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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: srnadiff
Commit: 2ce4af704106c389a476789586850a3bf70e69ef
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-12 09:36:25 +0200
Commit message:

 Update documentation.
 
Package: srnadiff
Commit: 5bc3c5662de2d933eea8fefdec51e0b0f285f985
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-11 17:32:50 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: srnadiff
Commit: 68bf0af8817e01c6a076a512e809dc3d5c15d264
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-11 17:30:33 +0200
Commit message:

 Version bump.
 
Package: srnadiff
Commit: 0a670df6f734f783ffae24eafbfbb19231702694
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-11 15:39:38 +0200
Commit message:

 Update package description.
 
Package: srnadiff
Commit: e5552b0452bf2460c69690eebd7c67bb930e2725
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-11 15:35:33 +0200
Commit message:

 Adding new tests.
 
Package: srnadiff
Commit: bed9a05459a177f483c3242cfebc20fc1bc9fcae
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-11 14:59:40 +0200
Commit message:

 Update code for the 'diffMethod' parameter.
 
Package: srnadiff
Commit: 605109cd22c936bf92193e3ef7647d238e0743d5
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-11 11:18:34 +0200
Commit message:

 Refactor to include the diffMethod parameter.
 
Package: srnadiff
Commit: c6fa4900d8156732c836166b469cf3df3d7e23de
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-10 17:03:34 +0200
Commit message:

 Add baySeq.
 
Package: srnadiff
Commit: cdd82f478f028b2f93c8fefd5cd6a8b01ff16a41
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-10 16:12:01 +0200
Commit message:

 Add edgeR.
 
Package: srnadiff
Commit: fe9d71376e52a853f96c3759a8c79dce6ce99a5b
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-10 11:10:36 +0200
Commit message:

 Encapsulate call to DESeq2.
 
Package: srnadiff
Commit: 6901eb85372a6dd7dd3cd39482b14fb87d0fa038
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-10 11:09:44 +0200
Commit message:

 Applying changes from 3.11 to master.
 
Package: srnadiff
Commit: d6f923673d30ceafc1da86237921403e9861fafe
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2021-05-10 09:52:17 +0200
Commit message:

 Applying changes from 3.11 to master.
 
Package: srnadiff
Commit: 05fb311818064c994379002319a23f2010e49993
Author: Matthias Zytnicki <matthias.zytnicki@toulouse.inra.fr>
Date: 2020-10-13 11:50:14 +0200
Commit message:

 Remove alternative visualization, which triggers errors.
 
Package: debCAM
Commit: 182ad9218393e970556a3903fb95ba21d975085a
Author: Lululuella <31086337+Lululuella@users.noreply.github.com>
Date: 2021-05-12 00:23:05 -0700
Commit message:

 replace DMwR with DMwR2
 
Package: debCAM
Commit: 53cef4a37cff034767ee2b09d317bc7c5505d56e
Author: ChiungTingWu <49213701+ChiungTingWu@users.noreply.github.com>
Date: 2021-03-12 00:55:24 -0500
Commit message:

 Update README.md 
Package: debCAM
Commit: d9a4149edae19daf3abdf6b14c2b5b812894542c
Author: Chiung-Ting Wu <ctwu@vt.edu>
Date: 2020-03-19 18:29:32 -0400
Commit message:

 Change version number to 1.5.1
 
Package: debCAM
Commit: 803181fe2744307deee77bfa3a0f52e6ef388744
Author: Chiung-Ting Wu <ctwu@vt.edu>
Date: 2020-03-17 20:10:48 -0400
Commit message:

 Add a parameter to decide perfrom quickhull or not.
 
Package: debCAM
Commit: 7597e0415bfa9c9ec477d355a5f6b12fc9284dd5
Author: Chiung-Ting Wu <ctwu@vt.edu>
Date: 2020-03-17 17:10:13 -0400
Commit message:

 test
 
Package: debCAM
Commit: 3763086c1528f488aa81ca24c25a22aff0112b1a
Author: Chiung-Ting Wu <ctwu@vt.edu>
Date: 2020-03-17 17:08:55 -0400
Commit message:

 test
 
Package: metapod
Commit: 9d385ed454ece4a55a7f58513455e840e215e058
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-12 00:09:49 -0700
Commit message:

 Typo fixes to the vignette.
 
Package: celldex
Commit: b24d9225633079381ecd5ea9033de6806ce39b47
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-12 00:03:11 -0700
Commit message:

 Automatically move the Hub caches to their new locations.
 
Package: scRNAseq
Commit: c61f25fd457fd69efbdd87f8e80b84167dfda902
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-11 23:38:38 -0700
Commit message:

 Auto-move Hub caches to their new locations.
 
Package: scRNAseq
Commit: c6cb50931030e875419cfaa067b621295630a4e2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-01 02:41:35 -0700
Commit message:

 Convert Bunis data to dgCMatrix.
 
Package: methylclockData
Commit: 705d7f9a18d65f41802a16d8c08f6a1441fdf7c6
Author: dpelegri <dpelegri@gmail.com>
Date: 2021-05-12 08:34:20 +0200
Commit message:

 Update make-metadata.R
 
Package: systemPipeR
Commit: 271b4c9cb701ef3a3d3580fab538298827b88625
Author: dcassol <danicassol@gmail.com>
Date: 2021-05-11 23:08:18 -0700
Commit message:

 module
 
Package: batchelor
Commit: f2af3ba575a4569e9b32312e814a6523390c10c1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-11 22:17:16 -0700
Commit message:

 Minor doc update.
 
