc.org <hpages@fhcrc.org@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-12-13 19:44:17
Commit message:

 bump versions to differenciate from newly created RELEASE_2_13 branch

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2646 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: f5b03f773dc4bb76a273ee916160c14672b6e8d1
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-11-13 01:21:28
Commit message:

 installation info updated removed instead of commented
 
Package: RforProteomics
Commit: 86a6a952375adc63615e8f23825281fe5adbc5ce
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-11-13 00:01:24
Commit message:

 installation info updated
 
Package: RforProteomics
Commit: 15ae420b0c523f0d329dd11dcc80321220a37163
Author: d.tenenbaum <d.tenenbaum@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-10-14 22:00:20
Commit message:

 version bump associated with 2.13 release

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2533 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 06523fb285990c3ff26f74fa25f899eb08d77b05
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-09-20 21:28:10
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2448 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: a279403c02179a27c9e353dae2282091bb398415
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-09-20 21:21:30
Commit message:

 don't clean too much
 
Package: RforProteomics
Commit: 94bf43d3f2bc9a0417e9e2932d1ac7325be2a145
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-09-20 21:02:08
Commit message:

 moved vig to vignettes
 
Package: RforProteomics
Commit: 43a48f65716c5c590dc9b04f45f739b08661bb56
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-09-19 22:13:41
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2445 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 72094edf9201e9ce96c69832d5a364fd8f060ab4
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-09-19 22:12:22
Commit message:

 vignette updates
 
Package: RforProteomics
Commit: 8a24aa737d61b83a745b8bc65e90d82700d36da0
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-09-18 01:49:44
Commit message:

 updating vignette
 
Package: RforProteomics
Commit: b1c4c0182007c83b1b068165822c29fa522b0a0f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2013-09-08 14:02:26
Commit message:

 adapt to MALDIquant 1.8
 
Package: RforProteomics
Commit: 38d3c4feb6dd6430dda271b1145b654137e626d2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2013-09-08 13:59:10
Commit message:

 fix typos
 
Package: RforProteomics
Commit: 105b1f276a234f3d669bc498f1722396ddfe735f
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-07-19 15:11:25
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2400 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 7db25d424968114ed4bb386afea07909cc5000cd
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-19 14:58:48
Commit message:

 cleaver enhances instead of imports
 
Package: RforProteomics
Commit: e82873a76044fc36c3a6ecfebef57e9ceceaebc5
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-12 18:34:18
Commit message:

 fixed twitter account
 
Package: RforProteomics
Commit: 031114c80d86f0f9e25c296c04aeab17c48b38a3
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-12 18:24:10
Commit message:

 add @RforProteomics to readme
 
Package: RforProteomics
Commit: 121b41309c2cd6a4a2208e90d5b817a1d96f9613
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-07-12 18:14:33
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2390 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: e3868b9bcce6d2e2e92256770e83597b930cbac8
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-12 18:06:22
Commit message:

 add Maintainer field in DESCRIPTION despite Author@R field - needed for Bioc web page propagation
 
Package: RforProteomics
Commit: 1eb0b080a5a9fa4fc1a9a84abfe5a6d4c4971117
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-12 13:44:18
Commit message:

 poster recognised as proper vignette
 
Package: RforProteomics
Commit: 65f311e694ab8c0181fe7800240c68f8fa38caba
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-12 13:37:16
Commit message:

 poster vignette stub
 
Package: RforProteomics
Commit: 904a9ad05fe6bc1be8ee34e6289a4b0f20b3516f
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-08 22:59:42
Commit message:

 readme clarifications
 
Package: RforProteomics
Commit: 1e086f84b51213957679ce0dcec8b744e8b14731
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-07-08 10:39:43
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2386 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 70789e6b80a2db5d7ae0ec820ec19078c9e3ce56
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-08 10:12:01
Commit message:

 typos, clarifications and R4P google group
 
Package: RforProteomics
Commit: a6e2e5418018fe351594414fb96b4ab4f5638a40
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2013-07-08 09:28:29
Commit message:

 Merge pull request #5 from sgibb/typo

fix typos 
Package: RforProteomics
Commit: 12272b491d6662543f21e78df9249140e486a952
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2013-07-06 20:51:36
Commit message:

 fix typos
 
Package: RforProteomics
Commit: c7cea69b8b3b8fe9400c195963db0e1ef4473003
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-07-06 00:16:58
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2383 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: caac99fb32fa962d7ff2dbec72dd4ce6bf8fc845
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-05 11:34:40
Commit message:

 fixed ugly fonts in vignette, document useDev, add Sebastian to vignette authors
 
Package: RforProteomics
Commit: 3cbea9d4953f6b6bd0c738bd55dffe950feafa3a
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2013-07-05 09:44:29
Commit message:

