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GIT Logs

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

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Package: Fletcher2013b
Commit: 88e87cc27f44ed2b095a8dbd6d60b57ceec32b39
Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2019-11-13 01:51:18 -0300
Commit message:

 regular maintenance
 
Package: RTNsurvival
Commit: 092ba1e54516ce2b1344f071d1334d77fd8f2675
Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2019-11-13 01:11:15 -0300
Commit message:

 regular maintenance
 
Package: RTNduals
Commit: 72bc86325031af06dc29e042430e8311c2bbb848
Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2019-11-13 01:00:31 -0300
Commit message:

 regular maintenance
 
Package: RTN
Commit: 4335bfb4854e4ea64dc8fcae13c0cbda30ee4247
Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2019-11-13 00:53:22 -0300
Commit message:

 regular maintenance
 
Package: ELMER
Commit: b5fddd7aedf9999f6fefec35c5bedc41803354f0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-11-12 21:11:31 -0500
Commit message:

 Bug fix
 
Package: RProtoBufLib
Commit: 6e2c023eabba9448af861815720e394bb6d3ad94
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 16:00:43 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: RProtoBufLib
Commit: d7242715641ba41b0de56e4d0a8789e55ba84543
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 16:00:29 -0800
Commit message:

 bump
 
Package: RProtoBufLib
Commit: 3d37d34753b2190b0e90d2affff8453de480f65b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 15:12:45 -0800
Commit message:

 fix ldflags
 
Package: RProtoBufLib
Commit: 6f4f8a81993b287ee297a278fa0896f473cd6c72
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 15:05:36 -0800
Commit message:

 skip loading dll for win
 
Package: RProtoBufLib
Commit: c86dd93a251ab443ec7900fc9b1799aacdf44e10
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 14:59:14 -0800
Commit message:

 update binaries for win. #8
 
Package: RProtoBufLib
Commit: 00e67268a64b910b5c34e40a12eb045908f06914
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 10:57:32 -0800
Commit message:

 up doc
 
Package: RProtoBufLib
Commit: 381864654ee55f3924bb419e8377d8fbdea68041
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 10:56:00 -0800
Commit message:

 rm reference to gsLib
 
Package: TCGAutils
Commit: a0a7e3232fe9bce89eb34dad04927835279cf70b
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-11-12 18:33:52 -0500
Commit message:

 version bump
 
Package: TCGAutils
Commit: a714a79f42f486500290b4d9aed855abaf116081
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-11-12 18:33:29 -0500
Commit message:

 update uniformBuilds, add more tests
 
Package: TCGAutils
Commit: 87c1e9cf0ece6c5e508330cde55b86bfeeb6e14a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2019-11-11 15:06:45 -0500
Commit message:

 bug fix: check builds with single value
 
Package: cytolib
Commit: e4848436085ff2625c3c3eb0824e471db3f7033f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-12 10:17:14 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: cytolib
Commit: ac2b1730bd306389d8bd9947e950b9e2218d67ef
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-10 17:08:39 -0800
Commit message:

 bump
 
Package: cytolib
Commit: e63c8d6b9f84d5774988978125bcdee1fb8688de
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-10 17:08:12 -0800
Commit message:

 rename pb::QUAD to pb::QUADRANT to avoid conflict with QUAD_MIN from clang4.0
 
Package: cytolib
Commit: 4353ae7ac54c2fd1fad0e8a67a002be1bda58ec2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 15:45:22 -0800
Commit message:

 resize the tar file to meet bioc rules
 
Package: tximeta
Commit: 37bcd638b687b396459198987a68ab7594474eae
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-11-12 13:00:31 -0500
Commit message:

 attempting to fix linkedTxome for Salmon 1.0
 
Package: cliqueMS
Commit: 9368dc610a85ea2a757cd3620080f1f6dcdcdff2
Author: osenan <oriol.senan@praenoscere.com>
Date: 2019-11-12 18:48:21 +0100
Commit message:

 Bug fix: error in defineEIC when the feature had only 2 elements
 
Package: MTseeker
Commit: 44c09b940acfeef092fc2a4820667ef3a9236774
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-12 11:29:23 -0500
Commit message:

 haplogrep jar is > 5MB, deleting
 
Package: MTseeker
Commit: afb0e4a9a207f67e7c638c793492798f37c0c48e
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-12 11:28:12 -0500
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/MTseeker
 
Package: MTseeker
Commit: 430644479991b779046b1d4fae920a20d5473363
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-12 11:25:56 -0500
Commit message:

 merging
 
Package: MTseeker
Commit: 66e4d3e8844d167daf93342e53168498d690726c
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-12 11:25:32 -0500
Commit message:

 merge
 
Package: MTseeker
Commit: 81325fe1d17bea6ba43325419ada3ef40235bdc6
Author: ttriche <tim.triche@gmail.com>
Date: 2019-11-12 11:21:21 -0500
Commit message:

 updates and cleanups for BioC 3.10 and 3.11
 
Package: MTseeker
Commit: 62e03e672141012b24b64e29c45953e658589c9a
Author: Tim Triche, Jr <tim.triche@gmail.com>
Date: 2019-07-22 09:49:05 -0400
Commit message:

 Merge pull request #39 from nsohail19/master

LGTM -- will see if it conflicts with the pileup changes later today.  Updating vignette and adding some unit tests for pileup (indels, calls, timing, etc.) should help too.  Eventually this needs to go into Travis or CircleCode (whatever Casey uses) so that reviews can be a little better automated.  Also Coveralls. 
Package: MTseeker
Commit: 9a231dcb06de99b1c7451e6795ebef486c84c0f6
Author: nsohail19 <koheenur@gmail.com>
Date: 2019-07-22 08:51:53 -0400
Commit message:

 fixed codonEnd
 
Package: MTseeker
Commit: ed278fa4af0fc72e2d201c2ce573d0fc3f8b4a1a
Author: nsohail19 <koheenur@gmail.com>
Date: 2019-07-21 22:16:46 -0400
Commit message:

 deals with overlapping gene deletions
 
Package: MTseeker
Commit: c643e969a6c2305a9f20d59bcc69b6b080daf1c3
Author: nsohail19 <koheenur@gmail.com>
Date: 2019-07-20 21:32:06 -0400
Commit message:

 plot single sample slowly
 
Package: MTseeker
Commit: b6892725ea61a84de1c577d08458db8ce1ef98ff
Author: nsohail19 <koheenur@gmail.com>
Date: 2019-07-19 10:05:45 -0400
Commit message:

 merging
 
Package: MTseeker
Commit: ea91022f8e71d75a39e023c8fce21967e5b34583
Author: ttriche <tim.triche@gmail.com>
Date: 2019-07-15 12:02:44 -0400
Commit message:

 pileupMT proto-support for indels (see warning message)
 
Package: MTseeker
Commit: 24fbb64442128d6d5d52b9aa8c4998f1fb7c2705
Author: ttriche <tim.triche@gmail.com>
Date: 2019-07-10 15:13:30 -0400
Commit message:

 fix pileupMT helper, bump version
 
Package: MTseeker
Commit: f6e47789414e5541d49a0e9929c76b49dbf808c7
Author: ttriche <tim.triche@gmail.com>
Date: 2019-07-10 15:11:12 -0400
Commit message:

 bump version
 
Package: MTseeker
Commit: 10c8aa8b8bf0b7734cdd3d2fc1fbd0d773a98e26
Author: ttriche <tim.triche@gmail.com>
Date: 2019-07-10 15:10:18 -0400
Commit message:

 fix seqlengths helper
 
Package: MTseeker
Commit: f43c6a77b1165fc366a280c1761fde3114f13366
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-07-08 16:33:21 -0400
Commit message:

 Merge pull request #38 from biobenkj/master

sync up dev branch 
Package: MTseeker
Commit: 1c39800ade19c6f270d25b954ae0ef301f3caf2f
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-06-19 16:19:59 -0400
Commit message:

 update vignette
 
Package: MTseeker
Commit: 78b6ee516c9b106547142a8efc26183079de79ea
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-06-19 15:37:44 -0400
Commit message:

 add an option to specify a java path
 
Package: MTseeker
Commit: d07a853025c748757e426bf8bb00897f83a3fa5f
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-23 11:42:30 -0400
Commit message:

 add a VCF export method for convenience
 
Package: MTseeker
Commit: 8bdd41a8858bbcc410ef10c3944e38edd43b86be
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-23 11:27:59 -0400
Commit message:

 fix HGVS names after any filtering operation
 
Package: MTseeker
Commit: af83c79676539285660c87322e02a19f9e7215dd
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-23 11:26:06 -0400
Commit message:

 fix a very stupid typo in filterMTvars!
 
Package: MTseeker
Commit: d22f80eb28d069d189c52c287e33e7e1f6cf6602
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-23 11:23:20 -0400
Commit message:

 housekeeping for pileupMT and downstream filterMTvars
 
Package: MTseeker
Commit: 537b2bfad98306363110e8374c969daa6161075f
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-23 11:15:45 -0400
Commit message:

 only add HGVS names for actual variants
 
Package: MTseeker
Commit: 8822eeca9c86e1f683ab29abfc20468b2f94fefe
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-23 11:11:29 -0400
Commit message:

 put bamFiles into a vector, not a DataFrame
 
Package: MTseeker
Commit: ab5de036b9871432e6f0eb552872a4f8b96ea53d
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-23 11:09:16 -0400
Commit message:

 streamline MVRangesList constructor and variant filtering
 
Package: MTseeker
Commit: decafac1d40b8183a57df187f7867b565c0bd856
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-23 10:43:36 -0400
Commit message:

 better variant filtering and pileup annotation
 
Package: MTseeker
Commit: fdb50515edf21aebadf743e8bd7fca2a9ebc15c8
Author: ttriche <tim.triche@gmail.com>
Date: 2019-05-22 14:49:24 -0400
Commit message:

 add pileup support
 
Package: MTseeker
Commit: b05cd7df7827232268c6467b5c863efe60f63d92
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-04-05 15:09:31 -0400
Commit message:

 update docs
 
Package: MTseeker
Commit: 43d7ae1a8a89d7682f0b605025e3c2d6bf429d8a
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-04-05 15:05:08 -0400
Commit message:

 update docs and add biscuit filter for importVCF
 
Package: MTseeker
Commit: 857f3e887e6fc8f25a50c14aae2cbf9e48f84813
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-04-05 14:09:54 -0400
Commit message:

 additional checks for haploMask
 
Package: MTseeker
Commit: aaf8dfbe80403c4d274c4c508d4f940c34fbc3b0
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-04-04 16:28:34 -0400
Commit message:

 Merge pull request #1 from trichelab/dev

sync up with dev 
Package: MTseeker
Commit: 0c33f3e02ca06086097b9025d0c2cbd05a7efd78
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-04-04 16:26:39 -0400
Commit message:

 Merge pull request #35 from heoly32/master

add support for biscuit VCF import 
Package: MTseeker
Commit: 8fdbce09d584681fc0ff3650da2962782b809dc5
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-31 23:18:07 -0400
Commit message:

 typos and bugfixes

Some hacks to get around multiple bugs. 1) in snpCall for
consensusString - appears to be a biobase issue; 2) haplogrep finds
more variants than in input… uhhh?
 
Package: MTseeker
Commit: a1797a6a91417aea88838e408c386ed9c693eb9e
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-31 22:30:11 -0400
Commit message:

 bugfixes for haploMask
 
Package: MTseeker
Commit: 7a4da3f0c2cbd72407136a222be5a53df70a1276
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-31 22:12:43 -0400
Commit message:

 haploMask fixes

These will fix if duplicate ranges come up and intelligently pick if
variants are found in the phylotree variant list.
 