Package: batchelor
Commit: ea913b61590defe883a0ab9f4bc18a2f4562e8ca
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-11 22:15:51 -0700
Commit message:

 Realize file-backed matrices prior to PCA.
 
Package: batchelor
Commit: 0fca00adbbfedccc6bdeaa3522b2d1cb1150ac4d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-11 21:57:20 -0700
Commit message:

 Updated test for fixed dqrng seed issue.
 
Package: scater
Commit: 207e91e80f42690394a450c2a908d082b4ca74bb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-11 22:19:01 -0700
Commit message:

 Realize file-backed submatrices prior to PCA.
 
Package: epigraHMM
Commit: 4ff57ce911f2feb2e05298c5b24615fbb557ede3
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-12 07:02:07 +0200
Commit message:

 Speeding up vignette
 
Package: epigraHMM
Commit: de49dd0b28e6fa8d4dbde09b059140b955fc5344
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-12 07:01:53 +0200
Commit message:

 Version bump
 
Package: beachmat
Commit: e693476acf4279e557d8829abdbe550a28d94606
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-11 21:55:10 -0700
Commit message:

 Actually try running the path method, to ensure it actually returns.
 
Package: genomicInstability
Commit: ec9d4c54eaaf1f79982a8accbd7a6da2c62e057b
Author: Mariano J. Alvarez <31012433+reef103@users.noreply.github.com>
Date: 2021-05-11 21:40:12 -0700
Commit message:

 Bumped version number
 
Package: genomicInstability
Commit: fba6e47b20be87c3f5619de77334ebcd65aa6230
Author: Mariano J. Alvarez <31012433+reef103@users.noreply.github.com>
Date: 2021-05-11 21:39:53 -0700
Commit message:

 Replaced sapply() by vapply()
 
Package: genomicInstability
Commit: 03b19828bdaf43e9f6945c3c9d7906af9db49c21
Author: Mariano J. Alvarez <31012433+reef103@users.noreply.github.com>
Date: 2021-05-11 18:41:18 -0700
Commit message:

 Replaced all sapply by vapply
 
Package: messina
Commit: 3d513a9abd615e37ca3a90cac571a29f8d933d04
Author: Mark Pinese <mpinese@ccia.org.au>
Date: 2021-05-12 03:02:46 +0000
Commit message:

 Replaced deprecated survival::survConcordance.fit with survival::concordancefit
 
Package: STexampleData
Commit: cabda478bbec57c6204896576009285d4765c71d
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-05-11 23:05:08 -0400
Commit message:

 version
 
Package: STexampleData
Commit: b2491e7d6b24c782fadfbec639d86104fa1ce7ec
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-05-11 23:04:59 -0400
Commit message:

 update vignette example
 
Package: BUSseq
Commit: 7f8a3d28011252644e323c378125a8419b57cbf5
Author: BUSseq <sfd1994895@gmai.com>
Date: 2021-05-12 10:39:16 +0800
Commit message:

 Support for Mac
 
Package: CARNIVAL
Commit: 858d08b1c299f3cce106601114e427aa43d0db76
Author: Olga Ivanova <>
Date: 2021-05-12 02:35:52 +0200
Commit message:

 Merge branch 'devel_2_1' into master_bioconductor

* devel_2_1: (95 commits)
  updating website
  updates to fix warnings and errors for packaging (bioc submission prep)
  lpSolve shift the negative values to positive space
  add packrat to gitignore
  Bug in inverse Carnival fixed! (was related to character type vs numeric in priorKnowledgeNetwork in Sign column). Multiple tiny style corrections and fixes
  removed visualisation files, setup solvers can do test runs now for each solver, inst folder updated for examples and test runs to work.
  All functions in z_obsolete marked as deprecated. Automatically identified cplex path possibility added (not fully implemented yet).
  All checks fixed. Introduced new API function to run precheck on carnival input
  Presentation
  solvers checks working again. Redundancy fully removed.
  updated api documentations; removed not needed file
  style updated in cplex parse log; corrected solve carnival - correct params list; generalising options checks - all solvers are checked in the same way. Not working code (yet).
  extensive documentation for solve carnival, added examples for basic api. Fixing packaging for which -> match in lp solve code (didn't work with devtools::check())
  updated API for options and default options, API functions with fewer arguments now.
  fixed: bugs in constraints 6 and 7 (several identical constraints were made), global reassignment of constraint 8; bug in constraint 9(when provided same node as measurement and perturbation); bug in measurements backward compatibility (wrong order)
  Merge branch 'devel_2_1' of https://github.com/saezlab/CARNIVAL into devel_2_1
  no message
  fixed incorrect constraints generation: constraints 8 and 9; hid global variables (now functions calls), corrected params list in obsolete and new functions
  no message
  no message
  ...

