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Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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: BrowserViz
Commit: 708d1a33ddf2d3f8294af07a03323d3d0653c7a8
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2018-04-23 14:35:49 -0700
Commit message:

 httpuv version must be 1.3.6

Package: wateRmelon
Commit: f5cc1b3ddc80e993aa9975f49cc90c9aebcf2031
Author: TJGorrie <tgorri@essex.ac.uk>
Date: 2018-04-23 19:05:50 +0100
Commit message:

 Final commit before Bioc3.7

Package: wateRmelon
Commit: 55bc62ddbec264f6e2df814447bd78bfb070b1a0
Author: TJGorrie <tgorri@essex.ac.uk>
Date: 2018-04-19 13:01:35 +0100
Commit message:

 Adding robust solution incase barcode format is changed

Package: wateRmelon
Commit: c80c1d49fad98161e1370ba2b3e48e0164e644fe
Author: TJGorrie <tgorri@essex.ac.uk>
Date: 2018-04-19 10:52:38 +0100
Commit message:

 Updating vignette

Package: wateRmelon
Commit: eb52276b81528fd913117326317152de72b23ab3
Author: TJGorrie <tgorri@essex.ac.uk>
Date: 2018-04-18 14:26:13 +0100
Commit message:

 Fixing ecc

Package: wateRmelon
Commit: 01aeeebf47fe1aacc28d365551b1dd1511d3de34
Author: TJGorrie <tgorri@essex.ac.uk>
Date: 2018-04-16 13:20:08 +0100
Commit message:

 Small fix to readEPIC

Package: wateRmelon
Commit: 4178e910b4c40c0e4af0713c5e20b5dcd6880dbb
Author: TJGorrie <tgorri@essex.ac.uk>
Date: 2018-03-15 17:11:45 +0000
Commit message:

 Adding estimateCellCounts to wateRmelon - porting various functions from bigmelon to wateRmelon that are used for this.

Package: VariantFiltering
Commit: 691d87b21ab1bcdbe71933c47e32ae55f46eb699
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2018-04-23 22:51:31 +0200
Commit message:

 Bugfix for windows build.

Package: rtracklayer
Commit: aec9f26c1e20a79edf0bad812c088cda80ef5f26
Author: Michael Lawrence <michafla@gene.com>
Date: 2018-04-23 13:38:33 -0700
Commit message:

 include '...' in tableNames<- formals due to R 3.5 bug in methods

Package: rtracklayer
Commit: 661428a635bfc54760a75dde4d5ca82a4328283d
Author: Michael Lawrence <michafla@gene.com>
Date: 2018-04-23 13:38:23 -0700
Commit message:

 clarify error message

Package: basecallQC
Commit: 8aac03d8f5fa67c51566227ed0919e6f01a1bc25
Author: Thomas Carroll <tc.infomatics@gmail.com>
Date: 2018-04-23 16:13:46 -0400
Commit message:

Package: basecallQC
Commit: e0e28597e8b2522ff2c8f24ee77cea458e63cd07
Author: Thomas Carroll <tc.infomatics@gmail.com>
Date: 2018-04-23 16:13:22 -0400
Commit message:

 Fix html_document to html_document2

Package: VariantFiltering
Commit: d3d247b1413d547e72cfd2442da197cb17300436
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2018-04-23 22:04:38 +0200
Commit message:

 Trying to spot the code that breaks the windows build.

Package: DESeq2
Commit: 2c0b0a74144207fc9311a89198807eb2e45366fb
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-04-23 15:16:12 -0400
Commit message:

 tweak vignette

Package: matter
Commit: c181f086c4c21084b134a20fb22ee005804d1933
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2018-04-23 14:47:16 -0400
Commit message:

 cleanup [base] links

Package: matter
Commit: eff1e505ac2f26ba7aa5248aa228f05230d1427e
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2018-04-23 14:43:46 -0400
Commit message:

 cleanup Rd links

Package: Cardinal
Commit: 2b5eef02ddee323bdcdab614c3e665aecf696d13
Author: kuwisdelu <k.bemis@northeastern.edu>
Date: 2018-04-23 14:32:49 -0400
Commit message:

 cleanup Rd links

Package: DESeq2
Commit: 6969808577df8f9fece3595f83c54638871549ad
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2018-04-23 14:00:21 -0400
Commit message:

 fix weights matrix subsetting for disp refit

Package: perturbatr
Commit: b3a3c9a4d1245c9b04ccba2f1a5ab564b3a6c819
Author: dirmeier <simon.dirmeier@bsse.ethz.ch>
Date: 2018-04-23 19:36:45 +0200
Commit message:

 Updates mrw after diffusr release v0.1.3

Package: unifiedWMWqPCR
Commit: 52b21d019115d3a45911dc44115d9f95b85bd37e
Author: Joris Meys <Joris.Meys@UGent.be>
Date: 2018-04-23 19:44:58 +0200
Commit message:

 Add news file

Package: RCyjs
Commit: d2efec7536463a132c1624a48695c307439575f2
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2018-04-23 10:28:16 -0700
Commit message:

 ask build to ignore inst/demo/

Package: SummarizedExperiment
Commit: 7562b4c8e683fb8b5bc9ba9bf5fddede37b5f5a3
Author: Marcel Ramos <LiNk-NY@users.noreply.github.com>
Date: 2018-04-23 13:09:46 -0400
Commit message:

 Merge pull request #9 from PeteHaitch/master

Add BACKEND argument to realize,SummarizedExperiment-method

Package: SummarizedExperiment
Commit: ca3944054cde0ec6149449a0c014c6185fbc9389
Author: Marcel Ramos <LiNk-NY@users.noreply.github.com>
Date: 2018-04-23 13:08:35 -0400
Commit message:

 update example to use `seq_len`

Package: SummarizedExperiment
Commit: 4db366bc41178fe60057d89c337113c3d8bae221
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-04-18 19:33:09 -0400
Commit message:

 Add BACKEND argument to realize,SummarizedExperiment-method

Package: GenomicInteractions
Commit: 0d1dabe5670aa05201910796d165dc5d2fa2b48e
Author: Liz Ing-Simmons <liz.ingsimmons@gmail.com>
Date: 2018-04-23 18:36:20 +0200
Commit message:

 version bump

Package: ChIPanalyser
Commit: 9fc07659a0d944d2495023b96d8890cdd79976be
Author: Patrick C.N. Martin <pm16057@essex.ac.uk>
Date: 2018-04-23 17:25:04 +0100
Commit message:

 version Bump

Package: diffcyt
Commit: 8cbbc0b358b812f311ec57266896d6e25213b127
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 18:23:48 +0200
Commit message:

 fix links in documentation

Package: diffcyt
Commit: c90e5503337517c41196b0892735cef2677ab81d
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 17:23:21 +0200
Commit message:

 return cluster IDs as factor

Package: diffcyt
Commit: b95d189c6defebd788b4a7b23397feaf7d42f798
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 17:06:22 +0200
Commit message:

 add alias for package help file

Package: ChIPanalyser
Commit: 20b08f505d2bf558f658e860decef75d84689aff
Author: Patrick C.N. Martin <pm16057@essex.ac.uk>
Date: 2018-04-23 17:21:07 +0100
Commit message:

 code doc mismatch

Package: ChIPanalyser
Commit: 86ec06a7e16c824a6c19a3215b4f55b11b17690e
Author: Patrick C.N. Martin <pm16057@essex.ac.uk>
Date: 2018-04-23 17:10:12 +0100
Commit message:

 Lazy Load

Package: IsoformSwitchAnalyzeR
Commit: 4ef66e25b05345286b8c6e45a5f89ff6c6bc6b28
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2018-04-23 17:53:34 +0200
Commit message:

 Correction of small bug

Package: ChIPanalyser
Commit: 560c0b2be3da5fdfd5a11d7e47899c6bfda4707d
Author: Patrick C.N. Martin <pm16057@essex.ac.uk>
Date: 2018-04-23 16:47:51 +0100
Commit message:

 NEWS Update

Package: ChIPanalyser
Commit: b6f20cd628f212f08c1baed512815a82eba40213
Author: Patrick C.N. Martin <pm16057@essex.ac.uk>
Date: 2018-04-23 16:43:31 +0100
Commit message:

 Remove old plotting function

Package: ChIPanalyser
Commit: e380b1eb8101901508ea1772bc6fbb109d464a83
Author: Patrick C.N. Martin <pm16057@essex.ac.uk>
Date: 2018-04-23 16:37:04 +0100
Commit message:

 v1.0.1 first commit

Package: eiR
Commit: 11b8cf5187dc7e32d3ac44163ca8708dfdb843d2
Author: khoran <khoran@cs.ucr.edu>
Date: 2018-04-23 08:22:51 -0700
Commit message:

 tweaked vinnette a bit

Package: GenomicInteractions
Commit: 8c3c48d7350c70986780de542c8e52ca76fa1253
Author: Liz Ing-Simmons <liz.ingsimmons@gmail.com>
Date: 2018-04-23 17:04:19 +0200
Commit message:

 deprecated function was still present in exports

Package: DaMiRseq
Commit: 8bc9d3070489c7793266d1c80b5db81de2f43547
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2018-04-23 17:04:29 +0200
Commit message:

 updates v1.3.9

Package: TCGAbiolinksGUI
Commit: 41e86087d8512e103de1cc524c314eb731ffc573
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-04-23 16:59:06 +0200
Commit message:

 Improving EA messages

Package: rgsepd
Commit: 17c35588bcb6d87a9520cfad6d7d52fa209c517f
Author: Karl Stamm <karl.stamm@gmail.com>
Date: 2018-04-20 16:44:26 -0500
Commit message:

 explicitly changing a matrix[1,1] into a vector before * for R 3.5's ego

Package: rgsepd
Commit: 3e6ba86d9d122dc4a88ead9f007d41e699de7e70
Author: Karl Stamm <karl.stamm@gmail.com>
Date: 2018-04-19 14:31:58 -0500
Commit message:

 tweaks to version number and requirements, bugfixing and no real changes.