Package: MTseeker
Commit: 558cb10207952b966583dc049a0333f2fd855a47
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-29 16:07:38 -0400
Commit message:

 Merge pull request #37 from biobenkj/master

Add haplogroup masking functionality 
Package: MTseeker
Commit: 4f06f5b079f2eb95b4261104529cf5cecec34c55
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-28 13:23:02 -0400
Commit message:

 Fix ref allele matching for haploMask
 
Package: MTseeker
Commit: 22784531112c2415489d0271bf5cf0c3cb2337cf
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-28 12:07:18 -0400
Commit message:

 Version bump
 
Package: MTseeker
Commit: 18bd72946922047ac9fc029e1bc3f5b03c878d97
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-28 12:02:24 -0400
Commit message:

 Add haploMask functionality
 
Package: MTseeker
Commit: ac7e4f64566d855e801fc69d2ab55d803c32442c
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-28 09:07:28 -0400
Commit message:

 Expose other options to injectMTVariants
 
Package: MTseeker
Commit: 618edf3eca170ac7d337318a12fbf0e22ea529d9
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-10 12:13:13 -0400
Commit message:

 Merge pull request #36 from biobenkj/master

Fixes for injectMTVariants and native annotation of MVRanges with AA changes 
Package: MTseeker
Commit: c17b7b0f588e5e149de8a3dc97ab462c7039ee25
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-10 10:33:04 -0400
Commit message:

 catch and fix codon 1 indels
 
Package: MTseeker
Commit: 9c85daa2a8b0f0e22f59ee15f70acc1a18a2668a
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-09 21:52:21 -0500
Commit message:

 remove locateVariants from getCoding
 
Package: MTseeker
Commit: 40184772f571e27157d1ed6c2a1b66de86c3870e
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-09 21:39:51 -0500
Commit message:

 check for overlapping gene hits
 
Package: MTseeker
Commit: 4e9f60553621ccc37f88a07b1d17a861d348139f
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-08 10:18:38 -0500
Commit message:

 typo
 
Package: MTseeker
Commit: 3d20498d7c38611c4efc44527581a5e90f959675
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-08 10:06:33 -0500
Commit message:

 catch and deal with large indels for annotation
 
Package: MTseeker
Commit: 3a69b0599dfa727fd4d7ad0481cfbff88bd51931
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-08 09:27:39 -0500
Commit message:

 more bug fixes for injectMTVariants and decomposition

Catch N bases and modify behavior of injectMTVariants. Appears to be an
off by 1 error when codon 1 is impacted.
 
Package: MTseeker
Commit: 4bcc9a6e7b89007b4df994cc64ef542974310196
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-07 21:59:26 -0500
Commit message:

 bug fix for codon and localStart and localEnd 0 indices
 
Package: MTseeker
Commit: b033a8cffdcec724f0ccdde85d4dd479354e8afe
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-07 17:38:46 -0500
Commit message:

 add one more layer of checking

The & statement wasn’t true and would result in an error of argument
length 0
 
Package: MTseeker
Commit: ae3547f8caf79b3e4cb8772de9ffc4089d5bb649
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-07 17:34:52 -0500
Commit message:

 typo fix
 
Package: MTseeker
Commit: 8ba6cbb9da286926522e150bac9fea8622cd7bb9
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-07 17:32:34 -0500
Commit message:

 check to see if a valid range exists in injectMTVariants
 
Package: MTseeker
Commit: ad49ae95ce26fde5189656176843229a1fee4352
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-07 17:28:00 -0500
Commit message:

 check for codon 1 bp changes

This is a “bug” that if the 1 bp is mutated in codon 1, the IRanges
calls the startCodon 0 and endCodon 0
 
Package: MTseeker
Commit: 1083afed8e2ccbe73c40028c09b1f49882e5d1d9
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-07 12:06:01 -0500
Commit message:

 add a check for having variants that overlap coding space
 
Package: MTseeker
Commit: 15995f11389cee92e01128d8c615b8a6a66b75e0
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-06 17:58:22 -0500
Commit message:

 add decomposition and annotation of variants

This is meant primarily to subset to things that cause AA changes for
plotting
 
Package: MTseeker
Commit: aa0db2fa45f39545cb2f724777ad36dfebec7b23
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-04 13:58:41 -0500
Commit message:

 update depth minimum
 
Package: MTseeker
Commit: 7b621b785c4e6103699231e388f4a9dc18a0f677
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-04 11:54:57 -0500
Commit message:

 bugfix
 
Package: MTseeker
Commit: 4fd3f1063c66a8c999d2fc910fede85e91912be0
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-04 11:05:18 -0500
Commit message:

 experimental minimum coverage filter
 
Package: MTseeker
Commit: 666031494948c0f38f1c134c439f5145b7134297
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-04 09:34:08 -0500
Commit message:

 Merge pull request #34 from biobenkj/master

stabilize parallel processing for callMT 
Package: MTseeker
Commit: 41476d5bc2835d64a895ccb441a19561203dd1e5
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-04 09:24:07 -0500
Commit message:

 stabilize parallel processing for callMT
 
Package: MTseeker
Commit: 9165b486a94ca597b79ea3eee71ca5bd5ae2e668
Author: heoly32 <heoly32@gmail.com>
Date: 2019-03-03 15:48:50 -0500
Commit message:

 Merge branch 'master' of https://github.com/heoly32/MTseeker
 
Package: MTseeker
Commit: a86e12a02039b919ac51f4e8cd4d196bb2d91dae
Author: heoly32 <heoly32@gmail.com>
Date: 2019-03-03 15:48:27 -0500
Commit message:

 Optimize code and correct typo
 
Package: MTseeker
Commit: 016877562e6bf0ac6b7c5cd8e3f384cecb9fd7bd
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-03-01 08:17:08 -0500
Commit message:

 Merge pull request #33 from biobenkj/master

Edge case bug fixes when looking at TCGA sliced bams 
Package: MTseeker
Commit: 46c8df36157fb8254253ac5dcd99795a00a5dc90
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-02-28 18:24:45 -0500
Commit message:

 pre-filter samples with 0 reads

filter out the metadata and GAlignments object prior to creating the
MAlignmentsList
 
Package: MTseeker
Commit: 5a04ac3e636284a0c3ff868c2e0f4c7b933a8733
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-02-28 18:01:59 -0500
Commit message:

 bug fix for genomeSize to be a list

This is an odd bug that came up when looking at sliced TCGA cases
 
Package: MTseeker
Commit: 2d77aecda3a97f11297c8d97b5a95279bdb6a58d
Author: heoly32 <37587081+heoly32@users.noreply.github.com>
Date: 2019-02-28 14:34:29 -0500
Commit message:

 Update NAMESPACE 
Package: MTseeker
Commit: a6f7ee470ab6a6028d0b2a9634b5e662b24c5dd1
Author: heoly32 <heoly32@gmail.com>
Date: 2019-02-28 14:08:30 -0500
Commit message:

 add importVCF function
 
Package: MTseeker
Commit: 3997911e78bd88db6efd2f7e010b3b67b069fa1a
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-02-28 13:12:31 -0500
Commit message:

 Merge pull request #32 from biobenkj/master

add combineMAlignments func 
Package: MTseeker
Commit: 1728dcb6957280aebc7cea897867316f1c7646f7
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-02-28 08:19:50 -0500
Commit message:

 temporary patch for validMetadata failing
 
Package: MTseeker
Commit: 6d42caf7b16230b973a63452f2c6f44bbbfe5f1a
Author: Ben Johnson <ben.johnson4343@gmail.com>
Date: 2019-02-28 08:14:41 -0500
Commit message:

 add combineMAlignments func
 
Package: annotatr
Commit: 611fc8d02a9e2a98ecf753d104353e6f8259ecff
Author: Raymond Cavalcante <rcavalca@umich.edu>
Date: 2019-11-12 09:57:11 -0500
Commit message:

 Update hg19 lncRNA URL

 
Package: ChIPanalyser
Commit: 432ad127a2788dc0ccf7ca30789dce5d37906f0b
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-11-12 15:39:50 +0000
Commit message:

 vbump
 
Package: ChIPanalyser
Commit: d01aa95e5dab090df0a14b5e56dd8eacfbc9f015
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-11-12 15:36:37 +0000
Commit message:

 methodCheck
 
Package: ChIPanalyser
Commit: 4196e22217b05864609328b67f4547757e857b7d
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-11-12 15:34:20 +0000
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: ChIPanalyser
Commit: 437fe7b755262a9e8f5667d1f7167d620fe769a1
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-11-12 15:30:17 +0000
Commit message:

 methodCheckUpdate
 
Package: GenomicAlignments
Commit: 2da2384358fc2c48dd1085d77d6d2577b5b4ac75
Author: Valerie Obenchain <obenchain.valerie@gene.com>
Date: 2019-11-12 06:08:53 -0800
Commit message:

 Fix bug in map_ref_locs_to_query_locs()
 
Package: evaluomeR
Commit: cc5aa8e2c748f80d27eab1c6dc57868226ef67af
Author: Neobernad
Date: 2019-11-12 13:20:29 +0100
Commit message:

 Version 1.3.1: Adding plotMetrics
 
</div>
Package: signatureSearch
Commit: 8c5b11c3489c26c8481e015db94382f1353d6ccb
Author: yduan004 <yduan004@ucr.edu>
Date: 2019-11-11 23:52:52 -0800
Commit message:

 Merge branch 'devel'
 
Package: signatureSearch
Commit: 873f213345810adb6290a4ffa59e39c2eb9353aa
Author: yduan004 <yduan004@ucr.edu>
Date: 2019-11-11 23:52:24 -0800
Commit message:

 docs: small edits
 
Package: signatureSearch
Commit: b9e1cc5461e467f2f0b252cdae6886d1ae9a5707
Author: yduan004 <yduan004@ucr.edu>
Date: 2019-11-11 23:39:47 -0800
Commit message:

 Merge branch 'master' of github.com:yduan004/signatureSearch
 
Package: signatureSearch
Commit: d817fff685b881b58e93f4811193d02a52ee8a65
Author: yduan004 <yduan004@ucr.edu>
Date: 2019-11-11 23:38:06 -0800
Commit message:

 feat: edit news, jump to 1.1.1
 
Package: signatureSearch
Commit: f2a196afea1186ec54e83e4ec54b67fba0b11c90
Author: yduan004 <yduan004@ucr.edu>
Date: 2019-11-11 23:19:44 -0800
Commit message:

 feat: support windows; use HDF5Array
 
Package: signatureSearch
Commit: fec46d20d881912a6b46981de3eae91eca61ae9c
Author: Yuzhu Duan <yduan004@ucr.edu>
Date: 2019-11-08 16:43:50 -0800
Commit message:

 add vignette link 
Package: simpleSingleCell
Commit: f5a5b3e24fab9bfaeee0bf8d517286f24f0dded6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-11 19:21:40 -0800
Commit message:

 Fix for removed variance modelling functions.
 
Package: chipseqDB
Commit: 7d3879ddf14175d39913e34feec66743330429e0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-11 19:18:24 -0800
Commit message:

 Fix for defunct filterWindows.
 
Package: KnowSeq
Commit: 96958938e1e5a1b82592788d4937693bd45283e5
Author: Daniel <dacacis@gmail.com>
Date: 2019-11-12 00:01:41 +0100
Commit message:

 KnowSeq V1.1.15
 
Package: TCGAbiolinks
Commit: d06d54a4467b0cdb6f23d1ed8764b6e6e8bac0b0
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-11-11 14:59:47 -0500
Commit message:

 Version bump
 
Package: TCGAbiolinks
Commit: c64efc0500eee382f27958d68799b4f1c7545846
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-11-11 14:59:20 -0500
Commit message:

 Fixing barcode in the gistic2 query
 
Package: TCGAbiolinks
Commit: 248027e09da703794f2a73d62540c4b16c8e20a3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-11-11 14:52:46 -0500
Commit message:

 Merge branch 'master' of github.com:BioinformaticsFMRP/TCGAbiolinks
 
Package: TCGAbiolinks
Commit: 407b7b5b2fae94d1ee73529d9865f5825f951959
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-11-11 14:52:40 -0500
Commit message:

 Fix GISTIC reading
 
Package: TCGAbiolinks
Commit: 357d091e5908309b0613acaab35254e0f23f075f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-11-08 09:50:47 -0500
Commit message:

 Merge pull request #363 from tiagomaie/patch-2

Update prepare.R 
Package: TCGAbiolinks
Commit: dc20e4bb9b6c88180d2acac5c7bc112592e70aa1
Author: Tiago Maié <tiagomaie@hotmail.com>
Date: 2019-10-23 19:29:56 +0200
Commit message:

 Update prepare.R

Because of the folder structure (and the previous change, keep.copy=FALSE), if we choose to run (for idat methylation files) GDCprepare several times or if we just run GDCprepare on some samples more than once, on the current state we will have the problem of either keep moving the files up until the base folder (eg. the default "GDCdata") or potentially having some idat files somewhere between the base folder and the file_id folder.

Since "readIDATDNAmethylation" only applies to files that are within the "Raw_intensities" folder anyway, this change makes it so that files that were to be moved outside this folder are not actually moved.

A more elegant solution would be better but this works for now. 
Package: ATACseqQC
Commit: a9c6339c1299b272bf087d54d48ff6cb1d39952a
Author: Jianhong Ou <jianhongou@Jianhongs-MacBook-Pro.local>
Date: 2019-11-11 08:55:20 -0500
Commit message:

 Add flag parameter for splitBam.
 