# Conflicts:
#	.gitignore
#	DESCRIPTION
#	NEWS.md
#	docs/404.html
#	docs/articles/CARNIVAL.html
#	docs/articles/index.html
#	docs/authors.html
#	docs/index.html
#	docs/news/index.html
#	docs/pkgdown.css
#	docs/pkgdown.yml
#	docs/reference/index.html
#	docs/reference/runCARNIVAL.html
 
Package: CARNIVAL
Commit: 3259cb7c1d5dc65e4acaa3b5b96a8ab1e621cb8f
Author: Olga Ivanova <>
Date: 2021-05-12 01:59:59 +0200
Commit message:

 updating website
 
Package: CARNIVAL
Commit: 7d8bdf337fcc7e3f671eed63cda7ee9dc1688496
Author: Olga Ivanova <>
Date: 2021-05-12 01:27:00 +0200
Commit message:

 updates to fix warnings and errors for packaging (bioc submission prep)
 
Package: CARNIVAL
Commit: 9b2fd2a20a99c2a100e15617203a660e7c7a4977
Author: Olga Ivanova <>
Date: 2021-05-08 14:54:57 +0200
Commit message:

 lpSolve shift the negative values to positive space
 
Package: CARNIVAL
Commit: 59c3dac6788bb387afbe37ad3dc63874b55ba698
Author: Olga Ivanova <>
Date: 2021-05-08 11:49:00 +0200
Commit message:

 add packrat to gitignore
 
Package: CARNIVAL
Commit: 19b0b03abcdf644a200b4ad61f4a5af2d75d645a
Author: Olga Ivanova <>
Date: 2021-05-08 11:33:41 +0200
Commit message:

 Merge branch 'pr/58' into devel_2_1
 
Package: CARNIVAL
Commit: 05e67565c81a36c3bd61bf65cf49ba8c48d3a09b
Author: Olga Ivanova <>
Date: 2021-05-08 09:49:02 +0200
Commit message:

 Merge branch 'devel_2_1' of https://github.com/saezlab/CARNIVAL into devel_2_1

* 'devel_2_1' of https://github.com/saezlab/CARNIVAL:
  Presentation
 
Package: CARNIVAL
Commit: 0e239850a9827eb4e9f4bdd81e6efaed764d201b
Author: Olga Ivanova <>
Date: 2021-05-08 09:45:56 +0200
Commit message:

 Bug in inverse Carnival fixed! (was related to character type vs numeric in priorKnowledgeNetwork in Sign column). Multiple tiny style corrections and fixes
 
Package: CARNIVAL
Commit: 4cdc964d85267705bb836a1c433c92d45c93e619
Author: ivanovaos <ivanovaos.09@gmail.com>
Date: 2021-05-07 12:05:54 +0200
Commit message:

 Merge pull request #60 from MatteoSpatuzzi/devel_2_1

Add Matteo Presentation 
Package: CARNIVAL
Commit: 02fb1906f0a40544661a30a5f9b58cd4f79e9769
Author: Olga Ivanova <>
Date: 2021-05-06 10:29:36 +0200
Commit message:

 removed visualisation files, setup solvers can do test runs now for each solver, inst folder updated for examples and test runs to work.
 
Package: CARNIVAL
Commit: e7af9259c9d7b0140f5c89e7b7d7894eabf1eafe
Author: Olga Ivanova <>
Date: 2021-05-05 23:18:20 +0200
Commit message:

 All functions in z_obsolete marked as deprecated. Automatically identified cplex path possibility added (not fully implemented yet).
 
Package: CARNIVAL
Commit: 9f96d79784f10a9f41f486626fb66a0a3fa22aa0
Author: Olga Ivanova <>
Date: 2021-05-05 20:04:56 +0200
Commit message:

 All checks fixed. Introduced new API function to run precheck on carnival input
 
Package: CARNIVAL
Commit: d92a3e4a6be145479e9aee24495498e11d281b70
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-05-05 12:31:16 +0200
Commit message:

 Presentation
 
Package: CARNIVAL
Commit: 30effaea2d3e3f3f572ea7b900a77e372b9809a0
Author: Olga Ivanova <>
Date: 2021-05-05 12:09:55 +0200
Commit message:

 solvers checks working again. Redundancy fully removed.
 
Package: CARNIVAL
Commit: 42a0fff551c37b54c47268ab1e62a98432bc5d37
Author: Olga Ivanova <>
Date: 2021-05-04 15:56:03 +0200
Commit message:

 updated api documentations; removed not needed file
 
Package: CARNIVAL
Commit: 1116e380b66da607fd0193268491b8c52f6baf30
Author: Olga Ivanova <>
Date: 2021-05-04 15:54:00 +0200
Commit message:

 style updated in cplex parse log; corrected solve carnival - correct params list; generalising options checks - all solvers are checked in the same way. Not working code (yet).
 
Package: CARNIVAL
Commit: 059f70cefb7bd27e004e916e2ae25c38e8db8fed
Author: Olga Ivanova <>
Date: 2021-05-02 11:11:25 +0200
Commit message:

 extensive documentation for solve carnival, added examples for basic api. Fixing packaging for which -> match in lp solve code (didn't work with devtools::check())
 
Package: CARNIVAL
Commit: f191d85a7537b3fc310190e15aa26f6d93438714
Author: Olga Ivanova <>
Date: 2021-05-01 16:18:21 +0200
Commit message:

 updated API for options and default options, API functions with fewer arguments now.
 