Package: ASICS
Commit: d6dc317f96baf8d8c39dfbe83eb4be34b3c058d6
Author: glefort <gaelle.lefort@inra.fr>
Date: 2018-04-23 16:40:04 +0200
Commit message:

 Merge branch 'dev'

Package: ASICS
Commit: 13b55b5ff37fe95f6e990daeaba7c639aaabebb2
Author: glefort <gaelle.lefort@inra.fr>
Date: 2018-04-23 16:39:24 +0200
Commit message:

 update package version

Package: ASICS
Commit: f66800cc7be3f3ac96468e7a5a8b2913871030ef
Author: glefort <gaelle.lefort@inra.fr>
Date: 2018-04-23 16:37:07 +0200
Commit message:

 Merge branch 'dev'

Package: ASICS
Commit: cd9a9c21a78cbb243650f41cd29736397c2fa18c
Author: glefort <gaelle.lefort@inra.fr>
Date: 2018-04-10 08:42:44 +0200
Commit message:

 fix a bug in quantification estimation

Package: ASICS
Commit: ebd5bed7d386c822f4a860e6ec1d76b8d98339da
Author: glefort <gaelle.lefort@inra.fr>
Date: 2018-04-09 10:45:23 +0200
Commit message:

 fix a bug in parallel environment for importSpectraBrucker function

Package: MAGeCKFlute
Commit: b370a5713b3fceac69f4275a5760df4a56c56468
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-04-23 22:12:42 +0800
Commit message:

 export cutoffcalling method

Package: methylKit
Commit: 63bb25c30cecbd288619846e9f248b0d87f5d233
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-04-23 16:05:54 +0200
Commit message:

 update NEWS and Version Bump

Package: DAPAR
Commit: 3b0fbe146aa2f8bceeb575fb1aebf1b3b4379c71
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 16:03:53 +0200
Commit message:

 Several bugs fixed

Package: DAPAR
Commit: e1be9c50486a70e8da6f55afd3d8a43d31b2406b
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:08:48 +0200
Commit message:

 Update normalize.R

Package: DAPAR
Commit: 736d23ed8dc8d75209b723b81268bd1ee9ea2787
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:08:13 +0200
Commit message:

 Update missingValuesImputation.R

Package: DAPAR
Commit: 2fb803cd90eed57f728114cf58d7e05389df19f0
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:07:33 +0200
Commit message:

 Update inOutFiles.R

Package: DAPAR
Commit: 8957f72f31340b0620ac39f20fcf7b361f7c8de9
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:06:50 +0200
Commit message:

 Update DiffAnalysis.R

Package: DAPAR
Commit: 09edab8b698c4b347445b30edaac7a219936ed93
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:06:12 +0200
Commit message:

 Update bioAnalysis.R

Package: DAPAR
Commit: 3fe51d9c2f8dce1cb107f4d3e13e5de0f3f950e6
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:05:27 +0200
Commit message:

 Update NAMESPACE

Package: DAPAR
Commit: f0bf684d584cb8e2dba3f3ed8903def6367f35b8
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:33:06 +0200
Commit message:

 Update inOutFiles.R

Package: DAPAR
Commit: fee674a00557a32e2c1ca8bbd9911bc7cf67032f
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:15:06 +0200
Commit message:

 Update normalize.R

Package: DAPAR
Commit: 01fd7b39a2523b0c3631869918c38cf4870227b0
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:14:10 +0200
Commit message:

 Update missingValuesImputation.R

Package: DAPAR
Commit: bbc40f1753e97e794f75122183b5809e3fe41ed8
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:13:12 +0200
Commit message:

 Update missingValuesFilter.R

Package: DAPAR
Commit: e907c75c21e2c9019c22cccb1a714f7796184f18
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:11:55 +0200
Commit message:

 Update inOutFiles.R

Package: DAPAR
Commit: 2c55de55928e938438db0691b7998bfa05025a72
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:10:52 +0200
Commit message:

 Update NAMESPACE

Package: methylKit
Commit: b42a46089163c80ffc57fed1000d33f4d135aff9
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-04-23 15:59:23 +0200
Commit message:

 check if tabix file exists and if yes rename output file

Package: methylKit
Commit: d784bd9352d1d2cddfc291890f62abbb66c0c7ea
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-04-23 15:58:31 +0200
Commit message:

 allow absolute paths for dbdir

Package: Prostar
Commit: 08a0ebd474d9b05846e66259b2fd44325219d019
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 15:56:37 +0200
Commit message:

 Several bug fixed

Package: Prostar
Commit: 0e0b488ae9120762d63438a7bf4433bb06e37f7f
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:13:23 +0200
Commit message:

 Update normalization.R

Package: Prostar
Commit: f03726afdfc5b50dc2b5181f4d2e33c5ee39cbdf
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:12:48 +0200
Commit message:

 Update modulesSrv.R

Package: Prostar
Commit: 6028bb25419979c164361aa5a070d261c3d44e27
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:12:21 +0200
Commit message:

 Update imputation.R

Package: Prostar
Commit: e1b613697d3b20db7c6574c181fbef7e17c07ba8
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:11:48 +0200
Commit message:

 Update GO_enrichment.R

Package: Prostar
Commit: 918bb69870f27cfb429e7805eb40625e30033c88
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:11:02 +0200
Commit message:

 Update anaDiff.R

Package: Prostar
Commit: ad6bfdb23a313bcf7ce24d9072ca615db5b6e0f7
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:10:15 +0200
Commit message:

 Update tabPanel_AnaDiff.R

Package: Prostar
Commit: 3525c6418d02d89d47380105fe3f39357eca4be4
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 06:09:39 +0200
Commit message:

 Update modulesUI.R

Package: Prostar
Commit: ec995a6a9f2e647477e4412790f9b6df97942fe7
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:23:40 +0200
Commit message:

 Update normalization.R

Package: Prostar
Commit: 96de277d6764aea3e9ce4c74952f7906abcb84ea
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:22:31 +0200
Commit message:

 Update imputation.R

Package: Prostar
Commit: 5d7fbf9b89a859b10401b1ae2abd59ccf3c9b4a2
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:21:20 +0200
Commit message:

 Update general.R

Package: Prostar
Commit: 23048ee20eca555a3b1b393f36f88d7d7b9db3aa
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:20:22 +0200
Commit message:

 Update filtering.R

Package: Prostar
Commit: 3c26b81dfb3319ebf57d31b11ddff53654102e25
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:18:47 +0200
Commit message:

 Update datasetManager.R

Package: Prostar
Commit: 6460d0bb878fdb3030ded09d3537d3e5d8ca19be
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-22 20:17:28 +0200
Commit message:

 Update anaDiff.R

Package: TCGAbiolinksGUI
Commit: ec762c5514ee2e0bcd4a1b8c779e499edd67f968
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-04-23 15:44:30 +0200
Commit message:

 Improving the text

Package: TCGAbiolinksGUI
Commit: 45c8aca19fa91437789709d3213e2d2b4eb124c6
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2018-04-23 15:37:13 +0200
Commit message:

 Adding exception handling for DEA analysis

Package: HDCytoData
Commit: d1e174e0a050603c16bc6672bad3780abb0b9fd4
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 15:24:08 +0200
Commit message:

 update vignette for new 'rowData' and 'colData'