Package: gwascat
Commit: 2b8cf90855a7019d64031a72339dc411b8d3c6cd
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-11-11 06:21:48 -0500
Commit message:

 passing check on R 4.0
 
Package: synergyfinder
Commit: c80972f6ff0875abe6366e4f8684878432fcc57b
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2019-11-11 11:37:39 +0200
Commit message:

 update news
 
Package: synergyfinder
Commit: 40aa9425a41329a38dfd9341759e3066e50b3df2
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2019-11-11 11:33:52 +0200
Commit message:

 update news
 
Package: synergyfinder
Commit: 7c1763e72ff4b497dd8c0bbd72b3508856aeb20f
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2019-11-08 11:38:43 +0200
Commit message:

 Bug fix FitDoseResponse function: if "LL.4" model fitting raise "Convergence failed" warning message, the model will not be fit and the error handler will be ignored. Solution: test  class of "drug.model", if it is not "drc" then fit L.4 model again.
 
Package: microbiome
Commit: df8fe90164c5943e659f9337d034e70d8183d573
Author: antagomir <leo.lahti@iki.fi>
Date: 2019-11-11 10:16:10 +0200
Commit message:

 Fixed core heatmap
 
Package: scRNAseq
Commit: ff4bed0e9d5c5e4ab9bf0eff1e4b5b50d35adfa0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 21:53:25 -0800
Commit message:

 Bumped version and date.
 
Package: scRNAseq
Commit: 1f327fa4b66958d44d83a6cd492d2fdd442836fc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 21:53:08 -0800
Commit message:

 Merge branch 'bugfix'
 
Package: scRNAseq
Commit: fd742a1515bb77969bbe8cebf3e132d5037442a4
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 21:51:22 -0800
Commit message:

 Implicit import of AnnotationDbi symbols.
 
Package: scran
Commit: b4398767760bb9bfa6df468f3dd7bb8c9f55f3e5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 21:44:35 -0800
Commit message:

 Reoxygenated, updated NEWS.
 
Package: scran
Commit: b7a34080aa77431094dd969dbd21443406d6d17e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 21:30:10 -0800
Commit message:

 Extended tests for bootstrapCluster.
 
Package: scran
Commit: bd42414a0c3759f16b6601f8adaa5581c08d7656
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 21:06:29 -0800
Commit message:

 Split off coassignment calculations from bootstrapCluster.
Robustified bootstrapCluster to missing clusters in bootstrap.
 
Package: gwascat
Commit: 6a642b3049f81babef810aad7aa0f8160f0219b2
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-11-10 22:00:23 -0500
Commit message:

 various upgrades including roxygenization
 
Package: csaw
Commit: 9115a71a5fe5af3d1d609bdc7dbe8ac19a200b5e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 10:51:12 -0800
Commit message:

 Added listing of defunct functions, closes #10.
 
Package: scater
Commit: 015579eb70c950302aec7931ccf0f08d689dce93
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 10:32:44 -0800
Commit message:

 Merge branch 'master' of https://github.com/davismcc/scater
 
Package: scater
Commit: 8738ae3076b07a892b941e466a077c89c4dd99f6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 10:31:12 -0800
Commit message:

 Bumped version and date.
 
Package: scater
Commit: 51ae13fbfc59ec26748d031cb4eed03f955ddd7f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 10:03:42 -0800
Commit message:

 Added listing of defunct functions.
 
Package: scran
Commit: 1d598c17f3c44dfd278b515bc3bb0f911bf5eeb2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 09:58:03 -0800
Commit message:

 Added listing of latest defunct functions to assist transition.
 
Package: scran
Commit: 52ee18da58c478d12bdba844fa25c41adc5e8b8f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 09:44:26 -0800
Commit message:

 Altered field name to be more explicit about summary.
Added flattening options for easier programmatic use.
Updated tests and docs, minor refactoring for easier reading.
 
Package: BSgenome
Commit: 9726318c35423ed71fcba683b0b5fb8a8a7c75dd
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-11-10 06:25:08 -0800
Commit message:

 Add extractAt() method for BSgenome objects

A cleaner/faster replacement for getSeq(). The plan is to deprecate
getSeq() at some point.
 
Package: RNAmodR
Commit: 595909eac676666edc15fe8411b9d53e62d4a555
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2019-11-10 11:11:34 +0100
Commit message:

 added missing implementation for compare and subset functions
 
Package: RNAmodR
Commit: da243723578681d272d70e1eab309113e516756f
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2019-11-10 09:48:50 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/RNAmodR
 
Package: RNAmodR
Commit: b53f0d704185606145147b6a3405d263cf993e8b
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2019-10-01 11:13:32 +0200
Commit message:

 Update README.md 
Package: scran
Commit: 27e0b56523719e61dd2c889791219de21a42752b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 01:44:37 -0800
Commit message:

 Bumped version, updated NEWS.
 
Package: scran
Commit: 5e0d64e3df32e69714f32bb6d2891c7917bd1a57
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 01:42:49 -0800
Commit message:

 Recompiled attributes and reoxygenated.
 
Package: scran
Commit: 018fa92a9561059ee9aeb556e535db3bf8468cb0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 01:42:36 -0800
Commit message:

 Reorganized combineMarkers docs.
 
Package: scran
Commit: 5349c88758ea687675ef1ba4d89f604052e07165
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-10 01:42:21 -0800
Commit message:

 Extended combineMarkers tests for new summary statistics.
 
Package: scran
Commit: f18987bea1e0683a9b512e3707a11e0af7842395
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-11-09 22:50:03 -0800
Commit message:

 Add a summary effect size to combineMarkers output.
 
Package: biocViews
Commit: 20624d450bff121fe34a7d8e91ebaf77cf1c8077
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-11-09 18:57:44 -0800
Commit message:

 genReposControlFiles() no longer writes the SYMBOLS file
 
Package: DEqMS
Commit: 3b79188129aba12bbde2e248bc250785eb51d7e4
Author: Yafeng Zhu <yafengzhu@Yafengs-MBP.cable.rcn.com>
Date: 2019-11-09 12:17:47 -0500
Commit message:

 ExperimentHub load error, add localHub=TRUE option
 
Package: DEqMS
Commit: 8821336665a12e513c3b5cc1fa27b4086e06379a
Author: Yafeng Zhu <yafengzhu@Yafengs-MBP.cable.rcn.com>
Date: 2019-11-09 11:53:44 -0500
Commit message:

 merge remote-tracking branch 'upstream/master'
 
Package: DEqMS
Commit: 7a0f2dd57c9217015e6028933bfe3106029bf83e
Author: Yafeng Zhu <yafengzhu@Yafengs-MacBook-Pro.local>
Date: 2019-05-05 20:01:36 -0400
Commit message:

 update readme for v1.2.0
 
Package: DEqMS
Commit: 704b27b6df7ed1ec16c83db373f14de07e4e54dd
Author: Yafeng Zhu <yafengzhu@Yafengs-MacBook-Pro.local>
Date: 2019-05-05 19:38:32 -0400
Commit message:

 update readme
 
Package: SWATH2stats
Commit: 8e264cb6f437f3cf87c9d1d58180533eb10ec664
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2019-11-09 17:34:48 +0100
Commit message:

 v1.17.1 merge commit
 
Package: SWATH2stats
Commit: f67b918f9fd2873c941033adab418dee07c96d63
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2019-11-09 17:27:15 +0100
Commit message:

 v.1.15.1: convert_protein_ids count unique ids
 
Package: Prostar
Commit: 956f6e2c35bfc04544b33c1bafd33dbaa2428f64
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-11-09 06:36:56 +0100
Commit message:

 update with previous commits of 1_19
 
Package: scTensor
Commit: eba2b39b748515a4ac0b651de37ceeb4681701b8
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2019-11-09 11:32:57 +0900
Commit message:

 v-1.3.1
 
Package: scAlign
Commit: 40a1a5caddc262afe5f2ef2119e0e1773162aecf
Author: UCDNJJ <njjohansen@ucdavis.edu>
Date: 2019-11-08 18:23:17 -0800
Commit message:

 desc
 
Package: scAlign
Commit: da8ed4345ef4f74d87189a71319c3dd6fb2ce74a
Author: UCDNJJ <njjohansen@ucdavis.edu>
Date: 2019-11-08 18:15:21 -0800
Commit message:

 bioc
 
Package: scAlign
Commit: 0d55b90a960f509bdaf546445c60dcf92ea07143
Author: Nelson Johansen <njjohansen@ucdavis.edu>
Date: 2019-11-08 18:07:40 -0800
Commit message:

 Update DESCRIPTION 
Package: scAlign
Commit: ffc0a92bfaf1ad347a3d174ad559fbd2cfec97f3
Author: Nelson Johansen <njjohansen@ucdavis.edu>
Date: 2019-11-08 18:06:08 -0800
Commit message:

 Update LICENSE 
Package: scAlign
Commit: 527d7f23264794e0e5a6e0119a265b67a9877c7f
Author: Nelson Johansen <njjohansen@ucdavis.edu>
Date: 2019-11-08 15:40:24 -0800
Commit message:

 Update README.md 
Package: scAlign
Commit: 476d2f92235efc59334ee424fbb418b30b8ef608
Author: Nelson Johansen <njjohansen@ucdavis.edu>
Date: 2019-11-08 15:10:07 -0800
Commit message:

 Packing related changes after merge.
 
Package: scAlign
Commit: 16d4f82a531187e1818d6022c03c5c8cda802ab6
Author: Nelson Johansen <njjohansen@ucdavis.edu>
Date: 2019-11-08 14:42:21 -0800
Commit message:

 Merge pull request #6 from cnk113/master

Accepted pull from cnk113: ported over Seurat V2's MultiCCA, removed PMA. Thanks! 
Package: scAlign
Commit: 2189258223e299645b1366ae5971558b2b4b1e80
Author: Chang <dfrontier1@gmail.com>
Date: 2019-11-08 14:21:07 -0800
Commit message:

 PMA MultiCCA has errors, and not suitable for scRNA-seq, added Seurat 2.0 MultiCCA
 
Package: scAlign
Commit: 720fc1bb08fa296cbcefc92d59907f91cbf54027
Author: Chang <dfrontier1@gmail.com>
Date: 2019-11-07 22:45:38 -0800
Commit message:

 small fixes
 
Package: scAlign
Commit: 5ca9d9ab93f55f299b438adc379d49dd7ffe8fd8
Author: Nelson Johansen <njjohansen@ucdavis.edu>
Date: 2019-09-11 16:03:20 -0700
Commit message:

 Update README.md 
Package: scAlign
Commit: c848c88c57f1f5c9780ec9c5c1cdbdea6862184a
Author: Nelson Johansen <njjohansen@ucdavis.edu>
Date: 2019-09-11 13:23:16 -0700
Commit message:

 Update DESCRIPTION 
Package: openCyto
Commit: afccaf8a76758d4089abebe9de1fb891f2650f27
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:22:22 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: openCyto
Commit: 918d27e76c32729cb06fab9c100065a84449ab41
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:21:39 -0800
Commit message:

 bum
 
Package: openCyto
Commit: b824218ce855e74156c279a513cff5a08923531c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:11:47 -0800
Commit message:

 Merge branch 'cytoset' into trunk
 
Package: openCyto
Commit: ca7e2ed39a85ed439423dbb444d26dff5d02dd21
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:37:09 -0400
Commit message:

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 
Package: openCyto
Commit: 258129090b46798d8d0d674a4d34fd4bce111044
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:08:50 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 
Package: openCyto
Commit: d9a96f0fe28145602f3d65f70171d00ca2d0183b
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-29 13:27:43 -0700
Commit message:

 pkgdown updates
 
Package: openCyto
Commit: 8f1abb5b7797d2cbba4a0ba8081cd48a7ab7a2ad
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-29 13:27:20 -0700
Commit message:

 Doc/vignettte consolidation and maintenance
 
Package: openCyto
Commit: e035cbfb8dd979cc5d3dd431ed376b01ab90ec2b
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-29 10:47:38 -0700
Commit message:

 Add CytoExploreR_exports
 
Package: openCyto
Commit: 731931336e59fff70ffb0ac0ae6f7eee752d3dc5
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-22 12:34:54 -0700
Commit message:

 Rebuild pkgdown branch off of cytoset branch
 
Package: openCyto
Commit: 59e12d90eedfffdbdd71c638682a094b1be6a2fa
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-11 16:30:21 -0700
Commit message:

 load flowCore
 
Package: openCyto
Commit: df9d7c8066480bf93acc1593bebb80f861744847
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-04 16:26:45 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/openCyto into cytoset
 
Package: openCyto
Commit: 605a294b5c79889207e70f44cecaef7e64d3b164
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-04 16:18:06 -0700
Commit message:

 load flowWorkspace
 
Package: openCyto
Commit: 345978b93ac355c0540ae3938396cc612ed5d4ee
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-04 13:07:35 -0700
Commit message:

 Add PAT to more lines in .travis.yml
 
Package: openCyto
Commit: a2ecf705209b6b2a50e5ce2fd8039179a531da50
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-04 12:50:41 -0700
Commit message:

 Update .travis.yml for issue with travis build script
 
Package: openCyto
Commit: cbaf751afe8637b367f7bc571b7e3d711859b90a
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-03 10:49:02 -0700
Commit message:

 Fix positive arg to gate_mindensity to match doc
 
Package: openCyto
Commit: 94fd6d8db87778b5cc49a8f42a25fa8737c769c1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 15:22:49 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/openCyto into cytoset
 
Package: openCyto
Commit: 4b20da372cb9def7f8ed35430df71b3d2962c52f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 15:20:58 -0700
Commit message:

 rm flowWorkspace from depends
 
Package: openCyto
Commit: c9d7dfcb21b3a8a3b01727aa600ce94158596fdf
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-24 10:18:41 -0700
Commit message:

 Update test reference for cytoverse API change
 
Package: openCyto
Commit: d35721552a59b97f39548a2adf6641ba131172c2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-28 14:12:17 -0700
Commit message:

 merge trunk
 
Package: openCyto
Commit: 50bc69297461d587b397063e364b904a6845ad50
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-21 12:51:42 -0700
Commit message:

 resolve pull conflicts
 
Package: openCyto
Commit: 6c9eb9af6a9f2fbc0f19125e2227ff0ab0a16901
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-21 12:48:37 -0700
Commit message:

 merge trunk
 
Package: openCyto
Commit: 40f3aa2e0236a36f2d4631420427e55563751bb2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-21 12:44:26 -0700
Commit message:

 more friendly error messasge for reporting empty dims in csv
 
Package: openCyto
Commit: 3bbf5511fa6f8b90a48385034cd0fab8ed07b8ab
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-20 16:53:11 -0700
Commit message:

 Update .travis.yml API token
 
Package: openCyto
Commit: e7dde2ac64b14ceb859db0f806e68b572a41cce6
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-20 16:24:12 -0700
Commit message:

 Update .travis.yml to access cytoset branches
 
Package: openCyto
Commit: 22d6581bec91a47fbf70beba71751e5ca7344b60
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-20 15:07:40 -0700
Commit message:

 A few more updates for cytoverse API changeover
 
Package: openCyto
Commit: 6a380b6cb0098d3dc024875977eb9049a6176d42
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-20 14:23:08 -0700
Commit message:

 Update gating-testSuite.R for cytoverse API and new-format gs
 
Package: openCyto
Commit: 57d1c8617e965c2daeb01d067929ab80343e59ae
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-20 12:10:38 -0700
Commit message:

 resolve pull conflicts
 
Package: openCyto
Commit: bce8436e11373322ffe73ad005cb981db753e87d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-20 11:51:00 -0700
Commit message:

 merge cytoverse
 
Package: openCyto
Commit: 262c439cacf73d6443ff222c2bf9cfd9850435d4
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-13 14:47:40 -0700
Commit message:

 Expand gate_tail doc
 
Package: openCyto
Commit: 062d1c80d6c37b138bc88dda8b34e1ec3b0ddb95
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-15 17:15:32 -0800
Commit message:

 Remove flowClust calls from add/remove_pop tests for speed
 
Package: openCyto
Commit: f870c59e3c18197b78af96d5d45cede97252582e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-15 15:14:53 -0800
Commit message:

 merge trunk
 
Package: openCyto
Commit: 3d05ad68204e71b9ed537182c33f59a50dffd718
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-30 15:57:17 -0800
Commit message:

 bump to 2
 
Package: openCyto
Commit: 1f280795de37e326b261bd2aab5245a853d9d747
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-22 13:30:12 -0800
Commit message:

 bump
 
Package: openCyto
Commit: ce77449c2b9222560783b615a0f44bf05bb8d11f
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2019-01-04 13:42:23 -0500
Commit message:

 Add ImmunoOncology biocViews term
 
Package: openCyto
Commit: 2b0e88972eb1927e4168f86273b5a2688eda68c6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-28 11:47:51 -0800
Commit message:

 replace plotGate with autoplot
 
Package: openCyto
Commit: 2bbb3524fcf50f02659c88cb763702a208fecf10
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-22 13:50:07 -0800
Commit message:

 skip recompute for ocRectRefGate
 
Package: openCyto
Commit: 1f947ab65c022de4aa5af80981cd80e94812a977
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-22 13:22:31 -0800
Commit message:

 fix the bug in refGate when reference 1d gate is open-ended at -Inf
 
Package: openCyto
Commit: 66b4ff6038b955aea42e156b832d69900b57e6bf
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-08 13:17:14 -0800
Commit message:

 update
 
Package: openCyto
Commit: 5c1277a76d589f1530a4405b8c3d16758ee0c13b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-08 13:14:25 -0800
Commit message:

 fix some test case issue temporarily
 
Package: openCyto
Commit: ef4ec174a034624be4e117d635b75367ef5bdb99
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-07 17:02:24 -0800
Commit message:

 update based on new cytolib
 
Package: flowStats
Commit: e7a3809234e347c9b023155e3b280dc1a978438c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:20:00 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: flowStats
Commit: 9264ba4c35fb3bb46ec99babfb4023ef3813417f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:18:43 -0800
Commit message:

 bump
 
Package: flowStats
Commit: f3f4f39243b9593ddb83789b16f168f516b0d654
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:17:14 -0800
Commit message:

 Merge branch 'cytoset' into trunk
 
Package: flowStats
Commit: 3c3a04f2c5a6825ea38515b58a17a7d70c098096
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:34:57 -0400
Commit message:

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
 
Package: flowStats
Commit: 4b9ec95959eafd2bb5e6be2a2693155216670aa3
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:08:05 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
 
Package: flowStats
Commit: 5da2709af454ec750b489db875118cd5cf7054b2
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-07-25 14:41:09 -0700
Commit message:

 Fix rrcov CovMcd import
 
Package: flowStats
Commit: 09307835cb9d017c704266206e78f218bcf76551
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-07-25 14:28:28 -0700
Commit message:

 Add rrcov covMcd import for norm2Filter
 
Package: flowStats
Commit: f4573557fae0a6dc307987a192fd805d485fabee
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-05 12:35:23 -0700
Commit message:

 Coerce cytosets to flowSets in vignette
 
Package: flowStats
Commit: d9102fae72044f320ed4ade9b30c894bf4119a4e
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-04 18:19:16 -0700
Commit message:

 Load flowCore where necessary after removal from Depends
 
Package: flowStats
Commit: 58e1ccb1b82ec4a67799e7e374e6bc4906430b72
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-03 12:49:51 -0700
Commit message:

 load flowCore in example code since now it is on imports
 
Package: flowStats
Commit: 2f20bffc2750e68c94df88bbc41894e218c437bc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-03 12:42:29 -0700
Commit message:

 add test cases for normalization
 
Package: flowStats
Commit: e4dc56d536ee279a4a56c9b112e79af586598edc
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-03 11:08:53 -0700
Commit message:

 Move dependencies to Imports section
 
Package: flowStats
Commit: 2c6e993d08592faabd2995ace68ac0a3be0b4ac7
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-29 13:32:03 -0700
Commit message:

 bump
 
Package: flowStats
Commit: 8fca1e67c40765e842fa8c2127ade0a8a9f25f29
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-29 13:30:54 -0700
Commit message:

 Merge trunk in to cytoset

Merge branch 'trunk' into cytoset

# Conflicts:
#	DESCRIPTION
#	R/gaussNorm.R
#	R/normalize-methods.R
#	R/warpSet.R
 
Package: flowStats
Commit: b8fba46fb52dab45fe58023b0492a959b24df593
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-07 15:12:47 -0800
Commit message:

 bump version
 
Package: flowStats
Commit: 83385e4f27aff75e99eaa55b08d360661c33bedf
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-07 14:23:25 -0800
Commit message:

 add warpSet.cytoset support #23
 
Package: flowStats
Commit: 53fcad7c7fa39cf88886561cfe3845f05b272364
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-07 12:06:02 -0800
Commit message:

 rm legacy code
 
Package: flowWorkspaceData
Commit: e38e48b14336f5b4ad2748ad080b22bec2cc8455
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:06:11 -0800
Commit message:

 Merge branch 'trunk' into devel
 
Package: flowWorkspaceData
Commit: d150d0c642c5af922ef19da3703db5bd5f3b1b72
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:04:51 -0800
Commit message:

 bump
 
Package: flowWorkspaceData
Commit: 386e3befe9cf84ad5c74a64a63a06fd458e29dd0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 16:03:22 -0800
Commit message:

 Merge branch 'cytoset' into trunk
 
Package: flowWorkspaceData
Commit: 61fac351811fb7a57dba83d133a23e82d28a6b17
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-30 12:46:01 -0800
Commit message:

 update archived gs with extendible ds
 
Package: flowWorkspaceData
Commit: 513a79c58ecc6a0173f530469c588eb589c4eb87
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-14 16:48:54 -0800
Commit message:

 convert legacy gs_bcell_auto
 
Package: flowWorkspaceData
Commit: e646a9d8cc90b92fea23c33880083b3342de2432
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:38:33 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
 
Package: flowWorkspaceData
Commit: 2abd148b82e4c298f31c7f93829d5be056e3dfc4
Author: nturaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 11:36:21 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 
Package: flowWorkspaceData
Commit: ede079869ce01c4bf031cd21c1bb33f26205b60d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-01 14:28:24 -0700
Commit message:

 update gs_manual
 
Package: flowWorkspace
Commit: 80cf4bfa110da5dff2aab10a216c00f1596c7406
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 15:57:36 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: e07e82e25426e87e8ffbdeac69a63b04b48be2d0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 15:53:35 -0800
Commit message:

 Merge branch 'devel' into trunk
 
Package: flowWorkspace
Commit: 823cea69376897e5ed82e055b1d096114b047ddd
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 12:22:53 -0800
Commit message:

 rm CYTOLIB_VERSION keyword when comparing to flowframe
 
Package: flowWorkspace
Commit: cef22317aa9101583aea656a1639a95479e25e5d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 12:11:51 -0800
Commit message:

 add cf_rename_channel
 
Package: flowWorkspace
Commit: ea520def28b3351f5eeb58cc5ca16ca6f8143dba
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-08 12:06:52 -0800
Commit message:

 add test case for rename marker to empty string
 
Package: flowWorkspace
Commit: e96b20c695278d76f672fb10b2590df4f4f7a040
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-11-04 11:55:30 -0800
Commit message:

 extend cytoset constructor to take a list
 
Package: flowWorkspace
Commit: 8f0b33430f25be62ad7ba6e2e7df88d89558f993
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-31 13:57:22 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: 3e31fcb1725cf8021628ed204e520d1192908eae
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-31 13:57:01 -0700
Commit message:

 add cf_rename_marker
 
Package: flowWorkspace
Commit: 8e38f477b6652a6bfa38e958bb6b9658fe9e6e04
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-28 17:06:33 -0700
Commit message:

 Merge branch 'pkgdown' into cytoset
 
Package: flowWorkspace
Commit: 165af761a0f94d84957b54ad37de038e4ffa69bb
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-28 16:47:25 -0700
Commit message:

 Doc/vignette updates/consolidation
 
Package: flowWorkspace
Commit: 92f316ae71058e0265fd468195db6aade1653899
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-28 16:49:39 -0700
Commit message:

 pkgdown updates
 
Package: flowWorkspace
Commit: 8d18d8883899756796bd1648a261c3646368e933
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-28 16:47:25 -0700
Commit message:

 Doc/vignette updates/consolidation
 
Package: flowWorkspace
Commit: f9b6e0d593e6b91a913200c62a6b1d7677f7a002
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-25 17:26:59 -0700
Commit message:

 doc consolidation
 
Package: flowWorkspace
Commit: c5aaefa1c0a54867a398aadc1d8446917fa7cdd0
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-25 17:30:23 -0700
Commit message:

 pkgdown site updates
 
Package: flowWorkspace
Commit: f40c7c908f2491cbfb1fcdf2dfe9f68f129d6d10
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-25 17:26:59 -0700
Commit message:

 doc consolidation
 
Package: flowWorkspace
Commit: e25a5c71a2451b436703403aff762e74dabcef37
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-15 13:18:50 -0700
Commit message:

 Fix gs_pop_get_stats_tfilter doc
 
Package: flowWorkspace
Commit: ec0f8c2883b9cab2381a5b7add8dae2fc2f22698
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-04 19:05:05 -0700
Commit message:

 Add gh_pop_get_stats_tfilter
 
Package: flowWorkspace
Commit: b815d010e2eb042a37a96fa537df927450ab5714
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-22 12:22:08 -0700
Commit message:

 Merge branch 'cytoset' into pkgdown
 
Package: flowWorkspace
Commit: 4e83e3e6834698ffa3104ce55927d1de5222c416
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-22 12:21:42 -0700
Commit message:

 Some required updates to DESCRIPTION/NAMESPACE
 
Package: flowWorkspace
Commit: 8f358791fb1a25ba1596c2a6947b4f97d8d3adcb
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-22 12:21:05 -0700
Commit message:

 Some doc consolidation
 
Package: flowWorkspace
Commit: 45e4b4e197952237a6b8dc04279f7a5b5775194f
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-10-22 09:48:28 -0700
Commit message:

 Rebuild pkgdown branch off of cytoset branch
 
Package: flowWorkspace
Commit: 79d2c1b3d8a1644bbae9b01eca26257d0b7a4b6b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-08 17:00:07 -0700
Commit message:

 support new quadGate c++ class RGLab/cytolib#16
 
Package: flowWorkspace
Commit: 3cda0415574493a4a2fd933ddcfa6d61138eada0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-10-01 11:09:14 -0700
Commit message:

 fix test case regarding to time channel scaling
 
Package: flowWorkspace
Commit: ec87f3f8f5a1fbcce75160395eb9b678716e485f
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-27 17:19:18 -0700
Commit message:

 Update logtGml2_trans for FredHutch/cytolib@4b71c4e
 
Package: flowWorkspace
Commit: 7c53f75c66716ef4a02cb2741c172759fe289f0e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-26 12:43:57 -0700
Commit message:

 assign the dummy legacy max_val for logTrans
 
Package: flowWorkspace
Commit: 4b54d26ea49c639342217f69738f5e7aa605771a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-25 16:21:45 -0700
Commit message:

 rm prefix from log trans
 
Package: flowWorkspace
Commit: 2185a68c73effbb4d92e936d5918556a411eff60
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-25 15:49:19 -0700
Commit message:

 flowjo_flog --> flowjo_log_trans
 
Package: flowWorkspace
Commit: d10af2089bcaef321d6390fd6d79d5291b133fef
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-25 14:27:56 -0700
Commit message:

 update according to the changes of locks in cytolib
 
Package: flowWorkspace
Commit: 7035c230d8f3b650a9e06e75ed7052898084bca4
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-24 16:02:14 -0700
Commit message:

 Add .onAttach message about cytoset changes
 
Package: flowWorkspace
Commit: 4bee3fefa347cd84f004b871e7bf6f8c284a69bc
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-24 15:13:05 -0700
Commit message:

 Switch vignette output to HTML
 
Package: flowWorkspace
Commit: 0639881ac90eba495d7041864f029957f1e119a6
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-24 15:02:39 -0700
Commit message:

 Some vignette metadata formatting
 
Package: flowWorkspace
Commit: 00722ccfe0aea4dd367b61ff9ec5f348ac392f1d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-24 12:43:13 -0700
Commit message:

 doc update
 
Package: flowWorkspace
Commit: c510e29766d3982a7d19dbc21580dfdd35070ea3
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-24 12:42:55 -0700
Commit message:

 Update for cytolib::LdFlags->cytolib::cytolib_LdFlags
 
Package: flowWorkspace
Commit: 82382f4070b3d01ce28710c62b5f295273f2e799
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-17 15:04:56 -0700
Commit message:

 Some minor cleanup of logtGml2_trans
 
Package: flowWorkspace
Commit: 563bfd5bad22706805df17ef38ae898cd09ebc28
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-17 14:57:21 -0700
Commit message:

 Restore some doc and namespace changes
 
Package: flowWorkspace
Commit: 544237bdcee92843b44bf98fbbb82dcb367b778e
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-17 14:55:52 -0700
Commit message:

 Detach logtGml2 from flowjo_flog
 
Package: flowWorkspace
Commit: a1a959fc2202f6288a6f2a82d794bee95e3e1835
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-17 12:29:57 -0700
Commit message:

 Revert "Update logtGml2 for 9e5a282"

This reverts commit a0d1931cbe7a5dc448d929e0879260af9b07e27c.
 
Package: flowWorkspace
Commit: 1105eacbe55afdd63143a3ee5ec415648f5c456a
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-17 12:29:11 -0700
Commit message:

 Revert "Update logtGml2_trans doc example for 9e5a282 and a0d1931"

This reverts commit f3cc1db12cd7435d00713f3e704d8b4b83a8d3d4.
 
Package: flowWorkspace
Commit: 166c079a9f374898319e878c0e4d74e45bb095c2
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-16 15:50:48 -0700
Commit message:

 Update logtGml2_trans doc example for 9e5a282 and a0d1931
 
Package: flowWorkspace
Commit: 1dd384261cbb801d8235a068690f1edf69884ef3
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-09-16 15:23:36 -0700
Commit message:

 Update logtGml2 for 9e5a282
 
Package: flowWorkspace
Commit: 83e5a31f9c6faa586e490d9f885bf6ee9321b4f5
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-09-18 12:48:22 -0700
Commit message:

 fix gh_get_transformations for fasinh
 
Package: flowWorkspace
Commit: 57e88f4de324c6f470d3c47d1a5a1b3ec6f4d10c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-23 13:50:24 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: 4dcc12e6e60c240d94368cb5822a51c1095c5fcb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-23 13:48:27 -0700
Commit message:

 update flog in R
 
Package: flowWorkspace
Commit: 962f6911c2a8aa54dbd2f4225a6b0115f3c60a60
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-08-08 12:52:19 -0700
Commit message:

 switch from gate * to shared_ptr
 
Package: flowWorkspace
Commit: 050cb46b9ac31b874510d7d970471174baf2b4e0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-22 15:58:05 -0700
Commit message:

 update according to the refactored cytolib
 
Package: flowWorkspace
Commit: 90b013924fc3797f7c2ca0be4deb5f2d59cab0b3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-17 16:16:14 -0700
Commit message:

 use non-header-only version of cytolib
 
Package: flowWorkspace
Commit: 01bff97f455132beb934d3aef807a01a2a9a55a7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-07-15 10:39:58 -0700
Commit message:

 make sure pd is synced to disk during load_cytoset_from_fcs
 
Package: flowWorkspace
Commit: 996df84d16a4a85ae79490a12d23bbfaa0341c64
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-19 17:40:53 -0700
Commit message:

 Updates for FredHutch/cytolib@ed43618
 
Package: flowWorkspace
Commit: 1ca1826843227958e4b7b9d966f6704d74271885
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-13 11:10:36 -0700
Commit message:

 fix old api call
 
Package: flowWorkspace
Commit: aa79d53409c1621cad3c91eb3f553eac23cc2c73
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-13 11:09:12 -0700
Commit message:

 rm legacy test block
 
Package: flowWorkspace
Commit: 730501d9c51d1d773987ec68517663825879221a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-13 11:05:12 -0700
Commit message:

 add test case to ensure meta won't be flushed to disk automatically for cytoframe
 
Package: flowWorkspace
Commit: 655787fb0f08abe03763fa46b53566db42eb30a0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-11 15:05:33 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: 628eff4056f5ac4bce01e3ef566227b4c9307738
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-11 15:05:17 -0700
Commit message:

 addd cytoframe-suite
 
Package: flowWorkspace
Commit: c80d1af82c1a65779eb4f874932ae12eb6d4c6db
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-11 14:56:30 -0700
Commit message:

 pass scale properly for flog
 
Package: flowWorkspace
Commit: 8c34f7c662dd4737e5955411a8bca69654853e2f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-10 16:31:09 -0700
Commit message:

 fix typo
 
Package: flowWorkspace
Commit: c458988b00655da5bce91b190cbf7b46f7b03654
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-10 14:24:59 -0700
Commit message:

 test in-mem version of cytoframe
 
Package: flowWorkspace
Commit: 7dd738a9e5c01e2761c071396a3ade051b43b542
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-10 13:30:14 -0700
Commit message:

 define cf_scale_time_channel API
 
Package: flowWorkspace
Commit: 1e73ef5783699d903d494df829d6a0d824bdcdbb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-07 13:36:20 -0700
Commit message:

 add tests for loading meta of locked cf
 
Package: flowWorkspace
Commit: 1dade5605f9c7d803c46a71eb10be184fca44740
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-07 10:30:15 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: c78a32d92a4a3b4f7385feda3efbf040c6aab150
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-07 10:29:51 -0700
Commit message:

 fix [[<- for cs
 
Package: flowWorkspace
Commit: bc0a10fb9159d37dd1857ab8cd5d09530672ba8a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-06 14:55:13 -0700
Commit message:

 write dummy replacement method [[<- for gs to enable the operations like 'markernames(gs[[1]]) <- newv'
 
Package: flowWorkspace
Commit: d7dcfada08fb13d9e9eadc32685806b95be511bd
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-04 17:39:07 -0700
Commit message:

 Add library(flowCore) to examples/vignette after removal from Depends
 
Package: flowWorkspace
Commit: f634f7d2c43194e2d51a2ac92b19a7b5f1079079
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-05 15:37:13 -0700
Commit message:

 Load flowCore in some examples and tests
 
Package: flowWorkspace
Commit: fc4dc9d2c9636b718c45eb0d13a43abf39751eae
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-05 15:36:37 -0700
Commit message:

 Ensure flowSet_to_cytoset leaves sampleNames unchanged
 
Package: flowWorkspace
Commit: 052c02a67a752e1b5432f680899d7d919d336519
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-04 16:09:40 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: 2e0c011a0d4cf69ffd83a75ae32d4494a82566bb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-04 15:33:10 -0700
Commit message:

 load flowCore
 
Package: flowWorkspace
Commit: 10c360fa48d02b7a51d20f6376f3c1c3a7ca57f3
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-06-04 12:45:06 -0700
Commit message:

 Update .travis.yml for issue with travis build script
 
Package: flowWorkspace
Commit: 6c3c971dacc48882dc23017ac3d0b952c45cd300
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-06-03 10:03:49 -0700
Commit message:

 rm Depends list
 
Package: flowWorkspace
Commit: 3cc9416d8813447ee7528acadf410b8017e69600
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 15:19:08 -0700
Commit message:

 make sure to clone gslist since gslist_to_gs call now points to the original gs
 
Package: flowWorkspace
Commit: b07368c035775ffdc5553c3f7111d52005b4ed52
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 15:13:02 -0700
Commit message:

 simplify test-merge code by using new api gh_pop_move/gh_copy_gate
 
Package: flowWorkspace
Commit: 5d6a16141a69f7cb14d6b8b9eddb5532a151b574
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 14:53:24 -0700
Commit message:

 deprecate GatingSet() with gh_apply_to_new_fcs in test case
 
Package: flowWorkspace
Commit: 028cbe3f75aa5d976904b5b6835b3c40cf6daedc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 13:10:10 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: c3df4dd93c4ecc692936bc435880f85ba4128e79
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 12:39:21 -0700
Commit message:

 refactor gh_apply_to_new_fcs
 
Package: flowWorkspace
Commit: 3dbc2be9cdfa9c2bb07c82bb23e0af3045598c30
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 11:53:58 -0700
Commit message:

 transform the data after gate copying for the trans that are not stored in c++
 
Package: flowWorkspace
Commit: 2bf919c7c228430243fac43cf8563fd1bf925409
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-31 11:11:36 -0700
Commit message:

 add more tests to transformation of gs
 
Package: flowWorkspace
Commit: fcc29ae240d0d437279f32df9eee391471d4788e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-30 15:22:45 -0700
Commit message:

 add range test to gh_apply_to_new_fcs
 
Package: flowWorkspace
Commit: a48ebafd0c8242e1e530cb684aedd6fa473485f6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-30 15:16:37 -0700
Commit message:

 fix [ method for gs
 
Package: flowWorkspace
Commit: bb9cdabf5acc49394264f65e406667423872daa6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-30 14:50:01 -0700
Commit message:

 copy over the R trans to new gs for gh_apply_to_new_fcs
 
Package: flowWorkspace
Commit: 521b3f6ccfd6c4a90323e03495a0eaab990dd14c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-30 13:21:16 -0700
Commit message:

 add gh_apply_to_new_fcs and its test case
 
Package: flowWorkspace
Commit: 175febae3c59eb983121ab5e3eb128d989768399
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-30 13:14:21 -0700
Commit message:

 fix phenoData<- for cs
 
Package: flowWorkspace
Commit: ce5042bdc92bf6c5a19a24b3fac3b9d7c1497221
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 14:28:35 -0700
Commit message:

 add stats comparison for new GatingSet based on the existing gating hierarchy
 
Package: flowWorkspace
Commit: 81870f2900ba2176d1a438f0634ae9a9b0774ad3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-29 11:05:44 -0700
Commit message:

 make a copy before transform to keep the original data intact from gs_cyto_data
 
Package: flowWorkspace
Commit: f27cad00b9362bf25333c1aaec7640a2d3022058
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-28 14:03:01 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: 4f4a969d364cc3ceaf44a3155b95b13baad54114
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-28 14:00:57 -0700
Commit message:

 merge trunk
 
Package: flowWorkspace
Commit: 33bf97f0bcf85364914364e3b0aab5c973653445
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-21 15:02:09 -0700
Commit message:

 fix some more cytoverse merge issues
 
Package: flowWorkspace
Commit: aec5eb55e9e08871132a871ee97ae96470d1c43a
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-21 10:21:02 -0700
Commit message:

 .travis.yml: Add BiocManager install
 
Package: flowWorkspace
Commit: 90bc9f96a5537413567e88593ad09ca6209d396e
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-21 09:52:37 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: 15782faebfbc371d41dcaf9c758cc6e98625f705
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-21 09:15:53 -0700
Commit message:

 Update .travis.yml to add token to packages with cytolib dependency
 
Package: flowWorkspace
Commit: 369118bfc739e85dafa54891391690c89d1bb9d0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-20 12:11:26 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: a7a2b86ce988e3e10c41104775489ea556eb06ac
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-17 12:03:06 -0700
Commit message:

 run roxgyen
 
Package: flowWorkspace
Commit: 55efc62b1fe6f8c28dfcf924771286235a7ea2a3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-05-16 17:35:12 -0700
Commit message:

 initial merge cytoverse with manual resolving conflicts
 
Package: flowWorkspace
Commit: 0c76d68089d80d7af3700d716ca70d61f1a038a1
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-05-09 09:18:15 -0700
Commit message:

 Update .travis.yml
 
Package: flowWorkspace
Commit: e7280d29edb5341f5287619abace223e5986c9c3
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-04-16 17:14:42 -0700
Commit message:

 Import graph::nodes() for plot_diff_tree()
 
Package: flowWorkspace
Commit: 02446c698cae356b3220631c90ac9f034a1e0c46
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-25 13:27:11 -0700
Commit message:

 Rework .travis.yml to avoid "cytolib" in install_deps
 
Package: flowWorkspace
Commit: 6e0acbc97a22e148f33fa531f06af7aa3f004514
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-25 12:51:23 -0700
Commit message:

 Update .travis.yml
 
Package: flowWorkspace
Commit: 846ffdf8d8cf5666d57ea1fa544ffeed325d324f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-22 14:50:17 -0700
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: 71d11e99d84246abcb7ba5a84763bb258925a998
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-21 15:37:50 -0700
Commit message:

 rm flowJo parser
 
Package: flowWorkspace
Commit: c91513041db92e40fd89e329e668515eb38e5cc9
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-22 10:58:57 -0700
Commit message:

 More .travis.yml cytolib fixes
 
Package: flowWorkspace
Commit: 876f15aa08119d15aaa2b955100fc04c03a159ec
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-22 10:23:21 -0700
Commit message:

 Re-order .travis.yml to fetch proper cytolib
 
Package: flowWorkspace
Commit: f2560daaf7855e2b7a9e33cde194cb122f5214ba
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-22 10:14:47 -0700
Commit message:

 Update .travis.yml for cytoset
 
Package: flowWorkspace
Commit: 7e4125c2f11bf16d2d299186f2e08a1b60a5613a
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-21 13:26:56 -0700
Commit message:

 Fix subset.GatingSet()
 
Package: flowWorkspace
Commit: bbe4e9454524db3d742f06f2ff9076d2062754c1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-18 16:24:33 -0700
Commit message:

 fix test case where cols in pdata change the order on mac (restore commit)
 
Package: flowWorkspace
Commit: 9cbf2a1c045f15a3f33f0c36eeb7c0d5708f8c33
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-18 16:09:38 -0700
Commit message:

 revert the change(mistakenly) to Makevars in regard of c++fs
 
Package: flowWorkspace
Commit: 77ba2e7d2884c434e8c607c184ba28a9e4709c02
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-18 15:18:35 -0700
Commit message:

 merge trunk
 
Package: flowWorkspace
Commit: e4b1315329ecc51d49ade8f4187206eef6ebe2d0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-15 15:47:07 -0700
Commit message:

 allow symlink directories in FCS searching
 
Package: flowWorkspace
Commit: 8574a9f60674493a99e82e33284caa4019d0473a
Author: Mike Jiang <Mike@C02QDX14GG77.pc.scharp.org>
Date: 2019-03-15 13:06:07 -0700
Commit message:

 link to c++fs instead of c++experimental for clang7.
 
Package: flowWorkspace
Commit: d1d0b4f3811105221fab0b85e9f1a5a861f23382
Author: Mike Jiang <Mike@C02QDX14GG77.pc.scharp.org>
Date: 2019-03-14 15:02:54 -0700
Commit message:

 fix test case where cols in pdata change the order on mac
 
Package: flowWorkspace
Commit: 5c4fdefe2a55d2fb9084d681c5398cecab557aaf
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-12 13:08:10 -0700
Commit message:

 update dep
 
Package: flowWorkspace
Commit: f17e662b28834daecc96823c58a7e6c092795fe0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-12 13:05:33 -0700
Commit message:

 Merge remote-tracking branch 'origin/cytoset' into cytoset
 
Package: flowWorkspace
Commit: f80f3ef2993c3373d93ff850902d91d1975fcca3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-12 10:41:20 -0700
Commit message:

 partial match CXX string to detect compiler type
 
Package: flowWorkspace
Commit: d2301313e81bc88389e58a7e20f4981b07264ad2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-11 16:21:51 -0700
Commit message:

 conditional linking to fs lib based on compiler
 
Package: flowWorkspace
Commit: 80c96e8c9b23760e53d58ef99a343cb4d8d4e578
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-11 15:01:37 -0700
Commit message:

 guard against unrecognized quadPattern
 
Package: flowWorkspace
Commit: 52966bf62e953f23a569cd2d80b8024142a51db8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-11 14:03:42 -0700
Commit message:

 undef FALSE to resolve RcppExports.cpp compiling warning (error on osx)
 
Package: flowWorkspace
Commit: b8c771d915c1f0dcb83ae99e7062df785f4000fb
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-08 16:22:14 -0800
Commit message:

 Update .travis.yml for cytoset
 
Package: flowWorkspace
Commit: 0fcb1ffe2e295fea62b9056f8809a4c220190ebb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-08 14:39:33 -0800
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: b94ab8c7f1c09abaf0c2d6f2eeae385bb63fe5d2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-08 14:38:55 -0800
Commit message:

 fix test-copyNode
 
Package: flowWorkspace
Commit: 1af8c8a1010009215f7359383dcb247f6af31eaf
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-08 14:38:30 -0800
Commit message:

 restore recompute = FALSE argument to keep 'add' backward compatible
 
Package: flowWorkspace
Commit: b222a3c27305ca9be48437067d59ebcf3f4f2346
Author: Greg Finak <greg.finak@gmail.com>
Date: 2019-03-08 14:24:28 -0800
Commit message:

 Update .travis.yml 
Package: flowWorkspace
Commit: 7ef9f3c0819c0c982b2211fcf569de09c6cc7ea7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-08 14:13:00 -0800
Commit message:

 fix getCompensationMatrices.GatingSet
 
Package: flowWorkspace
Commit: 8fe78c8ddb8bd52b34d1a6e86a8c114725ad2382
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-08 12:09:29 -0800
Commit message:

 Initial adaptation of IO-testSuite.R for load_cytoframe_from_fcs
 
Package: flowWorkspace
Commit: 1c3ba5d2f93e8433f5f7ec990adcc4df46c07624
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-07 16:59:50 -0800
Commit message:

 Change default value for dataset argument to load_cytoframe_from fcs to enable helpful warning
 
Package: flowWorkspace
Commit: 932f6cf01809b75351b983f191d6e59945f1d102
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-07 16:09:05 -0800
Commit message:

 merge from trunk
 
Package: flowWorkspace
Commit: 77ad60a93556085081c96fe8631fdb27f1c2dc7b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-07 15:51:37 -0800
Commit message:

 resolve pull conflicts
 
Package: flowWorkspace
Commit: 31d4e7a77756442b73fd5764f4c67b2a6004ecc9
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-01 16:07:11 -0800
Commit message:

 Add test for additional.sampleID
 
Package: flowWorkspace
Commit: e36c884652313a8e5b265c36484b9fea9a6951ac
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-01 12:33:42 -0800
Commit message:

 Add check for duplicate guid in parseWorkspace
 
Package: flowWorkspace
Commit: 520296228b825646c74481943123cddd9a780bb0
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-01 12:33:42 -0800
Commit message:

 Add check for duplicate guid in parseWorkspace
 
Package: flowWorkspace
Commit: 61346d2685b52df540436d6537f9cd15a9d443f9
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-01 10:56:49 -0800
Commit message:

 Revert "Add pre-check for duplicate guids before parsing samples in parseWorkspace"

This reverts commit 8b976040a37d92a7c157b2f213931ae7b4fbf24d.
 
Package: flowWorkspace
Commit: 8b976040a37d92a7c157b2f213931ae7b4fbf24d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-28 18:11:40 -0800
Commit message:

 Add pre-check for duplicate guids before parsing samples in parseWorkspace
 
Package: flowWorkspace
Commit: 454a508dbee1c4687f996aada86d4ae2120c43cd
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-28 18:10:58 -0800
Commit message:

 Update comments and cleanup guid strings in parseWorkspace
 
Package: flowWorkspace
Commit: ae3d8bd12d74cf264eb10dca452ec2c8ece5540d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-28 14:32:06 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: 3878eebc28c0481d107be77d8eedbba98e75d301
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-28 14:30:25 -0800
Commit message:

 Allow parseWorkspace to parse workspace opened from cwd
 
Package: flowWorkspace
Commit: 503100cda246cc8b35e9ae7422a7a5c4f58ecfba
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-28 14:27:47 -0800
Commit message:

 Add additional.sampleID option to parseWorkspace
 
Package: flowWorkspace
Commit: 7041a23b863524f202700e7c7f034f9f3b4dd7b2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-28 14:06:31 -0800
Commit message:

 fix test error
 
Package: flowWorkspace
Commit: 0bf01345140823439e2ce523d2cccf4b138bcbb1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-15 16:28:58 -0800
Commit message:

 fix recompute for GatingSetList
 
Package: flowWorkspace
Commit: 3dc69e999780e2533bbcb0fbc17a6960f921d9ef
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-15 16:11:38 -0800
Commit message:

 fix doc
 
Package: flowWorkspace
Commit: 730ab81df8bb7dece75fb0f10c5fdf5d20cfa1b3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-15 15:09:37 -0800
Commit message:

 merge from trunk
 
Package: flowWorkspace
Commit: b52085c60b48022db05f246ca839a892b394966d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-15 12:13:52 -0800
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: fd2c9a1782f5788f51ade51eb897923a110fbc20
Author: gfinak <greg.finak@gmail.com>
Date: 2019-02-15 11:40:39 -0800
Commit message:

 update
 
Package: flowWorkspace
Commit: a1be772b3a43c51cf2606ea9b68b720654389197
Author: Greg Finak <greg.finak@gmail.com>
Date: 2019-02-15 11:37:35 -0800
Commit message:

 Update DESCRIPTION 
Package: flowWorkspace
Commit: e780627f2b4069c820334fb42d7876d0ea6fc54f
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2019-01-04 13:33:20 -0500
Commit message:

 Add ImmunoOncology biocViews term
 
Package: flowWorkspace
Commit: caa214798ad07bdc26113776f5330ee98702f55d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-04 14:27:20 -0800
Commit message:

 Add guid slot to GatingSetList
 
Package: flowWorkspace
Commit: 8aee6f0677453cd1cd2a7c7bdd4dbe5f2f5e77e8
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-29 10:55:16 -0800
Commit message:

 Add docs for transform_gate methods
 
Package: flowWorkspace
Commit: 091afc563d71318b53313b2e2ab36d72b761609c
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-25 17:10:36 -0800
Commit message:

 resolve cherry-pick conflicts
 
Package: flowWorkspace
Commit: 88674429c583f9f130e42d3f0f29cf453e7bfa04
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-31 11:43:46 -0800
Commit message:

 add test case to ensure pdata is flushed to disk during gs_clone
 
Package: flowWorkspace
Commit: 0a28480180ebc6bf75b66f58bd47e4e0e559d611
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-30 15:09:47 -0800
Commit message:

 fix test-compensate
 
Package: flowWorkspace
Commit: c7f6270b54e72a15670d0b899054fb8b16b182da
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-30 12:26:46 -0800
Commit message:

 update test case for save_gs
 
Package: flowWorkspace
Commit: 9e48275d7189927645fb697cc2b534d86cc6cb58
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-29 11:57:03 -0800
Commit message:

 add convert_legacy_gslist
 
Package: flowWorkspace
Commit: 9ae394d0fc86f83c79b4e548a245891032d14d2b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-25 15:54:07 -0800
Commit message:

 optionally disable transform when execute is set to FALSE so that raw gate coordiates can be extracted for troubleshooting purpose
 