Package: CARNIVAL
Commit: 6f681f000c3e6e4376c6f24c04539d8476fb05a8
Author: Olga Ivanova <>
Date: 2021-05-01 09:10:38 +0200
Commit message:

 Merge branch 'pr/59' into devel_2_1
 
Package: CARNIVAL
Commit: f6e1564ad7249cf65c260d151d7fd933ad410c99
Author: Olga Ivanova <>
Date: 2021-05-01 00:35:17 +0200
Commit message:

 fixed: bugs in constraints 6 and 7 (several identical constraints were made), global reassignment of constraint 8; bug in constraint 9(when provided same node as measurement and perturbation); bug in measurements backward compatibility (wrong order)
 
Package: CARNIVAL
Commit: 2a07909597bf623240cca6fa93394bb6195ac5e8
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-30 16:54:47 +0200
Commit message:

 Merge branch 'devel_2_1' of https://github.com/saezlab/CARNIVAL into devel_2_1

# Conflicts:
#	R/solve_carnival.R
 
Package: CARNIVAL
Commit: f6f4fd3a2ee0ce1f7ab50a8001822a8499682e7e
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-30 16:46:01 +0200
Commit message:

 no message
 
Package: CARNIVAL
Commit: 1c8335f502aefcf1a5690cf548164a16390ab760
Author: Olga Ivanova <>
Date: 2021-04-30 14:17:11 +0200
Commit message:

 fixed incorrect constraints generation: constraints 8 and 9; hid global variables (now functions calls), corrected params list in obsolete and new functions
 
Package: CARNIVAL
Commit: 9f0bfc006ffe5ef6fa85a768b2cf62daf1ef724b
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-29 17:03:37 +0200
Commit message:

 no message
 
Package: CARNIVAL
Commit: 1e2f074bc38d342489532e1f4b748d4ccae2f6e7
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-29 13:32:32 +0200
Commit message:

 no message
 
Package: CARNIVAL
Commit: a7bc99cb342c2b93d018da94ad7153598bec909d
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-29 10:13:37 +0200
Commit message:

 Remove error in solve Carnival, update vignettes
 
Package: CARNIVAL
Commit: abf46d1fe011d8fd5c94133d5394598131ffc090
Author: Olga Ivanova <>
Date: 2021-04-28 11:53:27 +0200
Commit message:

 weighted version of carnival works within new code; fixed bug in creating objective function (wrong variables were used), added time to messages; removed os x from travis (not needed and fails with unclear reason on travis server)
 
Package: CARNIVAL
Commit: 1eb9eab65fbc9df1a5bdb4c331b901df4fa3502d
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-04-27 13:14:26 +0200
Commit message:

 fixing issue with negstove constrains for lp solve
 
Package: CARNIVAL
Commit: 59d5b0e59d0900970a1686fdd456af1303485ca7
Author: Olga Ivanova <>
Date: 2021-04-25 10:02:08 +0200
Commit message:

 renamed api function to avoid clashes with old API runCarnival -> runVanillaCarnival, updated roxygen, cbc solver recovered runs, R CMD check passes with 2 warnings
 
Package: CARNIVAL
Commit: 73ada831e26212d295a0475729cb2b25876646c0
Author: Olga Ivanova <>
Date: 2021-04-24 12:27:49 +0200
Commit message:

 working code. lpSolve works with new data representation. Started to rework lpSolve parsing lp file (see solvers_lpsolve_transform_input.R)
 
Package: CARNIVAL
Commit: c8ee9152f7763ccf5f579666efd1d75c2216a745
Author: Olga Ivanova <>
Date: 2021-04-24 01:36:19 +0200
Commit message:

 style corrections; preparing for packaging; fixing lpSolve for new data rep.
 
Package: CARNIVAL
Commit: 02883c0ecf20d04a4433e896b26a75aa12390177
Author: Olga Ivanova <>
Date: 2021-04-23 21:28:27 +0200
Commit message:

 yet another one travis fix.
 
Package: CARNIVAL
Commit: 600cfb969b29b9cf79ea3eb80fb9f051851ec512
Author: Olga Ivanova <>
Date: 2021-04-23 21:24:58 +0200
Commit message:

 travis update, fixing syntax; constraints style corrected
 
Package: CARNIVAL
Commit: 6f52498a7ea2a84d99a06a7b2f4b692037af82ae
Author: Olga Ivanova <>
Date: 2021-04-23 20:58:37 +0200
Commit message:

 travis update
 
Package: CARNIVAL
Commit: 14f88d4c69ea015c42b12fc14e1cb25b4f7a9777
Author: Olga Ivanova <>
Date: 2021-04-23 20:52:14 +0200
Commit message:

 travis update
 
Package: CARNIVAL
Commit: a9314c684a74e035932068ac3beec19fee3d1e1e
Author: Olga Ivanova <>
Date: 2021-04-23 20:49:15 +0200
Commit message:

 all tests are passing
 
Package: CARNIVAL
Commit: 8f633c864a0b4672ac39ea1eac7de530efb4b54d
Author: Olga Ivanova <>
Date: 2021-04-23 14:22:42 +0200
Commit message:

 correcting tests
 
Package: CARNIVAL
Commit: 96c407f250e56600edc5a059df91b6c3db965c24
Author: Olga Ivanova <>
Date: 2021-04-23 13:55:07 +0200
Commit message:

 Merge branch 'devel_2_1' of https://github.com/saezlab/CARNIVAL into devel_2_1

* 'devel_2_1' of https://github.com/saezlab/CARNIVAL:
  adding travis to devel readme
 