Package: DAPARdata
Commit: e9f2ffe7ac1cc96f791cb508ca4b7347954bfaf6
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 15:23:49 +0200
Commit message:

 updates in design

Package: DAPARdata
Commit: 5dbfc8f1cc6bef837d5ad8ecf96efa92c2905d66
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-04-23 15:12:49 +0200
Commit message:

 updates in design

Package: HDCytoData
Commit: d3ee92835b4ca6410f59e2ff28aecd02a2ed5f01
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 15:08:00 +0200
Commit message:

 update DESCRIPTION and NEWS

Package: PowerExplorer
Commit: 2226057706022fe869d06ea495f7375b21c61acb
Author: xuqiao93 <xu.qiao@utu.fi>
Date: 2018-04-23 15:49:22 +0300
Commit message:

 changes in package dependencies

Package: HDCytoData
Commit: 14698aa674ffb401a217ccababb977857f78b16f
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 14:51:03 +0200
Commit message:

 version

Package: HDCytoData
Commit: 1538a02819283f1bb312c76e957f16e44c9e36d0
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 14:34:04 +0200
Commit message:

 update structure of rowData and colData

Package: HDCytoData
Commit: 52072cd514ca18a5a0bd62fee3bdd55085bfe3b5
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 13:26:05 +0200
Commit message:

 clean up metadata script

Package: HDCytoData
Commit: 276b6bfba3d7e7921c1c2fcbe06e99338c242302
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-04-23 12:10:48 +0200
Commit message:

 update documentation and fix links

Package: MAGeCKFlute
Commit: b3abd11565100f8239929a377b26a43c9e60b095
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-04-23 20:40:58 +0800
Commit message:

 Remove warnings

Package: CrispRVariants
Commit: bcdc48bf87859d690d8de24c1c0afe507cbe454f
Author: Helen Lindsay <helen.lindsay@uzh.ch>
Date: 2018-04-23 14:31:46 +0200
Commit message:

 Add missing documentation

Package: CrispRVariants
Commit: 2a3a117aaff95676f0f7a6f7f5211a0493b46e5a
Author: Helen Lindsay <helen.lindsay@uzh.ch>
Date: 2018-04-23 12:58:01 +0200
Commit message:

 setup travis continuous integration

Package: CrispRVariants
Commit: 3e1cf8889d21fa5b2a3a4aa4579c9893cb05742e
Author: Helen Lindsay <helen.lindsay@uzh.ch>
Date: 2018-04-23 12:14:57 +0200
Commit message:

 Add test for renaming alleles

Package: CrispRVariants
Commit: 6c80be88cc0c37a6d2446640f688c160ec27a32c
Author: Helen Lindsay <helen.lindsay@uzh.ch>
Date: 2018-04-23 12:14:15 +0200
Commit message:

 Removed untested label functions for release

Package: scater
Commit: e1aa38b182b9da6802a067ba6ac943b443039b1b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 13:19:08 +0100
Commit message:

 Turned down version number.

Package: scater
Commit: 0b69a830045b27e34c44fd244e70f21bee177f9b
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 13:01:31 +0100
Commit message:

 Updates to documentation.

Package: scater
Commit: 1dc12df13d504ed266396d97f4a4ef0f33e1dfac
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 11:28:49 +0100
Commit message:

 Updated NEWS.

Package: scater
Commit: 92ff55ea3f6b25335675942d43067c72942dcbf5
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 11:26:17 +0100
Commit message:

 Bumped date, version number.

Package: scater
Commit: ff41526dc8f4e5e1ca934b7655764777f741202c
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 11:25:17 +0100
Commit message:

 Added checks when use_size_factors=FALSE for normalizeSCE.

Package: scater
Commit: 2422b1088f52e91df96d7f60fc3cf0e9ba24b8e4
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 11:20:05 +0100
Commit message:

 Bug fix to calculateCPM, updated calc-expression tests.

Package: scater
Commit: cbd33c6ab2fc93695269da020c6be38d94e0da42
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 11:14:21 +0100
Commit message:

 Expanded tests for normalizeSCE for new size factor interface.

Package: scater
Commit: 33637590698ea795e12554fe2f51fca218c61f20
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 11:07:04 +0100
Commit message:

 Bug fixes.

Package: scater
Commit: 098e4498251ae1b0e085a3ddd5a4c4c2955a8348
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 10:44:50 +0100
Commit message:

 Updated documentation for new interface.

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Commit: 764eb5ebb1fbffc410a9f6e522af0db5e7aaa168
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 10:31:32 +0100
Commit message:

 Streamlined calculateCPM.

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Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 10:30:23 +0100
Commit message:

 Standardized size factor-related arguments in calcAverage, normalizeSCE.
Created new function for size factor clearing and resetting.
Minor rewording to comments, updated docs.

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Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 10:10:59 +0100
Commit message:

 Refactored calcAverage to use centreSizeFactors. Moved naming into .compute_exprs.

Package: scater
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Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 09:56:33 +0100
Commit message:

 Used centreSizeFactors in normalizeSCE, removed centring from .compute_exprs.

Package: scater
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Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-04-23 09:47:07 +0100
Commit message:

 Added explicit function to centre size factors.

Package: scater
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Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-04-16 17:46:33 +0100
Commit message:

 Updated NEWS, bumped version number, date.

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Author: Arfa Mehmood <arfmeh@utu.fi>
Date: 2018-04-23 14:06:52 +0300
Commit message:

 Updating

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Author: Arfa Mehmood <arfmeh@utu.fi>
Date: 2018-04-23 14:06:18 +0300
Commit message:

 Updating

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Author: Arfa Mehmood <arfmeh@utu.fi>
Date: 2018-04-23 14:06:08 +0300
Commit message:

 Updating

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Author: Arfa Mehmood <arfmeh@utu.fi>
Date: 2018-04-23 14:05:52 +0300
Commit message:

 Updating

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Date: 2018-04-23 14:05:41 +0300
Commit message:

 Updating

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Author: Arfa Mehmood <arfmeh@utu.fi>
Date: 2018-04-23 14:05:14 +0300
Commit message:

 Updating

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Date: 2018-04-23 14:04:53 +0300
Commit message:

 Updating

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Date: 2018-04-23 14:04:30 +0300
Commit message:

 Updating

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Date: 2018-04-23 14:04:10 +0300
Commit message:

 Updating

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Author: Arfa Mehmood <arfmeh@utu.fi>
Date: 2018-04-23 14:03:48 +0300
Commit message:

 Updating

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Author: Arfa Mehmood <arfmeh@utu.fi>
Date: 2018-04-23 14:03:32 +0300
Commit message:

 Updating

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Author: Arfa Mehmood <arfmeh@utu.fi>
Date: 2018-04-23 14:03:16 +0300
Commit message:

 Updating

Package: qpgraph
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Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-04-23 13:04:38 +0200
Commit message:

 Updated NEWS file. Corrected src/Makevars.in to avoid a warning about LAPACK_LIBS and BLAS_LIBS.

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Date: 2018-04-23 11:57:36 +0100
Commit message:

 Reducing memory footprint of main example in man file

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Date: 2018-04-23 18:57:58 +0800
Commit message:

 as.phylo and as.treedata method for edgelist

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Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-04-23 12:54:26 +0200
Commit message:

 Updated README.md

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Date: 2018-04-23 12:50:01 +0200
Commit message:

 Updated NEWS and README.md files.

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Date: 2018-04-23 12:12:19 +0200
Commit message:

 Fixed conflicts version change

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Commit: 8f7e218f8f8417ea9e95cb55834688e1cbaa46c2
Author: Joris Meys <Joris.Meys@UGent.be>
Date: 2018-04-11 22:17:40 +0200
Commit message:

 Update documentation to remedy check warnings

Documentation is updated so all warnings regarding missing aliases, mismatches etc from R CMD chec are gone.

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Author: Joris Meys <Joris.Meys@UGent.be>
Date: 2017-08-25 18:56:56 +0200
Commit message:

 Trying again to setup travis

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Date: 2017-08-25 18:51:15 +0200
Commit message:

 Updated for bioconductor

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Date: 2017-08-25 18:43:53 +0200
Commit message:

 Removed travis badge

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Date: 2017-08-25 18:37:53 +0200
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 Updated gitignore and buildignore

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Author: Joris Meys <Joris.Meys@UGent.be>
Date: 2017-08-25 18:11:52 +0200
Commit message:

 updated readme.md

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Date: 2017-08-25 18:08:09 +0200
Commit message:

 Added travis support

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Date: 2018-04-23 17:36:19 +0800
Commit message:

 Update DESCRIPTION

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Date: 2018-04-23 17:35:27 +0800
Commit message:

 Update README.md

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Author: miaozhun <mz8@foxmail.com>
Date: 2018-04-23 17:34:54 +0800
Commit message:

 Update DEsingle.Rmd

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Author: miaozhun <mz8@foxmail.com>
Date: 2018-04-23 17:34:18 +0800
Commit message:

 Update NEWS

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Author: tanovsky <cristiano.oliveira@med.uni-heidelberg.de>
Date: 2018-04-23 11:08:56 +0200
Commit message:

 fix warning msgs

Package: SWATH2stats
Commit: 7fcbc266b66f670a6d33fea4e4f6f49d8f501054
Author: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Date: 2018-04-23 09:49:22 +0200
Commit message:

 v1.9.3 remove aLFQ link in man page

Package: GenomicScores
Commit: ee55fc3ca11218651df67123da181b893eb9326a
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-04-23 09:45:53 +0200
Commit message:

 Remove [] from cross-reference in man pages.