 Merge pull request #4 from sgibb/cleaver

add cleaver example 
Package: RforProteomics
Commit: f47e9e2293cc0fbca8c0cc2127d3ed01b2988611
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2013-07-03 21:35:52
Commit message:

 add Sebastian Gibb as contributor
 
Package: RforProteomics
Commit: cd5056c5f557a6cdf9067c742f7727d90b028e3a
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2013-07-03 21:34:30
Commit message:

 convert Author/Maintainer field to Author@R
 
Package: RforProteomics
Commit: a5c246d120400227c0ab8ed53d32accd4cc95984
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2013-07-03 21:26:17
Commit message:

 add cleaver example
 
Package: RforProteomics
Commit: 4d4b418f0b01616ed809c9faf510fb8d5761967b
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-03 01:45:26
Commit message:

 twitter hook
 
Package: RforProteomics
Commit: 26d46f5e49c7ef690cf23cb53bf1fb8754b25a61
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-03 01:28:30
Commit message:

 rbioc-sig-prot
 
Package: RforProteomics
Commit: 92a046effa69f33b35fcc9c7c705ad502674d5a0
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-07-02 23:46:28
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2382 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: f64ebb35d5df2f3be6f5d377834d2bf62c5cdaa2
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-02 23:45:03
Commit message:

 readme and vignette update
 
Package: RforProteomics
Commit: 85d5d56c4a025ebbd32affb214654fc65f5d6a49
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-07-02 20:23:17
Commit message:

 added links/refs
 
Package: RforProteomics
Commit: 4ee3fd620ddbabe38550324fdafaff969aae4ff7
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-06-07 21:18:27
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2370 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 9a0a5e997e04027d8d84aa1985cd7b412ff117dc
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-06-07 21:17:21
Commit message:

 fix citation
 
Package: RforProteomics
Commit: 2d3124a24ff1114b059a72d77525d4e658b49115
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-06-07 21:12:10
Commit message:

 rebuild vignettes to use updated bib refs
 
Package: RforProteomics
Commit: 50cb8478bd1841b2170da488c77c7b4b0cb22b03
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-06-07 20:35:24
Commit message:

 version and news
 
Package: RforProteomics
Commit: 921d6d971202717a93235a8db9453497734b428d
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-06-07 20:33:20
Commit message:

 add citation file
 
Package: RforProteomics
Commit: 31316ff7bdd32170a2a61dbf77afb7474d409a17
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-06-07 20:32:59
Commit message:

 update refs
 
Package: RforProteomics
Commit: cd779969d65a9bfb5940c0e76a396a9036d72480
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-05-24 00:24:19
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2363 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 02c81c3045d14847d71181efe0a9316a2538c36d
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-05-24 00:23:11
Commit message:

 regenerate vignette pdf with latest version
 
Package: RforProteomics
Commit: fda5044a1ac7f2a63c188e57e464259bf1186825
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-05-23 23:51:11
Commit message:

 bump version
 
Package: RforProteomics
Commit: fe68735a5354a930e371c4a0aa547e3769929e01
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-05-23 23:17:25
Commit message:

 updated vignette pdf with Sebastian's latest updates
 
Package: RforProteomics
Commit: 51bf169fbb424eefaae7048014ea0f84557ebdae
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2013-05-23 19:48:26
Commit message:

 Merge pull request #3 from sgibb/fixMovingAverage

MALDIquant: remove misleading length calls 
Package: RforProteomics
Commit: 9a3035f31d81c717929d6eb741cc2f07b5b16825
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2013-05-23 18:13:15
Commit message:

 MALDIquant: remove misleading length calls
 
Package: RforProteomics
Commit: 2d6bf689b44829f0b4798f73a9651b149125578a
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-05-01 20:33:51
Commit message:

 udpated vignette with latest MALDIquantForeign and Sebastian's pull request
 
Package: RforProteomics
Commit: 528ae382e247953c9959d9b8818ae28f4635c693
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2013-05-01 19:30:44
Commit message:

 Merge pull request #2 from sgibb/nonVerbose

importBrukerFlex: set verbose=FALSE 
Package: RforProteomics
Commit: 72113a8b1f2d85b612b583ec514b3b7d7e632f67
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2013-05-01 09:22:29
Commit message:

 importBrukerFlex: set verbose=FALSE
 
Package: RforProteomics
Commit: 96b4e77bb7b930d0669f17ac44d04d411b00e1fc
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-04-26 17:24:34
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2336 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 8a9d7f6fef52b26275d922853593e7b0be068405
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-04-26 17:22:11
Commit message:

 udpate vignette pdf
 
Package: RforProteomics
Commit: f4e9ad16e29c79c587a1654b1f37bd6f52d5689f
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-04-26 16:52:00
Commit message:

 version bump
 
Package: RforProteomics
Commit: 20f573a4d3453696e458dffc65699582c3ef3deb
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2013-04-26 16:47:16
Commit message:

 Merge pull request #1 from sgibb/cleanMALDIquantExample

remove deprecated library/function calls 
Package: RforProteomics
Commit: b80df52e1430d665961c60acd88744d472dc364e
Author: Sebastian Gibb <sebastian.gibb@studserv.uni-leipzig.de>
Date: 2013-04-26 16:03:50
Commit message:

 remove deprecated library/function calls
 
Package: RforProteomics
Commit: 956dcc268ee7bfbfa3049474ed23bab378cf525c
Author: l.gatto <l.gatto@db2202da-8704-0410-b924-b125b3cd84ef>
Date: 2013-04-24 01:09:10
Commit message:

 Merge branch 'master' into local-hedgehog

git-svn-id: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RforProteomics@2334 db2202da-8704-0410-b924-b125b3cd84ef
 
Package: RforProteomics
Commit: 84ff758da39b42d6e0cd7461692224bfcd639e63
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-04-24 01:06:48
Commit message:

 more netcdf deps
 
Package: RforProteomics
Commit: 612fff8dd75648c07d6afb9b435186cc3252dcbf
Author: Laurent <laurent.gatto@gmail.com>
Date: 2013-04-19 12:51:48
Commit message:

 netcdf deps
 

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