Package: CARNIVAL
Commit: 779133512c6e4330dba4ec4c993d9e565d1e1115
Author: Olga Ivanova <>
Date: 2021-04-23 13:54:26 +0200
Commit message:

 passing test 1, separating dummy data creation
 
Package: CARNIVAL
Commit: 79c9f8290cb2f18cc717ba544bd44095ca77076f
Author: ivanovaos <ivanovaos.09@gmail.com>
Date: 2021-04-23 12:20:01 +0200
Commit message:

 adding travis to devel readme 
Package: CARNIVAL
Commit: 713d373fd55b9bd06db8eb92a9887114d1cde21e
Author: Olga Ivanova <>
Date: 2021-04-23 12:14:26 +0200
Commit message:

 tests folder structure/naming unified
 
Package: CARNIVAL
Commit: 410319812738556dde1f55a60fc4e776813ef3f1
Author: ivanovaos <ivanovaos.09@gmail.com>
Date: 2021-04-23 12:03:41 +0200
Commit message:

 Merge pull request #57 from MatteoSpatuzzi/Testing_constraints

Testing constraints 
Package: CARNIVAL
Commit: 7ded28a61ab62a7cde476c90b375fde6a1a7f9fa
Author: ivanovaos <ivanovaos.09@gmail.com>
Date: 2021-04-23 12:00:49 +0200
Commit message:

 Merge branch 'devel_2_1' into Testing_constraints 
Package: CARNIVAL
Commit: 24d727f23e9c5d0e08153fe4cf105f46024949f0
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-23 10:26:55 +0200
Commit message:

 Improved R/check_solver_param.R , now with new functions to check cbc and lpSolve params
 
Package: CARNIVAL
Commit: 3766cce815e8b271d75090ab35d47ea63c3ddf8d
Author: Olga Ivanova <>
Date: 2021-04-22 16:09:38 +0200
Commit message:

 small fixes and updates in the docs, added travis support
 
Package: CARNIVAL
Commit: 6c0a0dbe49ecb599449fa175f8bb963e6e59e5a2
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-22 15:28:27 +0200
Commit message:

 no message
 
Package: CARNIVAL
Commit: c2f3ef51de93617c27daf4d65e7f980cc7ebd23b
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-22 15:05:58 +0200
Commit message:

 Reorganization of the unit tests and new unit tests
 
Package: CARNIVAL
Commit: 251a16573a304b1110bc06e4960e859d54c2ab2e
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-22 12:36:47 +0200
Commit message:

 Second unit_test
 
Package: CARNIVAL
Commit: b513d12488bb9521ea35bd7af51a2cb85f44c20c
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-22 12:25:19 +0200
Commit message:

 First Unit_test for createVariablesForIlpProblem subfunctions
 
Package: CARNIVAL
Commit: 0c53be19fe13ff64510db5befcd6c2c8e0d82c9f
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-22 11:46:12 +0200
Commit message:

 Corrected the functions so they can deal with networks with the same sign for all edges
 
Package: CARNIVAL
Commit: 10ebd962d407a4508da57dce0ba56c382abc618b
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-22 10:05:44 +0200
Commit message:

 New Unit testing scripts
 
Package: CARNIVAL
Commit: 37bc2f1a6f834ea00cc0c77c1f9bd02392cd9b10
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-21 17:38:40 +0200
Commit message:

 no message
 
Package: CARNIVAL
Commit: 6df0332c249047802443db422feaeb42f8b4eed8
Author: Olga Ivanova <>
Date: 2021-04-21 17:13:49 +0200
Commit message:

 documentation is partially updated, also for obsolete code; aphaweight removed as a param from everywhere.
 
Package: CARNIVAL
Commit: ff239b0956c8773e0c1527054515cec4833b14de
Author: Olga Ivanova <>
Date: 2021-04-21 14:55:33 +0200
Commit message:

 updated test
 
Package: CARNIVAL
Commit: e0a3cdf426798e272624cf60052f43039211d702
Author: Olga Ivanova <>
Date: 2021-04-21 14:35:39 +0200
Commit message:

 updated test for constraint 1.
 
Package: CARNIVAL
Commit: fb469337a8750e35b17da35d30fbdccc9134132e
Author: ivanovaos <ivanovaos.09@gmail.com>
Date: 2021-04-21 14:12:15 +0200
Commit message:

 Merge pull request #56 from MatteoSpatuzzi/Testing_constraints

First test for constraints 
Package: CARNIVAL
Commit: 8fa98263a4ecbc4ce4b53665cb9ec49d1dd673d5
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-21 12:30:50 +0200
Commit message:

 Adding new unit testing function
 
Package: CARNIVAL
Commit: 1e0a32dacb5eaeafb0a66b67c6d763ce90b6df19
Author: MatteoSpatuzzi <matteo.spatuzzi@gmail.com>
Date: 2021-04-20 10:45:18 +0200
Commit message:

 First test for constraints
 
Package: CARNIVAL
Commit: 39053c0432b7e3b48f92bbae8e52b70784162b54
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2021-04-19 19:26:45 +0200
Commit message:

 fix small bug with old data representation
 
Package: CARNIVAL
Commit: cf5413b79342295881ef32e471daf84d04a4e1ff
Author: ivanovaos <ivanovaos.09@gmail.com>
Date: 2021-04-19 17:34:10 +0200
Commit message:

 Merge pull request #55 from ivanovaos/devel_2_1

minor fixes, updating the exporting code to be in line with the previ… 
Package: CARNIVAL
Commit: 6b9a5e57716a53886896afeb410891b659b057e5
Author: Olga Ivanova <>
Date: 2021-04-16 16:19:57 +0200
Commit message:

 minor fixes, updating the exporting code to be in line with the previous export results.
 
Package: CARNIVAL
Commit: 7e31e3b01ddd4c8427d33f5ab0883e4531016b68
Author: Olga Ivanova <>
Date: 2021-04-09 14:21:13 +0200
Commit message:

 first (dirty) version of new export from new data representation. Requires refactoring and checks.
Renaming constraints functions.
 