Package: GenomicScores
Commit: 1f3e6c1351b53bfab2f311bb22901d6d9c947d70
Author: [rcastelo] <[robert.castelo@upf.edu]>
Date: 2018-04-23 09:32:13 +0200
Commit message:

 Added metadata for AnnotationHub resources phastCons46wayPlacental and phastCons46wayPrimates, and updated NEWS file.

Package: Rsubread
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Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2018-04-23 17:29:26 +1000
Commit message:

 (1) fixed find bin start bug in FC
(2) removed some warning messages

Package: Rsubread
Commit: 8aa64146e87b525cb0b7cc9c5d8ea239f2f39cdf
Author: Wei Shi <shi@wehi.edu.au>
Date: 2018-04-23 14:31:13 +1000
Commit message:

 Update users guide.

Package: RTNsurvival
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Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2018-04-22 23:28:50 -0300
Commit message:

 regular maintenance

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Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2018-04-22 23:19:38 -0300
Commit message:

 regular maintenance

Package: RTN
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Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2018-04-22 23:09:26 -0300
Commit message:

 regular maintenance

Package: RCy3
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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-22 17:49:40 -0700
Commit message:

 fixed conflict

Package: RCy3
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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-22 17:36:10 -0700
Commit message:

 cleared a warning and note; bump

Package: RCy3
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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-22 16:35:01 -0700
Commit message:

 added cyndex2 functions and vignette; bump


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 updated vignettes and docs; bump


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 added example to vignette


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Date: 2018-04-13 13:56:09 -0700
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 updated docs and vignette to note loss of undirectedness in round-trip iGraph conversions


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 expanded edge coloring cases; fixed layout case; corrected docs; bump


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 added error messages from POST


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 minor tweaks


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 New vignette and fixes; bump


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 more tests; fixed typos; bump


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 added section to vignette


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 new vignette; fixed minor formatting on all vignettes


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Date: 2018-04-07 12:03:24 -0700
Commit message:

 bump


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 shifting order of operations to fix styling in createNetworkFromIgraph


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Date: 2018-04-05 22:46:02 -0700
Commit message:

 fixed edge cases for unhideAll; more tests


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Date: 2018-04-05 18:36:53 -0700
Commit message:

 fixed headers in all vignettes for html


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Date: 2018-04-05 16:14:20 -0700
Commit message:

 completed deps and defuncts


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Commit message:

 bump

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Package: RCy3
Commit: 0e2ff8f19740f33868a341cd3c968064d5ea1962
Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2018-04-05 12:38:08 -0700
Commit message:

 removed old formatting syntax

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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-05 12:13:53 -0700
Commit message:

 added link to old bioc page


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-05 12:09:20 -0700
Commit message:

 updated all vignette; using BiocStyle; excluding Rproj


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-05 11:25:50 -0700
Commit message:

 added version check to cytoscapePing


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-03 22:27:23 -0700
Commit message:

 bump


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-03 22:26:57 -0700
Commit message:

 more tests and mionr fixes


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-04-03 16:02:52 -0700
Commit message:

 Merge branch 'master' of github.com:cytoscape/RCy3


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Date: 2018-04-03 16:02:42 -0700
Commit message:

 bump for PR


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Date: 2018-04-03 16:00:39 -0700
Commit message:

 Merge pull request #18 from rmflight/na_getNetworkSuid

getting the suid into an actual numeric

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Author: Robert M Flight <r.flight79@gmail.com>
Date: 2018-04-02 16:37:49 -0400
Commit message:

 getting the suid into an actual numeric


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-03-31 23:06:24 -0700
Commit message:

 docs are done!


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-03-31 14:31:50 -0700
Commit message:

 more docs


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-03-30 19:41:35 -0700
Commit message:

 bumped R req


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-03-26 21:03:58 -0700
Commit message:

 more tests


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-03-26 20:30:17 -0700
Commit message:

 fixed bioccheck warning


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Date: 2018-03-25 16:51:29 -0700
Commit message:

 upped version


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Date: 2018-03-25 16:50:22 -0700
Commit message:

 removed completed todo note

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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-03-25 16:08:28 -0700
Commit message:

 fixed doc error


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Date: 2018-03-25 15:53:17 -0700
Commit message:

 groups added and docs


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-03-25 13:39:49 -0700
Commit message:

 added diffusion and docs


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-03-25 13:24:19 -0700
Commit message:

 Merge branch 'master' of github.com:cytoscape/RCy3


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Date: 2018-03-25 13:24:16 -0700
Commit message:

 Added command and cybrowser, plus docs


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Commit message:

 adding travis widget

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Commit message:

 adding travis-ci


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Commit message:

 upped version


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Date: 2018-03-24 17:23:56 -0700
Commit message:

 A few minor fixes and tweaks


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Date: 2018-03-22 22:11:27 -0700
Commit message:

 adding tests


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Date: 2018-03-18 12:50:22 -0700
Commit message:

 updated all vignettes


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Date: 2018-03-18 12:15:35 -0700
Commit message:

 testing numbering of vignettes


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Date: 2018-03-18 12:11:03 -0700
Commit message:

 fixing installation for vignettes

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Commit message:

 fixing installation for vignettes

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Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2018-03-18 12:09:48 -0700
Commit message:

 fixing installation for vignettes

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Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2018-03-18 12:09:13 -0700
Commit message:

 fixing installation for vignettes

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Date: 2018-03-18 12:07:51 -0700
Commit message:

 fixing installation for vignettes

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Package: RCy3
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Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2018-03-18 12:03:48 -0700
Commit message:

 Update DESCRIPTION

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Date: 2018-03-18 12:02:00 -0700
Commit message:

 fixing installation for vignettes

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Date: 2018-03-18 11:53:34 -0700
Commit message:

 Update Cytoscape-and-igraph.Rmd

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Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2018-03-18 11:52:15 -0700
Commit message:

 add igraph dep

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Date: 2018-03-18 11:43:39 -0700
Commit message:

 Fixed other selection returns

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Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2018-03-18 11:40:46 -0700
Commit message:

 Fixed return for selectNodes

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Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2018-03-18 11:26:44 -0700
Commit message:

 Added alt app installation

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Date: 2018-03-18 11:18:48 -0700
Commit message:

 Update README.md

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Date: 2018-03-18 11:15:52 -0700
Commit message:

 Update README.md

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Date: 2018-03-18 11:12:42 -0700
Commit message:

 Update README.md

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Commit message:

 added updated repo mgmt


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 Merge complete


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 1.99.3; vignettes; docs; sync


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 0 errors | 0 warnings | 2 notes


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 more vignettes; pdfs


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 fixed indents

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 Update README.md

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 updated docs


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 more docs


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 cleanup of vignettes


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 another vignette, fixes and docs


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 another vignette and fixed commands parsing


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 more vignettes ready


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 importing data vignette is good; added networkImportFromFile()


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 intro vignette is good


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 major refactor; builds and checks


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 updated news with latest Milestone notes


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 Update README.md

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 bumping to build clean


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 0 errors | 0 warnings | 2 notes


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 finished refactor of StyleMappings


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 renamed defaults for consistency; docs


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 progress on refactoring StyleMappings


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 passes devtools::check()


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 Merge branch 'master' of github.com:cytoscape/RCy3


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 completed docs for apps


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 Update README.md

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 Update README.md

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 Update README.md

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 added version check for prerelease commands/api functions


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 more docs


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 more docs


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 more docs


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 All panel functions updated and doc'd


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 more docs


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 updated simple samples to all be the same


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 fixed and tested makeSimpleGraph and makeSimpleIgraph


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 utils cleaned and documented


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 cleaning up RCy3 package and utils


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 updated docs


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 added cool idmapper function!


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 docs and tweaked loadTableCol to catch pre-existing cols


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 all network create fxns work and preserve integers!


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 graph to/from network working via igraph!


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 create from DF and iGraph updated and tested


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-02-15 16:57:06 -0800
Commit message:

 minor tweaks


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Date: 2018-02-15 16:54:19 -0800
Commit message:

 createSubnetwork updated and tested


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Date: 2018-02-14 23:31:10 -0800
Commit message:

 first set of Groups functions


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Date: 2018-02-14 23:30:46 -0800
Commit message:

 new util function and start on createSubnetwork


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Date: 2018-02-14 21:46:12 -0800
Commit message:

 providing sample session for openSession(); improved messenging


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Date: 2018-02-14 21:36:50 -0800
Commit message:

 fixed network and view export and session save as


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Date: 2018-02-14 21:36:15 -0800
Commit message:

 fixed base.url arg in all app fxns


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Date: 2018-02-13 22:42:22 -0800
Commit message:

 4 new fxns for Collections


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Date: 2018-02-13 17:21:52 -0800
Commit message:

 13 new app management functions!