Package: flowWorkspace
Commit: d2525b9a362d15d8611d825e128d9ccc9f7c6d16
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-25 13:52:05 -0800
Commit message:

 pass which.lines correctly to c parser to speed up test cases of big FCS
 
Package: flowWorkspace
Commit: 46c44291d018551ba273a8a1806c2b4bb60cc24c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-25 12:16:38 -0800
Commit message:

 mute prints optionally
 
Package: flowWorkspace
Commit: 32b1287235eaf014e57acef71afab598f153dcb0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-25 12:02:06 -0800
Commit message:

 add validity checks on tree structures for parser
 
Package: flowWorkspace
Commit: 4964057f8831273378b2c36b5700051337ae9e73
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-25 11:59:38 -0800
Commit message:

 document more details on how to suppress errors from libxml
 
Package: flowWorkspace
Commit: 271baa4938bee9b04f001859e7a3589f427b1830
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-25 10:36:41 -0800
Commit message:

 refine sampleRef xpath to skip ManuallyIncludedSamples node
 
Package: flowWorkspace
Commit: 101685c888f05e379e96d5e9ada7720dbf8828fe
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-24 16:22:04 -0800
Commit message:

 use ws version specific xpath to parse group name
 
Package: flowWorkspace
Commit: 68ac322ba88a1d61cb8f1f2d768d3224f233237b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-24 16:03:00 -0800
Commit message:

 optionally mute workspace type print
 
Package: flowWorkspace
Commit: 0fffcf3b4b88030be4ecd7522ec3c3579c76ab0f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-24 15:41:51 -0800
Commit message:

 add argument fcs_file_extension to parser
 
Package: flowWorkspace
Commit: 4ab80ecddc1f1dd636ed6b3b8bd4ee4830b40a9e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-24 15:11:12 -0800
Commit message:

 revamp get_sample_groups so that it is lightweight and does not traverse entire xml
 
Package: flowWorkspace
Commit: b57f54c2abbdb85a60169f4beb4cd4135309fe32
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-23 14:27:43 -0800
Commit message:

 simplify Rcpp API parse_workspace by dispatching fcs_parse_arg parsing to dedicated Rcpp Wrap
 
Package: flowWorkspace
Commit: b6e5bba87f687164e1ba0c2fdee2530929b2e3ac
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-23 11:06:08 -0800
Commit message:

 merge
 
Package: flowWorkspace
Commit: 7168d1608e19cd6c7b7ff1431c3bf60c623cb6e6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-23 10:50:19 -0800
Commit message:

 pass RNG state from R to c++
 
Package: flowWorkspace
Commit: bc5f51ed9639da45d795de8ff3545a45e1ef2049
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-22 16:46:37 -0800
Commit message:

 add swap_colnames
 
Package: flowWorkspace
Commit: bae8c8c2717e644c90aac924ccf5000a8ad8d94e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-23 11:00:06 -0800
Commit message:

 test the set.seed effect for which.lines
 
Package: flowWorkspace
Commit: 3f6a6958b83e0a040627667f7a266aa837d36236
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-16 13:26:13 -0800
Commit message:

 write test case for load_cytoframe_from_fcs where which.lines is specified
 
Package: flowWorkspace
Commit: a0bc98144f4febe0bfb8a7c87b154a48c7f7a70f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-16 13:26:13 -0800
Commit message:

 write test case for load_cytoframe_from_fcs where which.lines is specified
 
Package: flowWorkspace
Commit: 1895955d5c1f417d71537554188fdea4153c1f6e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-16 10:19:24 -0800
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: e9474cbf87bd49316a61e997461d98909867f266
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-15 14:41:29 -0800
Commit message:

 normalizePath for parseWorkspace
 
Package: flowWorkspace
Commit: 255b64496d09c5c9fa296135f3d252fe8b4a4ae2
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-15 16:56:04 -0800
Commit message:

 Update docs for added cytoset/cytoframe APIs
 
Package: flowWorkspace
Commit: 48e896fb73299c458e688f33315afdf5e948b566
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-15 14:41:29 -0800
Commit message:

 normalizePath for parseWorkspace
 
Package: flowWorkspace
Commit: 4191cbd72461b9b9842f10cef7cc6936a9a0cf51
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-15 14:00:49 -0800
Commit message:

 replace references to csApply with lapply
 
Package: flowWorkspace
Commit: e87cd40c35477317a8e4079c98f95b1f9c915dd8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-15 10:22:27 -0800
Commit message:

 add flush_meta/load_meta and lock/unlock for on-disk cytoframe
 
Package: flowWorkspace
Commit: 656064c2e2ea31cdab365f3a9d6d148810c77ba1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 14:38:56 -0800
Commit message:

 importFrom dplyr group_by
 
Package: flowWorkspace
Commit: 0b8d3416e0778ff9499573f6cf95e697e2718c59
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-10 16:02:54 -0800
Commit message:

 bump RProtoBufLib version dependency for isGML2
 
Package: flowWorkspace
Commit: d2fa78cc30d94e6ffa00e70992fc20b1efd754e9
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 15:21:15 -0800
Commit message:

 update CytoML section
 
Package: flowWorkspace
Commit: 5e0d49e1c4ad717f8567619562d70b7f6a434bd1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 15:18:48 -0800
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: f33178939834217ac24c7cd10f38d61ac6cf15b3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 15:12:14 -0800
Commit message:

 normalizePath in save_gs
 
Package: flowWorkspace
Commit: 4d5a03ec302bf5e7d669d230dcfceb674855cafd
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-10 14:52:12 -0800
Commit message:

 Update vignette for cytoframe/cytoset
 
Package: flowWorkspace
Commit: a83194f8adcdf3e2ca629ff7ed3971dd3d32bc04
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 14:45:44 -0800
Commit message:

 create s3 for getSamples
 
Package: flowWorkspace
Commit: f3421fd48bc8d0c86ae88be14d06c3ccdefc9bc4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 12:48:32 -0800
Commit message:

 parse_transformer properly from flowJo_biexp
 
Package: flowWorkspace
Commit: 38e7666744b28881f24594526a85f2b1133d70c2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 12:16:03 -0800
Commit message:

 pass M to logicleTrans constructor properly for logicleGml2
 
Package: flowWorkspace
Commit: dafa3712b44c5f0efa55b19c4d8cf18268524dc8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-10 11:14:00 -0800
Commit message:

 catch and handle logicle constructor exception
 
Package: flowWorkspace
Commit: b875a4de49c7187d1b42deb99a97238c98a52c2c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-09 13:00:45 -0800
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: 83d0104772ccd7b0a3ab11b114dfb18eeb323eff
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-09 12:07:05 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: dc914444d4e1c8d96a603527ef16a1ccdd360ddf
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-09 12:02:09 -0800
Commit message:

 Create S3 generic for parseWorkspace methods
 
Package: flowWorkspace
Commit: 8035eb59d50967b7b1a46a37397b4bd2ad876406
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-09 10:39:41 -0800
Commit message:

 Merge branch 'cytoset' of github.com:RGLab/flowWorkspace into cytoset
 
Package: flowWorkspace
Commit: 1943af9601798e0fb9122ca69cc5aea1bc840fbf
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-09 09:53:27 -0800
Commit message:

 Fix typo in cf_write_h5
 
Package: flowWorkspace
Commit: f841da91284f21c159362086d89173f6938bf71e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-08 15:54:22 -0800
Commit message:

 import %>%
 
Package: flowWorkspace
Commit: 9690cc10c34f536a62a063ee5d54409a791f1dc6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-08 15:06:42 -0800
Commit message:

 use gh.check_ungated_bool_node
 
Package: flowWorkspace
Commit: 8daf077f5d37597c92cbe6c6290c9f8b7565dd24
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-08 10:57:04 -0800
Commit message:

 exprt gs_clone
 
Package: flowWorkspace
Commit: 943ff55415aa5e08464691c3b7fb1ba28e1d3265
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-08 10:53:38 -0800
Commit message:

 normalizePath in load_gs
 
Package: flowWorkspace
Commit: d38281386a49a7581c9613a653040f6c705c6171
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-08 10:52:10 -0800
Commit message:

 recompute the root node right after constructing an empty gs
 
Package: flowWorkspace
Commit: 7391f9cdce736e74fc28407e4a1ac500f57d601d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-07 16:06:45 -0800
Commit message:

 take care of even older legacy gs archive.
 
Package: flowWorkspace
Commit: bd7c143bfbeb49c3a3aeef920110a24949ef3f2c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-07 15:25:31 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: 1e47ebf836e3ba55581938885518fa445127e0a7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-07 15:22:45 -0800
Commit message:

 remove recompute option from .addGate
 
Package: flowWorkspace
Commit: 7345e44d0a93e92be403598f863d34e5f5029432
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-03 16:07:50 -0800
Commit message:

 link dynamically to RProtobufLib
 
Package: flowWorkspace
Commit: 904177ae7e9fd5c7797ed3a1d405e7bb8b32e6f7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-03 13:17:57 -0800
Commit message:

 resolve merge
 
Package: flowWorkspace
Commit: fd7e50031e1d35020f45feecefada8212a23e3bf
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-03 13:04:25 -0800
Commit message:

 execute tbb::serial when thread number is 1. #268
 
Package: flowWorkspace
Commit: efcb465d985364e7d68a00d363738b962221c73d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-03 12:10:54 -0800
Commit message:

 add print message for missing FCS. #268
 
Package: flowWorkspace
Commit: 89047a7b4f1f826e4b765b592c42cf30d0688a0e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-02 15:59:36 -0800
Commit message:

 add h5 locks. #268
 
Package: flowWorkspace
Commit: cbe2d70683b68be1005000c06f3a82dc5a6d027f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-02 13:11:35 -0800
Commit message:

 link to RcppParallel through importing it so that tbb shared lib is automatically loaded by RcppParallel and make symbol available at runtime
 
Package: flowWorkspace
Commit: 70f8eaa5fe8148219a5a3c1366a79ea84b74e90d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-02 12:57:10 -0800
Commit message:

 set linker flags for RcppParallel
 
Package: flowWorkspace
Commit: e685e5a5c384776bf007c63ef971e3b6a46e2075
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-30 17:45:45 -0800
Commit message:

 add lock for getTransformation calls. #268
 
Package: flowWorkspace
Commit: 448c04f4f205519443b7ee947f635541e6519b00
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-29 17:07:53 -0800
Commit message:

 use TBB. #268
 
Package: flowWorkspace
Commit: 6afdf739f00d78e52570f3d5f0d4db665bbdc290
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-27 18:22:21 -0800
Commit message:

 wrap the loop logic into separate function to be able to use thread
 
Package: flowWorkspace
Commit: 5e14004b505c7a8567f759d8bca35ce8ac5d1f79
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2018-12-21 16:05:40 -0800
Commit message:

 Remove RBGL dependency from DESCRIPTION
 
Package: flowWorkspace
Commit: 62b8996e3af27283fe01a61adc2587db5654bb6a
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2018-12-21 15:52:02 -0800
Commit message:

 Defunct plotGate and eliminate legacy viz pkg dependencies
 
Package: flowWorkspace
Commit: aa5f1aa572617bebafa9af5d6f9c60e840f82e01
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-21 15:17:47 -0800
Commit message:

 replace omp lock with critical statment. #268
 
Package: flowWorkspace
Commit: 5891b9e787f67f4c42f4e66d521074512f32a9c0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-21 12:44:35 -0800
Commit message:

 modify search_for_fcs to avoid creating temporary cs container thus avoid the extra omp lock. #268
 