Package: CARNIVAL
Commit: 135cf3b5d6cd3869f4331e6a7374247d18af9317
Author: Olga Ivanova <>
Date: 2021-04-09 00:47:25 +0200
Commit message:

 moving the code around: old lp file creation went to z_obsolete files. Collapsed short files in one.
 
Package: CARNIVAL
Commit: 13f72a6c952ce6073c6065be6f53f6d8eba603aa
Author: Olga Ivanova <>
Date: 2021-04-08 21:49:00 +0200
Commit message:

 introducing new internal representation everywhere, cleaning the code, returning constraints_8 back (was removed accidentally). Only post processing xml parsing is not working atm with new data representation.
 
Package: CARNIVAL
Commit: ea8a74fa272f1077eb2d36285b21ff356d745a75
Author: Olga Ivanova <>
Date: 2021-04-08 19:18:44 +0200
Commit message:

 collapsing similar constraints in one function, moving old constraint code in one file (keeping it for testing purposes)
 
Package: CARNIVAL
Commit: eff222ab0cdeb4b9f390ba464ec87d98eba49666
Author: Olga Ivanova <>
Date: 2021-04-08 15:44:25 +0200
Commit message:

 preparing for tests of new internal data representation
 
Package: CARNIVAL
Commit: 1fd6f0b425ac023765d88e828b4a817e9cf743de
Author: Olga Ivanova <>
Date: 2021-04-08 15:26:35 +0200
Commit message:

 further update of constraints and objective function code, adapted for the new internal data representation
 
Package: CARNIVAL
Commit: 747d98fcda7891d7eb60943af745b4f292ee56e1
Author: Olga Ivanova <>
Date: 2021-04-06 19:42:13 +0200
Commit message:

 constraint 8 adapted for new internal representation
 
Package: CARNIVAL
Commit: 417f8dcbe87b43a8200005949eec8f06f78be82e
Author: Olga Ivanova <>
Date: 2021-04-06 16:43:14 +0200
Commit message:

 constraints 6 and 7 are updated for new internal representation
 
Package: CARNIVAL
Commit: 475202cce0b059b964867072b064ade439ec5111
Author: Olga Ivanova <>
Date: 2021-03-31 22:55:42 +0200
Commit message:

 update of constraints code 1-5 for the newly made internal data representation
 
Package: CARNIVAL
Commit: 193036eeb8ecfb69e2f6a0dcaf3fbea8f5ef8d62
Author: Olga Ivanova <>
Date: 2021-03-31 19:20:13 +0200
Commit message:

 first ideas of different internal representation of data and variables (for easier constraint generation).
 
Package: CARNIVAL
Commit: f600bee1ab90b170935f7e643e7f22176985c81c
Author: Olga Ivanova <>
Date: 2021-03-29 11:40:55 +0200
Commit message:

 cleaning majority of todos
 
Package: CARNIVAL
Commit: 3b619c9019594b9d69fff49960f18a2c9286ca8e
Author: Olga Ivanova <>
Date: 2021-03-27 21:35:59 +0100
Commit message:

 big refactoring on functions params in all parts of the code. Added flexibility on new solvers additions. Removed duplication in exports from all solvers.
 
Package: CARNIVAL
Commit: 0049dc4ba5404c48d407bdb8d8a401fef0fec77f
Author: Olga Ivanova <>
Date: 2021-03-27 11:56:56 +0100
Commit message:

 cleanup carnival update after refactoring
 
Package: CARNIVAL
Commit: 2415545df7ed153ddd286ea73d772ceae82faa3b
Author: Olga Ivanova <>
Date: 2021-03-27 11:35:16 +0100
Commit message:

 small (further) refactoring of constraints
 
Package: CARNIVAL
Commit: 6d83d9abed882146801458aa02d6b9402b0a9017
Author: Olga Ivanova <>
Date: 2021-03-26 12:15:02 +0100
Commit message:

 Major clean up of constraints writing functions: removing multiple experimental conditions code, small refactoring. Removing multiple experimental conditions from variables and dataMatrix (now dataVector)
 
Package: CARNIVAL
Commit: c483f3892959b697b29b3e71026736bf5ba8c71b
Author: Olga Ivanova <>
Date: 2021-03-25 11:21:52 +0100
Commit message:

 small refactoring of constraints - updating names, partial removing experimental conditions code; implemented inversed carnival flavour in new api; minor fixes after regression tests
 
Package: CARNIVAL
Commit: c79f938ce442cb15a0a481967633d86409352286
Author: Olga Ivanova <>
Date: 2021-03-25 00:54:02 +0100
Commit message:

 generating file names in one place; minor refactoring of constraints
 
Package: CARNIVAL
Commit: 8749ca4d8431b65f3bc50b2a5e5b742380e0370b
Author: Olga Ivanova <>
Date: 2021-03-23 23:34:08 +0100
Commit message:

 cbc solver works in new API
 
Package: CARNIVAL
Commit: 0fb424bb94cda4d1f40aab5270e3cc6903292111
Author: Olga Ivanova <>
Date: 2021-03-23 22:11:29 +0100
Commit message:

 fixes for packaging (R CMD build passes, but not R CMD check). Quick and dirty temp fixes for vignette building - will be corrected later.
 