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Date: 2018-02-13 17:06:54 -0800
Commit message:

 fixed importFrom and typos


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Date: 2018-02-13 12:00:18 -0800
Commit message:

 Update DESCRIPTION

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Commit message:

 Update LICENSE

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Date: 2018-02-11 23:47:51 -0800
Commit message:

 Add support for loading integer data values


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Date: 2018-02-11 23:25:34 -0800
Commit message:

 getTableColumns now preserves integers and longs; new column type fxn


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Date: 2018-02-11 22:38:37 -0800
Commit message:

 Simplified table fxns and tested


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Commit message:

 more docs; converted some fxns to internal/utils


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Commit message:

 refined docs for suid and name getters


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Commit message:

 using new view suid function


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Commit message:

 more docs; new function for getting network view


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Commit message:

 more doc warnings fixed


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Commit message:

 more doc warnings fixed; updateStyleMappings fixed


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Commit message:

 Passes CHECK... with tons of warnings


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Commit message:

 Updated maintainer list


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Commit message:

 updated maintainer list


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-02-09 18:49:11 -0800
Commit message:

 docs; updated dep and bypass functions; improved error handing/reporting in cyrest and cmd calls


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Date: 2018-02-09 11:00:21 -0800
Commit message:

 added view param per lastest fixes from Scooter


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Commit message:

 organized and doc'd


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Date: 2018-02-08 21:38:38 -0800
Commit message:

 fixes to style getters/setters


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Commit message:

 tweaks to bypass options for style settings; docs


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Commit message:

 minor fixes


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Commit message:

 massive rewrite of styles; new functions; lots of new docs


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Commit message:

 replaced all objects and methods


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Commit message:

 docs and formatting for Networks


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Commit message:

 minor fixes


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Date: 2018-02-07 21:05:49 -0800
Commit message:

 minor fixes


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Commit message:

 addGraphToGraph-defunct; addCyNodes; addCyEdges; docs


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Commit message:

 Tables done; started on addGraphToNetwork; more docs and formatting


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Commit message:

 doc skeletons inserted


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Commit message:

 formatted code; documented sections


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Commit message:

 StyleDirects done


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Commit message:

 StyleDefaults done


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Commit message:

 Main Styles done; added StyleDeps


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Date: 2018-02-04 12:56:32 -0800
Commit message:

 Sessions done


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Date: 2018-02-04 12:10:14 -0800
Commit message:

 cleaned up utils... a bit


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-02-04 12:00:16 -0800
Commit message:

 NetworkViews done


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Date: 2018-02-03 23:53:19 -0800
Commit message:

 first pass on all methods in Networks


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Date: 2018-02-03 17:41:19 -0800
Commit message:

 upgraded cyrestX and commandsX methods


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Date: 2018-02-03 12:38:23 -0800
Commit message:

 progress on Networks; POST for commandRun working


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Commit message:

 implemented POST support for commandRun()


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Date: 2018-02-01 21:23:05 -0800
Commit message:

 progress through Networks


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Commit message:

 updated TODO lists and imports


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Commit message:

 Layouts done


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Commit message:

 continuing object-less refactor; more docs


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Commit message:

 swapping CytoscapeConnectionClass with default character string


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Commit message:

 updated deprecation link


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Commit message:

 completed CytoscapeSystem; roxygen based NAMESPACE


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Date: 2018-01-29 21:32:12 -0800
Commit message:

 more refactoring to match CyREST


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Commit message:

 tests pass


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Commit message:

 updated DESCRIPTION;bump to version 1.99.0


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Date: 2018-01-28 19:14:12 -0800
Commit message:

 reorg functions into CyREST chunks; more docs


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Commit message:

 more docs; updated description


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Commit message:

 Merge pull request #13 from cytoscape/add-license-1

Create LICENSE

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 Create LICENSE

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Commit message:

 Update README.md

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Commit message:

 Update README.md

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Commit message:

 Update README.md

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Commit message:

 added details regarding connection to bioconductor repo

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Commit message:

 more docs


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Date: 2018-01-26 16:18:39 -0800
Commit message:

 fixed getFirstNeighbors; cont docs and sep


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 begining docs and separate files; tests pass


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Commit message:

 new rstudio project file


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Commit message:

 Update README.md

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Commit message:

 Update and rename README to README.md

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Commit message:

 Additional deprecations; tests pass


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Commit message:

 restored getNodePosition to its former glory; refactored all remaining functions; cleared test


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Commit message:

 refactored and debugged save/restoreLayout


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Commit message:

 All "Direct" mapping functions now work with a CW


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Commit message:

 fixed null case


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Commit message:

 added support for style names with spaces


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Commit message:

 fixed style methods to handle spaces in style names


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Commit message:

 added support for continuous mapping via EdgeLineWidthRule; added another vignette


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Commit message:

 minor shuffling and notes


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Commit message:

 final vignette migrated and tested


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Date: 2018-01-14 19:48:33 -0800
Commit message:

 simplified a couple functions; tests pass!


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Date: 2018-01-14 19:24:51 -0800
Commit message:

 lots of merging; advanced cancer networks and data protocol works!


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Date: 2018-01-14 13:36:11 -0800
Commit message:

 udpated references to r2cytoscape


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Commit message:

 another r2cytoscape vignette cleared


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Date: 2018-01-14 13:09:34 -0800
Commit message:

 More merging; another vignette tested; started to update DESC


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Package: RCy3
Commit: f52e3ae75d5c497891da63d5a430e62c81750113
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-01-14 11:37:22 -0800
Commit message:

 runable vignettes and all tests pass


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-01-14 10:45:26 -0800
Commit message:

 updated unavailable layout alog referenced in vignette


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-01-14 10:08:05 -0800
Commit message:

 completed deprecations so far


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Commit: d84eb0e1e61572638f2d7be19a21499e464d1748
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-01-13 20:47:41 -0800
Commit message:

 started to include supported deprecations


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-01-13 20:35:10 -0800
Commit message:

 progress on merge... tested


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Commit: 49200283e9e1271ec4ec24ed361af7d48fb5b338
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-01-13 19:55:17 -0800
Commit message:

 updated handling of obj in rename fxn


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-01-13 19:03:21 -0800
Commit message:

 progress on merge...


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Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-01-13 18:06:40 -0800
Commit message:

 initial work to merge with r2cytoscape


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Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-10-30 12:54:16 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch


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Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-10-30 12:41:08 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch


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Package: RCy3
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-12 22:34:19 -0700
Commit message:

 update CITATION

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-12 22:29:28 -0700
Commit message:

 Add setDefaultEdgeLineStyle

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Package: RCy3
Commit: b619dfdb04e303e2621503d7920236abb28e95fe
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 22:55:54 -0700
Commit message:

 update description

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Package: RCy3
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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2017-06-11 22:21:13 -0700
Commit message:

 avoid overwriting of function c() by variables named c


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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2017-06-11 22:01:03 -0700
Commit message:

 create new function setDefaultEdgeLineStyle


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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 21:36:26 -0700
Commit message:

 update NEWS with current improvements

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 21:32:20 -0700
Commit message:

 Create setDefaultEdgeLineStyle.Rd

Former-commit-id: 4ce7bf0f138f18e1b8989bbe0775910d03df2da6
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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2017-06-11 18:00:06 -0700
Commit message:

 rule-based functions have an extra parameter for the visual style


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Date: 2017-06-11 17:57:06 -0700
Commit message:

 setNodeTooltipRule for different visual styles

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:57:02 -0700
Commit message:

 setEdgeTooltipRule for different visual styles

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Date: 2017-06-11 17:54:59 -0700
Commit message:

 setEdgeLabelRule for different visual styles

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Date: 2017-06-11 17:53:05 -0700
Commit message:

 setNodeLabelRule for different visual styles

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:49:47 -0700
Commit message:

 setEdgeSourceArrowColorRule for dif visual styles

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Date: 2017-06-11 17:47:44 -0700
Commit message:

 setEdgeSourceArrowRule for different visual styles

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Date: 2017-06-11 17:46:21 -0700
Commit message:

 setEdgeTargetArrowRule for different visual styles

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Date: 2017-06-11 17:44:08 -0700
Commit message:

 setEdgeTargetArrowColorRule for dif visual styles

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Date: 2017-06-11 17:41:49 -0700
Commit message:

 setEdgeLineWidthRule for different visual styles

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:38:59 -0700
Commit message:

 apply setEdgeLineStyleRule to a visual style

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Date: 2017-06-11 17:35:54 -0700
Commit message:

 apply setEdgeOpacityRule to a visual style

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:33:02 -0700
Commit message:

 apply setEdgeColorRule to a particular style

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:30:29 -0700
Commit message:

 apply setNodeSizeRule to a particular style

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:27:30 -0700
Commit message:

 Create setNodeShapeRule.Rd

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:22:35 -0700
Commit message:

 Create setNodeBorderWidthRule.Rd

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:19:25 -0700
Commit message:

 Create setNodeBorderColorRule.Rd

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:16:33 -0700
Commit message:

 Create setNodeOpacityRule.Rd

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Package: RCy3
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:14:12 -0700
Commit message:

 add vizmap.style.name = 'default'

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Package: RCy3
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-06-11 17:03:11 -0700
Commit message:

 Create setNodeColorRule.Rd

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Package: RCy3
Commit: bbd24e8c1080ea36ceeca6b4b1a5ccd871bfd564
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2017-06-11 16:45:20 -0700
Commit message:

 support boolean for edge attributes


Former-commit-id: 5e762b09cd0e1df9d6be334b6c274460180e5f0b
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Package: RCy3
Commit: 3f0f191e87276d666aab1d633bca47bf98c3470e
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2017-06-11 16:42:38 -0700
Commit message:

 update data types for node and edge attributes when copying from Cy graph


Former-commit-id: 5e67b387d4ca5a8d310709f561c81ab624ec0a0f
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Package: RCy3
Commit: 2027b00b51cd7f8d5564de96a8fb80982a8e9793
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2017-06-06 23:29:20 -0700
Commit message:

 bug fix: missing support for boolean in initNodeAttribute; additional support for Java Long datatypes


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Package: RCy3
Commit: 506fdd700bc4aea38afcbe2b9df07b868cd42d26
Author: Herve Pages <hpages@fhcrc.org>
Date: 2017-04-24 19:50:57 +0000
Commit message:

 bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

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Package: RCy3
Commit: 6cc8a79150500eea4448eeddb3b25605ac65ddbb
Author: Herve Pages <hpages@fhcrc.org>
Date: 2017-04-24 19:25:24 +0000
Commit message:

 bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

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Package: RCy3
Commit: 4e23bdf8cac5cfe674e7403cf91f687740a8a1c2
Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2017-01-06 05:07:31 +0000
Commit message:

 bug fix: url format in vignette

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@125719 bc3139a8-67e5-0310-9ffc-ced21a209358

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Package: RCy3
Commit: 1d78c1b3f601c0f6eb9aa008498fc4c4cc80addc
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2017-01-03 00:10:45 -0800
Commit message:

 Update DESCRIPTION

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Package: RCy3
Commit: 43abc12f2430b48cd946ad07ce550ebdaa1f67e7
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2017-01-03 00:09:40 -0800
Commit message:

 add \url around url in vignette and remove pdf


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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-28 16:55:47 +0000
Commit message:

 add Julia s vignettes

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-28 09:53:58 -0700
Commit message:

 update version number and cyREST min version req

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Author: Herve Pages <hpages@fhcrc.org>
Date: 2016-10-17 19:10:43 +0000
Commit message:

 bump x.y.z versions to odd 'y' after creation of 3_4 branch

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Author: Herve Pages <hpages@fhcrc.org>
Date: 2016-10-17 18:45:06 +0000
Commit message:

 bump x.y.z versions to even 'y' prior to creation of 3_4 branch

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Package: RCy3
Commit: 43367aa05702db47a5e7d4c90af4854392fc44f5
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-16 22:08:54 +0200
Commit message:

 fixed some errors found by Tanja and R Cmd check.


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Commit: bb44cb2a62247b732e69de59a4d1e9d117c79f29
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-15 10:16:08 -0700
Commit message:

 Merge pull request #39 from tmuetze/potential_vignettes

Julia's additional vignettes (examples and use cases)

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Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-15 13:59:32 +0200
Commit message:

 added in data needed for co-occurence data vignette.


Former-commit-id: a490aae8dba26eefd0a4bbf7c12eac6983defbba
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Commit: bd36a2e0d2ff80aa18bc77e9be1047a6834c1a6f
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-15 13:59:10 +0200
Commit message:

 set paxtoolsR vignette chunks to eval = FALSE


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Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-15 13:57:32 +0200
Commit message:

 added paxtoolsr vignette


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Commit: 234fe98bd86d5091ae6c7082df77282238e734d9
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-15 13:52:41 +0200
Commit message:

 set chemviz chunks to eval false


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Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-15 13:51:26 +0200
Commit message:

 adding chemviz vignette


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Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-15 13:45:12 +0200
Commit message:

 co-occurence vignette chunks set to eval=FALSE.


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Commit: 88ec271e115ba49470dacdef620b3a452ef765cd
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-15 13:43:18 +0200
Commit message:

 added co-occurrence network vignette for perusal.


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Commit: 9f2f3c5d6a0d75bf491a6794dabdb4f5b6115f84
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-10-15 13:42:10 +0200
Commit message:

 Added new functions and wrapped all roxygen examples in dontrun.


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Package: RCy3
Commit: 3e6781b5b215250637ca9527faa3bdccb8b91348
Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-13 20:22:58 +0000
Commit message:

 correct mistake \dontrun

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@122389 bc3139a8-67e5-0310-9ffc-ced21a209358

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Commit: 9930cdba08f6d9c89f28544028e5192be68b51da
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-13 13:20:24 -0700
Commit message:

 update version


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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-13 13:18:40 -0700
Commit message:

 bug fix: escape dontrun


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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-13 12:15:06 -0700
Commit message:

 Update DESCRIPTION

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-13 16:38:11 +0000
Commit message:

 remove .BBSoptions to allow build on Mac and Windows and update version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@122376 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-13 01:16:50 +0000
Commit message:

 remove old files

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-13 01:06:17 +0000
Commit message:

 disable code execution on build system

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@122335 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-12 17:37:08 -0700
Commit message:

 disable code execution of man pages on build system


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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-12 17:33:13 -0700
Commit message:

 Update deleteSelectedNodes.Rd

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-12 17:32:54 -0700
Commit message:

 Create selectAllNodes-CytoscapeWindowClass-method.Rd

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Commit: 67bc83454407534920e0313a241cb92116293df3
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-12 17:32:39 -0700
Commit message:

 Update selectAllEdges-CytoscapeWindowClass-method.Rd

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-12 17:31:40 -0700
Commit message:

 add keyword graph

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-12 17:25:25 -0700
Commit message:

 add keyword graph

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Commit: 446ce1126daa0b03638ae6ba155e35fe8dfab37a
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-10-12 16:27:37 -0700
Commit message:

 disable code execution of tests and vignette on build system


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Commit: a0c156e63daba96b7eda61933eb9f8ce02661adb
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-12 16:20:32 -0700
Commit message:

 Update DESCRIPTION

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Commit: 0adc54a7ea140317d3b3c35f24f7fd277b947455
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-12 16:19:52 -0700
Commit message:

 update version and email

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Package: RCy3
Commit: 4d548ac5c362a9eb75f59a8a34944dfa23a5b61c
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-10-12 14:24:07 -0700
Commit message:

 Merge pull request #37 from tmuetze/image_scaling

Removed scale argument and added h to saveImage function.

Former-commit-id: fd87d1def6b1373e209639b39b7ed93631a24e5b
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Package: RCy3
Commit: 70e76d82027410f3094896e1f0fb3fd050a49a22
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-08-16 09:17:43 +0200
Commit message:

 Removed scale argument and added h to saveImage function.

The scale argument is not an option for resizing images using cyREST so it was removed. For images of type 'png' there is an option to set the height of the image and this argument was added for pngs. Closes #35


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Package: RCy3
Commit: d5fd385bc1ebbd5f2ab904d6c0574b36cf9da35d
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-08-04 14:09:57 -0700
Commit message:

 Merge pull request #31 from tmuetze/selecting_and_copying

Functions for selection and for copying

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Package: RCy3
Commit: b8237ee0bd31747091006ea703a37d6032f68100
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-08-04 14:47:16 +0200
Commit message:

 functions to copy and rename networks in Cytoscape.


Former-commit-id: f28d84a34466c975d6cb07815488fd45426e6d65
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Package: RCy3
Commit: abe7855bab5a093bac6c66ec311484a4569e7064
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-08-04 14:40:35 +0200
Commit message:

 added functions that allow the selection of all nodes and of all edges in a Cytoscape network.