Package: flowWorkspace
Commit: 31d3e0b35bf82e87fee10ec65a98bbf1eaea54ad
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-19 12:45:15 -0800
Commit message:

 support parallel parseWorkspace with openMP. #268
 
Package: flowWorkspace
Commit: 81584736bb4849d3aee8389b50b0169aa8bd0d0b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-18 14:48:03 -0800
Commit message:

 update keywords during gs_transform_data
 
Package: flowWorkspace
Commit: a65067e75a3d53f9dbbb4cadd54bbbb4fe2c9919
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-18 13:00:21 -0800
Commit message:

 update package dependencies
 
Package: flowWorkspace
Commit: 6712514d8bcd7da547780dea7b65ffd7db8f746f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-18 13:00:00 -0800
Commit message:

 update flowCore_PnR keywords to reflect the transformation for the load_legacy
 
Package: flowWorkspace
Commit: 29fafedd5571653bc1dfb7807820d409cedd4c5b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-17 15:43:53 -0800
Commit message:

 fix shallow_copy_cytoset to ensure copy has the separate view of cytoframes
 
Package: flowWorkspace
Commit: f8a8ab8985e6613b3c2fd8a12e138a998ccb510b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-17 11:05:48 -0800
Commit message:

 fix merge gs test cases
 
Package: flowWorkspace
Commit: 093710c313b5605a1304d7faefeeef2d4bb87c24
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-14 16:45:00 -0800
Commit message:

 fix convert_gs_legacy and write test case for it
 
Package: flowWorkspace
Commit: ca9a3433213cf22c14bb55c03473c7285da6ba10
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-14 14:20:50 -0800
Commit message:

 fix and pass addGate testsute
 
Package: flowWorkspace
Commit: 44a4b66db228b5d82636e4feee01ea0ee76e7c46
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-13 13:03:52 -0800
Commit message:

 transform and store gs with logicle
 
Package: flowWorkspace
Commit: 062a32ba9ed73d8a13689da3c0fa2ec4bfc9d843
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-12 16:34:54 -0800
Commit message:

 fix transform method for gs
 
Package: flowWorkspace
Commit: 842cb703d681c9cf6738e2011fcb7ae1a0361ae2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-12 15:23:24 -0800
Commit message:

 fix cs_compensate
 
Package: flowWorkspace
Commit: 7a65f5d1c7f09db837965f96ed96ad5e92acb1ae
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-11 14:10:34 -0800
Commit message:

 fix subset.cytoset
 
Package: flowWorkspace
Commit: b6546811b5c014968d6430132a8898a319af0614
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-11 11:45:11 -0800
Commit message:

 add test case for h5_readonly
 
Package: flowWorkspace
Commit: dbc0e19208e30c813def680ed20b846b7f1062f9
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-10 12:27:44 -0800
Commit message:

 do in-place compensation for gs
 
Package: flowWorkspace
Commit: 8320e17a7f90857c552b0a104efa860c22065bfa
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-10 11:13:13 -0800
Commit message:

 fix updateChannels
 
Package: flowWorkspace
Commit: f9c831429223f9fdd90b642d3a6737cebf7ebe7a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-10 10:26:06 -0800
Commit message:

 update doc
 
Package: flowWorkspace
Commit: a88cd6d4d1666548a3abbbd659862134a007f2c6
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-07 11:26:31 -0800
Commit message:

 optionally parse pData from ws in c++ and add validity checks
 
Package: flowWorkspace
Commit: a1141906518672dcedf208fd23d3fc7fe7aac317
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-06 17:01:39 -0800
Commit message:

 add h5_set_error_handler to redirect h5 error print to R error console
 
Package: flowWorkspace
Commit: cd78006f68ff6629264c3207cafa11fc3ddba37b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-04 13:05:05 -0800
Commit message:

 set default access mode for load_cf_from_h5 as readonly to prevent h5
from being tampered accidentally by various reference copy
 
Package: flowWorkspace
Commit: 9d013ced141759d0103bc62c5271278a43496cc5
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-04 11:50:51 -0800
Commit message:

 refactor cytoFrame/cytoSet to eliminate the leading capital letter
 
Package: flowWorkspace
Commit: 8209de1be9a21043ffa7237687b38227d461d7fb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-04 11:30:13 -0800
Commit message:

 transform methods for cf and cs
 
Package: flowWorkspace
Commit: 20a76cb7dfc09e1b23a8ba14d133a28e6169c392
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-12-03 09:53:12 -0800
Commit message:

 replace CXX1X with CXX11
 
Package: flowWorkspace
Commit: 7c354d896e4cffb3b7c8afb5ae89153b96c17575
Author: Greg Finak <greg.finak@gmail.com>
Date: 2018-11-30 15:26:57 -0800
Commit message:

 Update .travis.yml 
Package: flowWorkspace
Commit: 63637a036f462acc657b64f1da87ae427f0d72b9
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-30 13:09:10 -0800
Commit message:

 fix setKeyords Rcpp api
 
Package: flowWorkspace
Commit: 12a48cdf0369e628681630764fda49948909aa81
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-29 16:47:32 -0800
Commit message:

 add parameters<- for cytoframe
 
Package: flowWorkspace
Commit: 7f1f334521d4a7fe2acc27098598c5f029d33cff
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-29 14:40:22 -0800
Commit message:

 add test cases for cytoframe
 
Package: flowWorkspace
Commit: 815272a579d83b06a658c3d712d6422b477a4c9f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-29 14:00:29 -0800
Commit message:

 add data setter for cf and cs
 
Package: flowWorkspace
Commit: d95122d104a9657a80816d65243d8d55ca1db9d0
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-29 11:39:52 -0800
Commit message:

 use gs id as the default h5_dir
 
Package: flowWorkspace
Commit: 4ae4a6563b62ce87db44d15dbba9572c8cd6f947
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-28 12:04:48 -0800
Commit message:

 support loading single FCS as H5CytoFrame
 
Package: flowWorkspace
Commit: 90281b44e474b67f0dc979c3571bf1e285e4deba
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-28 10:58:07 -0800
Commit message:

 add subset.cytoSet
 
Package: flowWorkspace
Commit: 0eaa72e6c501db9d46736bf28fcafe95e4826941
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-28 10:37:31 -0800
Commit message:

 add phenoData accessors to cytoset
 
Package: flowWorkspace
Commit: 2d2850dc9f50c9f05068caa8050a07f7626d8119
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-27 15:41:40 -0800
Commit message:

 filter PnX keywords on the subsetted cytoFrame
 
Package: flowWorkspace
Commit: 047b054b0f4ea13dae383efe28b866c524df3b24
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-27 13:55:11 -0800
Commit message:

 retain the original  in subsetted fr through [[ method for cs
 
Package: flowWorkspace
Commit: abbae20bf3e786b715d22752e2e638f04e355854
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-21 11:13:07 -0800
Commit message:

 add test case for cytoset
 
Package: flowWorkspace
Commit: 7bcf8504095cd48aa9ca4fb866215ebe18773eba
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-20 16:18:33 -0800
Commit message:

 store and perform transformations through Rcpp
 
Package: flowWorkspace
Commit: fbf865b91622dc898b9922ea86b4903cdd34438f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-20 16:17:37 -0800
Commit message:

 add flowFrame_to_cytoframe
 
Package: flowWorkspace
Commit: c071f4305a14415f72c61009066da4a2e215398e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-20 16:16:49 -0800
Commit message:

 add parse_transformer
 
Package: flowWorkspace
Commit: 73420ec8ea47234ccab01101269f6fafd8dd10e8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-19 15:22:33 -0800
Commit message:

 fix compensate methods
 
Package: flowWorkspace
Commit: 4880ea04f3343974e4c013ac553e5d2ce802dbfa
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-19 13:00:31 -0800
Commit message:

 fix typo
 
Package: flowWorkspace
Commit: f4befd7fffcc06edc84609d2f7de2396b6d780ae
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-05 10:53:48 -0800
Commit message:

 merge swap_data_col commit
 
Package: flowWorkspace
Commit: 2c1bc18c5bbade49ecafcb78bb43f44306f5e0f1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-05 11:30:23 -0800
Commit message:

 update doc
 
Package: flowWorkspace
Commit: 122ab52a9c1311b7c7b1b82a4811252fed98d792
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-19 12:30:42 -0800
Commit message:

 import read.AnnotatedDataFrame
 
Package: flowWorkspace
Commit: daa1adf2ec45e19a04ec75c1c6a6b08a11055089
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-19 12:21:13 -0800
Commit message:

 explicitly define S4 (x='cytoSet', spillover='list') to avoid dispatching to (flowSet,list)
 
Package: flowWorkspace
Commit: b71c708f1f89def86da3e1166cea38a743817d15
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-19 11:14:27 -0800
Commit message:

 fix external comps
 
Package: flowWorkspace
Commit: 296c398225b96ac010daae461433d743e80e940e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-16 16:55:52 -0800
Commit message:

 add fpermissive flag to avoid type conversion error from R_useDynamicSymbols(dll, FALSE)
 
Package: flowWorkspace
Commit: fbbbc4bd9c290ee9d1a892ce2a283a05f32a4491
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-16 10:34:56 -0800
Commit message:

 fix external comps
 
Package: flowWorkspace
Commit: a237dafe234936b8c854064adaaa18e680610cdb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-11-15 14:15:19 -0800
Commit message:

 add linker flags for blas&lapack to link to armadillo code properly
 
Package: flowWorkspace
Commit: ea572694441c066bb10eeb91fc3149359f9fc163
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-23 14:59:18 -0700
Commit message:

 support external compensation
 
Package: flowWorkspace
Commit: 8e32a6b2b3c255ebbda98c46d26b4be91c84258c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-22 15:08:43 -0700
Commit message:

 use generate_unique_dir to set default h5_dir
 
Package: flowWorkspace
Commit: 6101d2efd96dc9386be9281313f6521efa53e0d1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-19 12:14:33 -0700
Commit message:

 R API for gs contructor based on gating template of existing gh
 
Package: flowWorkspace
Commit: 448ec2147727ed3a2f851b9ab5595a278a310b5f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-18 16:02:37 -0700
Commit message:

 doc the behavior of keyword value changing during convert_gs_legacy
 
Package: flowWorkspace
Commit: 5d9a3903c84d9db270a4f0e2f9787a683cc90707
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-18 13:48:46 -0700
Commit message:

 do in-place update in colnames<- and markernames<- for gs/cs to avoid triggering the classical cascade effect of R replacement method [[<-
 
Package: flowWorkspace
Commit: 7cb799e20167110b5f5d43ef0c1a65d9def04700
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-18 13:08:30 -0700
Commit message:

 fix get_pheno_data
 
Package: flowWorkspace
Commit: 7ec80d90a0440c31cc25c5f239f539572d31f1b9
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-17 13:10:09 -0700
Commit message:

 keep pData order consistent with sampleNames API
 
Package: flowWorkspace
Commit: 90eedc74e8c85cd9de49b1e4fe8daaf3570d2a82
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-16 11:25:09 -0700
Commit message:

 fix test cases where sample order is now preserved
 
Package: flowWorkspace
Commit: dc2a4fc953ed58c57ffe54700e3afb417109355e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-15 15:55:22 -0700
Commit message:

 fix load_gslist
 
Package: flowWorkspace
Commit: 0c40d8909928ca437229a15d68f2029da075c1b1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-12 14:04:31 -0700
Commit message:

 update according to the latest changes in cytolib
 
Package: flowWorkspace
Commit: a78009596bbdfd4cc6869663f052d3d210db9a00
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-09 15:56:43 -0700
Commit message:

 skip derived parameters. #262
 
Package: flowWorkspace
Commit: 32279ee551ee09b87288fdc5b00edf0c7629bbab
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-09 11:57:39 -0700
Commit message:

 fix flog issue. #261
 
Package: flowWorkspace
Commit: 721b442c281910ea3ca0fb66d195857b02e460d8
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-08 11:00:03 -0700
Commit message:

 drop dep on cytoCore
 
Package: flowWorkspace
Commit: 469675d559a6af1b98d3ad065b0c1f094e8bb3ed
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-03 16:39:30 -0700
Commit message:

 replace deep_copy with realize_view
 
Package: flowWorkspace
Commit: 26cc2649a7c4228586b500830141a2066c68788e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-10-01 15:09:39 -0700
Commit message:

 add getter/setter for gs guid
 
Package: flowWorkspace
Commit: e259886c7c0382f3a91318d5a5c1a15bfe45f838
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-28 16:44:54 -0700
Commit message:

 add convert_legacy_gs
 
Package: flowWorkspace
Commit: fe51e4447deba236c10e1004f49194763a55149a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-28 10:54:54 -0700
Commit message:

 rewrite recompute in c++
 
Package: flowWorkspace
Commit: 85151f2f3133724fc8a3bd9d69b2d879f855c600
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-27 12:53:11 -0700
Commit message:

 add constructor GatingSet_from_CytoSet
 
Package: flowWorkspace
Commit: 5bb9f390a9a1db64061139718d38125ec105d120
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-27 12:52:33 -0700
Commit message:

 add coerce function from fs to cs and vice versa
 
Package: flowWorkspace
Commit: 6621d83a21a9844d790f00066b1324a1028c43a3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-25 16:55:22 -0700
Commit message:

 add colnames and markernames setter for cs
 
Package: flowWorkspace
Commit: 4d3a0e645328f37742ecc4c6c22b04c629142427
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-25 15:48:39 -0700
Commit message:

 fix the Rcpp API name conflicts
 
Package: flowWorkspace
Commit: aef2c14b1e02b951c9e8b26c73005e39b37ede84
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2018-09-25 14:56:53 -0700
Commit message:

 merge cytoCore source
 

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