Package: CARNIVAL
Commit: 264cd01a1800e7d1a0bc94697ee98f1c5554ee7c
Author: Olga Ivanova <>
Date: 2021-03-21 20:26:44 +0100
Commit message:

 lpSolve is working now in changed API. Minor improvements in lpSolve data preparation for running the solver.
 
Package: CARNIVAL
Commit: 1845520875003d54642a960bcf6a683c82fe7031
Author: Olga Ivanova <>
Date: 2021-03-20 00:25:43 +0100
Commit message:

 More code clean ups, introducing new param: output folder
 
Package: CARNIVAL
Commit: 6ac42facb252b57bb96f378555777eab55f06581
Author: Olga Ivanova <>
Date: 2021-03-19 00:33:41 +0100
Commit message:

 fixing two bugs in the output: one with an extra space appeared in Sign column in weightedSIF results, another is missing S/T in Attributes (both introduced with new API)
 
Package: CARNIVAL
Commit: 4340fa4cbebbaaacfae4ec7c560b7540fcb5dffd
Author: Olga Ivanova <>
Date: 2021-03-18 23:18:02 +0100
Commit message:

 adding timestamp and salt to the file names in cplex, also small fixing and clean up
 
Package: CARNIVAL
Commit: 999213d2e93a451be607286176a39c64037f5353
Author: Olga Ivanova <>
Date: 2021-03-18 11:38:51 +0100
Commit message:

 Merge branch 'reading-from-lp-file' into changing-api

* reading-from-lp-file:
  implemented a simple version of loading preparsed data and lp files, v.1
  Updates to the vignette and the README files. Removed redundant Mybib2 file.

# Conflicts:
#	R/check_inputs.R
#	R/control_node_identifiers.R
#	R/create_variables_all.R
#	R/run_carnival.R
#	R/solve_carnival.R
#	R/solve_carnival_single.R
#	R/write_lp_file.R
#	R/write_solver_files.R
 
Package: CARNIVAL
Commit: eccb5c33a926c38f5397d87689cc192ad2ca2902
Author: Olga Ivanova <>
Date: 2021-03-17 20:06:31 +0100
Commit message:

 Introducing json parameters (partial implementation)
 
Package: CARNIVAL
Commit: c44ddc3daaee85b2617b31c6fa5d0f2a881e3ecc
Author: Olga Ivanova <>
Date: 2021-03-16 21:57:12 +0100
Commit message:

 partial constraints clean up
 
Package: CARNIVAL
Commit: a0ecd35dfa94abbad3d2b2de1d6cef5b98b85fd6
Author: Olga Ivanova <>
Date: 2021-03-16 10:29:04 +0100
Commit message:

 fixes for refactored code: now updated API works.
 
Package: CARNIVAL
Commit: d014854c6fde18b599f9ec7c3e33804089e338cc
Author: Olga Ivanova <>
Date: 2021-03-15 00:20:30 +0100
Commit message:

 separating exports of solvers to different folders
 
Package: CARNIVAL
Commit: e2d5a0150439821e25b00c29d7e239f977c48d2c
Author: Olga Ivanova <>
Date: 2021-03-14 21:35:59 +0100
Commit message:

 Adding further clean up of parameters list for carnival options, updating checking functions, removing conditions and repIndex (was not in use). Code is not tested yet!
 
Package: CARNIVAL
Commit: b3ed6041211c596a2b215cecba296d847fb35b07
Author: Olga Ivanova <>
Date: 2021-03-12 20:20:45 +0100
Commit message:

 fix of error message from cplex (line 64 in example 1 generated LP file was empty if as.data.frame transformation skipped for prior knowledge network)
 
Package: CARNIVAL
Commit: f6982ce9b148c05bd91236eb5dfb692f9db5c6f7
Author: Olga Ivanova <>
Date: 2021-03-12 19:40:11 +0100
Commit message:

 more small cleanups and fixes before push
 
Package: CARNIVAL
Commit: 2012f2ce07ba95ff221228744c965578d2d0f092
Author: Olga Ivanova <>
Date: 2021-03-12 17:54:22 +0100
Commit message:

 further prepush clean up
 
Package: CARNIVAL
Commit: 528cb08e38a80c70068f2910d7088f43bff44dd0
Author: Olga Ivanova <>
Date: 2021-03-12 15:38:45 +0100
Commit message:

 pre push clean up
 
Package: CARNIVAL
Commit: 208aeb4481c97bec93373b29867a4ef80622f9a0
Author: Olga Ivanova <>
Date: 2021-03-12 15:18:27 +0100
Commit message:

 minor formatting changes, control index identifiers - new function, old removed
 
Package: CARNIVAL
Commit: 2b607aee5ed7340597ec3057f167a87daeb2aee6
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2021-03-12 12:59:43 +0100
Commit message:

 API changes: half cooked
 
Package: CARNIVAL
Commit: f2e8b3759bcbfec8451745f06dd7b561380da2d2
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2021-03-08 16:46:10 +0100
Commit message:

 tiny cleanup
 
Package: CARNIVAL
Commit: 101fa8ee547df2b9dd989c349c826d1b361de00d
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2021-03-04 22:51:01 +0100
Commit message:

 implemented a simple version of loading preparsed data and lp files, v.1
 
Package: CARNIVAL
Commit: f5ecbf2b5b73a97857bba18a243e9d886a4fcee7
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2021-03-02 20:10:44 +0100
Commit message:

 api changes, not working code!
 