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Package: RCy3
Commit: 37d5390ddc547d684231de5079f59a797269b912
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-07-28 13:49:12 -0700
Commit message:

 update version

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Package: RCy3
Commit: 1af76fb881cb933b691c4e49722f52f665c090a1
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-07-27 17:17:48 -0700
Commit message:

 add to commit ce3ddb001cc102a540095f34945db28e8f0bed0f [formerly 4143f6f9699825fc849fe16e09c1c4d82715859f] [formerly 630deb424d464f1da0ae49c45a89afd8a8be2f06]: no parentheses in getGraphFromCyWindow


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Package: RCy3
Commit: ce3ddb001cc102a540095f34945db28e8f0bed0f
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-07-27 16:50:55 -0700
Commit message:

 add warning if nodes have parentheses when copied over from an existing window


Former-commit-id: 630deb424d464f1da0ae49c45a89afd8a8be2f06
Former-commit-id: 4143f6f9699825fc849fe16e09c1c4d82715859f

Package: RCy3
Commit: d612929f3ba6a9e454b10f85b8232458aa1f4965
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-07-13 12:27:12 -0700
Commit message:

 update documentation for permissible filetypes

Former-commit-id: 1b5111cf3ee6d19f06fb56ad45307b83fa050218
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Package: RCy3
Commit: ffc6cc92b4753297651230036c16ec65f83c80ad
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-07-08 18:24:27 -0700
Commit message:

 remove hard coded fix to cyREST bug after recent CyREST bug fix in setEdgeLineWidthRule


Former-commit-id: 3dd3535e1ca4107eae31ba113acc2eec53a6a652
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Package: RCy3
Commit: e4f550b990bdf26207e6ef53546014df5c5781d4
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-07-08 16:58:02 -0700
Commit message:

 add checks for color formats


Former-commit-id: 20f6d69dc5cb80b424c709c62586d46a91af1fa1
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Package: RCy3
Commit: 5ea387ac16fd6cc9c1d31c96fa5f1eee5410cfef
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-07-08 16:18:09 -0700
Commit message:

 Update setNodeColorRule.Rd

Former-commit-id: 698e676202c35813b2f0354183001617baab73b5
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Package: RCy3
Commit: 09bcd2bb10a0587e2ac2c5354f5e4e63abc35d50
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-07-06 18:36:11 -0700
Commit message:

 move color formatting check into separate function


Former-commit-id: 3887a19c5f4574aeeeb39d9d8178a67f5b2f81ba
Former-commit-id: e85ac40fc8968e0c9168e38e5da37059160d85f9

Package: RCy3
Commit: a4567edbe01d65783a79808222eb8ba590d844cb
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-07-06 16:30:47 -0700
Commit message:

 bug fix: check if color is a hex in setDefaultBackgroundColor


Former-commit-id: 793fe27471a2a61947fbbf1d0248bf42a1956bb8
Former-commit-id: f9068785ef5f2c9fa10586835bb1a6b53310e1e2

Package: RCy3
Commit: 3f4590c975d074de9fd90e676876e1468654fa6f
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-06-29 14:14:47 -0700
Commit message:

 Merge pull request #27 from tmuetze/cyplot_fix_idea

Fixing issue with cyplot and nodes without attributes

Former-commit-id: 66f46587f48e5a3196c471ef24e5d52f0c574f6c
Former-commit-id: a323eca1d4325aabec497aba87e1d5f3a6c2f716

Package: RCy3
Commit: ae6d4909466ad9dffb4c99a3b4037a80ff19e2f4
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-06-29 11:27:43 +0200
Commit message:

 incorporated changes from @m-grimes cyplot.2 function into my proposed cyplot() function


Former-commit-id: 845467f92fb08d9457c27f3b67dbba48a1589e2d
Former-commit-id: 636d24a305f7705356dd07e997a085896d4efd1e

Package: RCy3
Commit: f74e8a7d08bfcb723398ac25a8940e75048387b9
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-06-29 10:27:46 +0200
Commit message:

 add github page and issues to Description


Former-commit-id: e6c3e89098a5539bea7e4a2402312331ee52f674
Former-commit-id: 44d26c9f33c28a193deda3860f236dcc434d2836

Package: RCy3
Commit: ee52b811fc4b46dc6a77e25f44bebc9f4c33ec0d
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-06-27 15:48:53 +0200
Commit message:

 For cyplot, dealing with cases where edge table is only a list of edge connections.


Former-commit-id: ba609966f2dbc548074037f7f645f3c0f3e67c5d
Former-commit-id: d5ae69fa179b2915de06a7f62b8c8fde3a2cfcef

Package: RCy3
Commit: a3ee7e3ac0eadb895a8701d6a4f7c3501cbe8c93
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-06-27 15:19:24 +0200
Commit message:

 Fixing issue with cyplot and nodes without attributes

Attempted to fix behaviour cyplot when nodes do not have any attributes. Only adds the attributes if there are more than 1 columns in the node table.


Former-commit-id: a32e4c55b52b45f57c83d3927baa793067aae0c7
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Package: RCy3
Commit: aa94af49fda88424ba90bb4cce4a0e90d29eb2ae
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-06-23 15:16:49 -0700
Commit message:

 ensure user provides color as hex code in setDefaultBackgroundColor


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Package: RCy3
Commit: 891fda00015a5b281cdda96693b6a20751358396
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-06-20 23:01:43 -0700
Commit message:

 Merge pull request #26 from tmuetze/help_docs

Added package help file. More info to be added soon.

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Package: RCy3
Commit: 0e04f81ab6f9da56acea1ff62c362c83e88714eb
Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-06-17 16:18:20 +0200
Commit message:

 Added package help file. More info to be added soon.

Generated via roxygen2 and devtools::use_package_doc()


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Package: RCy3
Commit: 21f53bd680085fece8eabc7122e95fc6a703b78a
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-05-24 07:41:19 +0930
Commit message:

 Merge pull request #23 from tmuetze/develop_typo_fixes

small change to quotation characters in vignette

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Author: Julia Gustavsen <j.gustavsen@gmail.com>
Date: 2016-05-23 13:27:54 -0700
Commit message:

 changed quote characters so that they reflect forward and backward quotes in latex


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Author: Dan Tenenbaum <dtenenba@fhcrc.org>
Date: 2016-05-03 21:30:44 +0000
Commit message:

 bump version after creating 3.3 branch


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Author: Dan Tenenbaum <dtenenba@fhcrc.org>
Date: 2016-05-03 21:20:18 +0000
Commit message:

 Bump versions prior to creation of 3.3 branch


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Dan Tenenbaum <dtenenba@fhcrc.org>
Date: 2016-04-05 23:59:08 +0000
Commit message:

 mark as unsupported on non-linux


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@115846 bc3139a8-67e5-0310-9ffc-ced21a209358

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Commit: e8a998fde3b8c6f59e2183a27f63d1505ea9386b
Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-04-03 23:39:24 +0000
Commit message:

 clarify message for lockNodeDimensions function and update version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@115709 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-04-04 09:08:37 +0930
Commit message:

 update lockNodeDimensions message


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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-04-04 09:07:59 +0930
Commit message:

 Update DESCRIPTION

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-04-03 23:37:18 +0000
Commit message:

 clarify message for lockNodeDimensions function

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@115708 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-04-02 21:43:24 +1030
Commit message:

 Update lockNodeDimensions.Rd

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-23 11:52:32 +0000
Commit message:

 update version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@115164 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-23 22:21:09 +1030
Commit message:

 update version

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-22 00:17:59 +0000
Commit message:

 outcomment all tests

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@115083 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-21 23:32:07 +0000
Commit message:

 outcomment test.zoom as it times out

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@115081 bc3139a8-67e5-0310-9ffc-ced21a209358

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Package: RCy3
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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-18 14:41:55 +1030
Commit message:

 out comment all tests


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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-18 14:42:08 +1030
Commit message:

 update version

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-17 22:58:06 +0000
Commit message:

 outcomment a few tests to avoid timeout of the Bioconductor build system

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@114940 bc3139a8-67e5-0310-9ffc-ced21a209358

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Package: RCy3
Commit: 3d34c27f22a5936cc9a931a4b85c9c554d7952bd
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-18 09:21:39 +1030
Commit message:

 Update DESCRIPTION

Former-commit-id: 5aa5d21118769419d45f242bc062d211dbaf2fed
Former-commit-id: cfca73caed143721dc51f3ef79e1439e8b199ab7

Package: RCy3
Commit: 845477005788decf5d71b11aba927ac46d5be06a
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-18 09:18:38 +1030
Commit message:

 out comment a few tests to avoid time out on the Bioconductor build system


Former-commit-id: c94e5318648bd209ac5752b07c59cc7d1fa4e847
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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-14 22:20:32 +0000
Commit message:

 outcomment test that times out on the Bioconductor build system

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@114764 bc3139a8-67e5-0310-9ffc-ced21a209358

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Package: RCy3
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-15 08:48:46 +1030
Commit message:

 Update hideSelectedEdges.Rd

Former-commit-id: 69feb60115ab92e039d1d793b65ab972ed49c16e
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-15 08:47:00 +1030
Commit message:

 Update DESCRIPTION

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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-15 08:46:05 +1030
Commit message:

 out comment test that fails on Bioconductor build system


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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-10 23:56:39 +0000
Commit message:

 undo versions behind packages

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@114629 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-11 10:24:21 +1030
Commit message:

 Update DESCRIPTION

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-11 10:22:58 +1030
Commit message:

 Update DESCRIPTION

Former-commit-id: b0552a0df929c2d504d6d320eecf87fde3527353
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-11 10:21:40 +1030
Commit message:

 Update DESCRIPTION

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 11:33:55 +1030
Commit message:

 Update hideSelectedEdges.Rd

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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-10 11:06:55 +1030
Commit message:

 update test.unmatchedAttributesError


Former-commit-id: 7bdbf936d4559c4a4f0056c43d1e86ffe57a64b7
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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-10 00:23:06 +0000
Commit message:

 update package version requirements

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@114576 bc3139a8-67e5-0310-9ffc-ced21a209358

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 10:51:15 +1030
Commit message:

 Update DESCRIPTION

Former-commit-id: 7c324aa13e82ecec1be3a684da13ef362bda976a
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 10:50:23 +1030
Commit message:

 Update DESCRIPTION

Former-commit-id: d7af09bbde0c65de12ffdd7855f884ca63a8ea4d
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 10:48:49 +1030
Commit message:

 Update DESCRIPTION

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Author: Tanja Muetze <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-09 23:13:23 +0000
Commit message:

 fix bugs and remove some tests to increase speed

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RCy3@114565 bc3139a8-67e5-0310-9ffc-ced21a209358

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Package: RCy3
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Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-03-10 09:28:45 +1030
Commit message:

 change tests and add TODO for setNodeImageDirect


Former-commit-id: a37bf3d78c82e2c0ea104e1f25068ad4ec965a53
Former-commit-id: a250b5094d6550baf3754bb8b6cc4227ab8e6844

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 09:28:05 +1030
Commit message:

 Update DESCRIPTION

Former-commit-id: 8b18e1188b3d1118bc72bb488fe5b5eed90bf289
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 09:19:25 +1030
Commit message:

 Update setEdgeLabelColorDirect.Rd

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 09:18:24 +1030
Commit message:

 Update hideSelectedEdges.Rd

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 09:16:43 +1030
Commit message:

 Update setEdgeOpacityDirect.Rd

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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 09:15:33 +1030
Commit message:

 Update getGraphFromCyWindow.Rd

Former-commit-id: ac14e1acb0165475a2788fa63e01c9b47d26b107
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 09:14:27 +1030
Commit message:

 Update setCenter.Rd

Former-commit-id: 39c2d9ade00f53e1b700368a5025377782569c3e
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 09:10:46 +1030
Commit message:

 Update setVisualStyle.Rd

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Package: RCy3
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Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-03-10 09:03:44 +1030
Commit message:

 Update setEdgeLabelColorDirect.Rd

Former-commit-id: c2325890f80ae9f3772008380bf6e162759a1efa
Former-commit-id: 89bf996d08eaf251c605ab33483d0cf0b5aa1d8b

Package: RCy3
Commit: 11d8896e616a88968861907dc892c3b368508f75
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-11 12:27:37 -0800
Commit message:

 Update setNodeImageDirect.Rd

Former-commit-id: 18c29ee0a2e3802a5af1fbab33308ae128674710
Former-commit-id: db473cbe0c7a8286d4d6949a589890a3ddf95ca3

Package: RCy3
Commit: 230a8cbdb7bbcbe8e7d7345b69f188431e5dafaf
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-02-11 11:44:44 -0800
Commit message:

 incomment setNodeImageDirect


Former-commit-id: bfc30870077ddf8a6d2f07271cf05b91485e1164
Former-commit-id: b3a2ee2f0c64003abaa1344e8a25778b5ad7d60e

Package: RCy3
Commit: 6e02e09fd06dbe691f8476e55239f18d9b6e1d55
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-11 11:35:51 -0800
Commit message:

 node position rather than image url

Former-commit-id: f4afe8dd1dc3aae7c3f623cdbac7e2efe0fd62af
Former-commit-id: 9667a9093eb2d7f1fb90210b297aed09e0839881

Package: RCy3
Commit: 800257389c403cf3e06710af652dffd0201a785c
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-11 11:18:06 -0800
Commit message:

 Update DESCRIPTION

Former-commit-id: 2e992d07be7a6266a99187d89fd05bad10a5cb2c
Former-commit-id: 839f01a04539f1e6611918150d9f9a3aa611aece

Package: RCy3
Commit: 7a9f7302839318d0b192f1ab810284e49d07a6fd
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-02-11 10:33:19 -0800
Commit message:

 mark setNodeImageDirect as unimplemented


Former-commit-id: 61e19193f433d6e542da55bf3e910ffbb5c8cd39
Former-commit-id: 527f3b30373eda9ef8960653190f230f428e8881

Package: RCy3
Commit: 770e7c423fedb0d6f5d8c5b7bb63b03c7a21c181
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-09 17:39:50 -0800
Commit message:

 Update RCy3.Rnw

Former-commit-id: e9158801214c02d00a291d71f7ca4b4d6410a355
Former-commit-id: 93e2bfd0c06348c2c49cb7d247ab988518553bb2

Package: RCy3
Commit: 2d0879c86e7307fdd2e626c964c237d92d8d97d6
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-02-09 17:38:21 -0800
Commit message:

 update vignette


Former-commit-id: 8349d30cdc2395235a5682cc5fe59ba7c4eba29b
Former-commit-id: f650037b67dfe463acf17280aae9fcf7297a8ef9

Package: RCy3
Commit: ca734c9b1479a59c7b56b47cd99fd8a7447529c4
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-09 17:16:29 -0800
Commit message:

 update installations

Former-commit-id: f3942206c4e90c10a60f69690811443476770f0a
Former-commit-id: ab1d7974b72b770be56979b4afc19e582e48a112

Package: RCy3
Commit: d521dcda8f43754c91409f6379e4935936d68fad
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-09 17:15:36 -0800
Commit message:

 Delete README.md

Former-commit-id: b80a82eead3cdf7da42c95a8ebb00df7cfbcda17
Former-commit-id: 1cc036df49c7fffff9bc528bd2379e42485dcf7f

Package: RCy3
Commit: ea7216892af73025ed33e4cf627d649c45919d20
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-02-08 00:59:57 -0800
Commit message:

 spacing


Former-commit-id: a01f27077982c863b6bf30320ea429965e83a01d
Former-commit-id: d7e2b267748c7c92a6e5fc66e25835a71eed63ee

Package: RCy3
Commit: fe1be2e278a06fb7c9f7cd856f6b26c9c0a6739a
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-07 12:42:37 -0800
Commit message:

 Update DESCRIPTION

Former-commit-id: 932c06b7d25dbe96487cc7a59475e9aee5ff5a1a
Former-commit-id: 8e7cf0cd1b210cd312a16aa9faa71dec4272eb77

Package: RCy3
Commit: 16da3756221ac3daa66d28b11e1dd79229b52cb9
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-02-07 12:41:21 -0800
Commit message:

 spacing


Former-commit-id: 326256247126164b904dcd013974a9538dafae8f
Former-commit-id: c430d51022260f56eb15f04d6a556dc4b27f9dfb

Package: RCy3
Commit: 28dbd6bf7911156905182a501acb389503db9388
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-07 12:17:31 -0800
Commit message:

 Update DESCRIPTION

Former-commit-id: a8b96785c6931499f6140568b74f9c7c105cd655
Former-commit-id: 79905a87d70a23b934c42583f012d33e543b7ca9

Package: RCy3
Commit: dcd48062b8d913f7f0c21cabe0081a7291ef3d6d
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-02-06 18:37:19 -0800
Commit message:

 outcomment test.setEdgeLabelColorDirect


Former-commit-id: a6b13b8c8c93c4cc965846e03109ef77d6d1edac
Former-commit-id: bd32440855283790c3708e5c574d7f575c84a0b6

Package: RCy3
Commit: 57b24b5c1c0c3013b35b57f129402d9e74ad97fa
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-06 18:31:36 -0800
Commit message:

 required minimum version for RJSONIO

Former-commit-id: 9cdb24bc93cc623a49fe2d2a31468cb639327cd5
Former-commit-id: ca813d6108c7d0aed2b621ffef2a59417a6e6b45

Package: RCy3
Commit: 7fda9b27e8bcf7f20db2e9324b82a9924dc90799
Author: Tanja <tanja.muetze14@imperial.ac.uk>
Date: 2016-02-06 18:22:04 -0800
Commit message:

 getNodeAttributeNames requires a displayed graph


Former-commit-id: 6fd4201c60ed0cfcd99b962a24864441d1e1c00d
Former-commit-id: 3a0979d59dfef9ea31727cf93103c0b537b041ff

Package: RCy3
Commit: d1559366e33ea9e18c975e772957d8c8d5b2c5a2
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-06 18:15:42 -0800
Commit message:

 inform user to run displayGraph before

Former-commit-id: 6d68f5c3016e71680cca87896bed0fe816760116
Former-commit-id: 5b91cb63ef3a91d027bb9d446398dc14d847ab48

Package: RCy3
Commit: 6704ef7c6e33100dc423c7e475aede250a02b2b0
Author: Tanja <tmuetze@users.noreply.github.com>
Date: 2016-02-06 17:59:14 -0800
Commit message:

 correct typo: size instead of color

Former-commit-id: 75ac75cb4d841f2fc909840a9bfed7848ab817c6
Former-commit-id: e6e624eed90f563d9935a41ec5095850114efe86

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