Package: CARNIVAL
Commit: 92c4823b6f88b7f6054e385754eb6165d0c02c08
Author: ivanovaos <ivanovaos.09@gmail.com>
Date: 2021-02-09 15:00:03 +0100
Commit message:

 Merge pull request #49 from BartoszBartmanski/devel_2_1

Updates to the vignette and the README files 
Package: CARNIVAL
Commit: 5962771a61a51fbc4d2791b1117c0b8af276fa69
Author: Bartosz Bartmanski <bartoszbartmanski@gmail.com>
Date: 2021-02-01 11:38:08 +0100
Commit message:

 Updates to the vignette and the README files. Removed redundant Mybib2 file.
 
Package: CARNIVAL
Commit: b1e2cb220ae9344738b9844b63637bd15f9f7a8f
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2020-12-18 16:46:32 +0100
Commit message:

 Merge branch 'devel_2_1' into changing-api

* devel_2_1:
  adding unit test for parse_cplex_log
  fix detection of phases when a convergence table is missing
  - pipe cplex log to a temp file and to stdout - got rid of stringr and used baser - fixes for small case studies
  adding parser for CPLEX log
 
Package: CARNIVAL
Commit: 6af47b588a00c489ddc9127242b81b1290c8030e
Author: ivanovaos <ivanovaos.09@gmail.com>
Date: 2020-11-24 16:06:21 +0100
Commit message:

 Merge pull request #46 from saezlab/gabora_cplex_log

adding unit test for parse_cplex_log 
Package: CARNIVAL
Commit: 4215aab2c24d179f5817b205862cf54b19f8835c
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2020-11-16 15:39:52 +0100
Commit message:

 adding unit test for parse_cplex_log
 
Package: CARNIVAL
Commit: 6b92f10013ce1ef42785c6ba1982204e4829cd56
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2020-11-16 11:55:21 +0100
Commit message:

 Merge commit '696d4b4e6fd9160b4035b090005e7dd925c0e56e' into devel_2_1

* commit '696d4b4e6fd9160b4035b090005e7dd925c0e56e':
  fix detection of phases when a convergence table is missing
  - pipe cplex log to a temp file and to stdout - got rid of stringr and used baser - fixes for small case studies
  adding parser for CPLEX log

# Conflicts:
#	R/run_carnival.R
 
Package: CARNIVAL
Commit: 696d4b4e6fd9160b4035b090005e7dd925c0e56e
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2020-11-16 11:30:56 +0100
Commit message:

 fix detection of phases when a convergence table is missing
 
Package: CARNIVAL
Commit: 427df0ad370b7ddca82a6b2c602ffa69fb7971fc
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2020-11-09 13:21:08 +0100
Commit message:

 - pipe cplex log to a temp file and to stdout
- got rid of stringr and used baser
- fixes for small case studies
 
Package: CARNIVAL
Commit: 717edfcb5cd5968a4da9094a99ead3af56e0484c
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2020-11-05 16:01:19 +0100
Commit message:

 adding parser for CPLEX log
 
Package: CARNIVAL
Commit: e8ad7a51bb87096c6223aef41130cf30b96d6cdc
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2020-10-21 17:22:36 +0200
Commit message:

 introducing default cplex options and default Carnival cplex option, starting to change parameters checks
 
Package: CARNIVAL
Commit: 963b99e5fae03f4c917403fdbc4a116cbb5dba19
Author: Olga Ivanova <ivanovaos.09@gmail.com>
Date: 2020-10-21 15:45:25 +0200
Commit message:

 unified file names
 
Package: chromhmmData
Commit: eac7645dff45982637f04ecfaac44c206dfbc496
Author: Mahmoud Ahmed <mahshaaban2@gmail.com>
Date: 2021-05-12 09:37:55 +0900
Commit message:

 add vignette
 
Package: NanoMethViz
Commit: 41fa09493fc1beffc8b291a4439be68cc02d43ea
Author: Shians <registertonysu@gmail.com>
Date: 2021-05-10 10:43:36 +1000
Commit message:

 Fixed `plot_agg_regions()` handling of list of regions
 
Package: edgeR
Commit: 43d8f81756a6452f9f81a9231eb913025e8ae93d
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2021-05-12 10:31:55 +1000
Commit message:

 edgeR 3.33.5
- Remove the "BCV" method in plotMDS.DGEList();
- Update the edgeR User's Guide;
- Update NEWS.Rd;
- Update test files.
 
Package: Dino
Commit: 23e1deed89a965040681f40bfb2a8e30b2944cdc
Author: brown46 <brown46@brown46.local>
Date: 2021-05-11 18:44:32 -0500
Commit message:

 Rebuild Bioconductor submission
 
Package: OmnipathR
Commit: 2633ec7cb1584f74b3653458c0472438cfab6d2d
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-12 01:26:42 +0200
Commit message:

 Merge branch 'master' into bioc-2021-spring
 
Package: OmnipathR
Commit: b694660b28b22660683663cbf7181c6bb1ff3a14
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-12 01:26:28 +0200
Commit message:

 donttest for kegg_pathway_download (due to issues with Bioc Windows build server)
 
Package: OmnipathR
Commit: af2abb0d270eeb308b5a174f0a9dcf263781de6b
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-10 01:16:27 +0200
Commit message:

 v2.99.19 in news
 
Package: universalmotif
Commit: 3d79bab65de4d96cfb7f228b7e2d29ce2897861c
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2021-05-12 00:37:10 +0200
Commit message:

 TEMPORARILY disable motif_tree(...,layout=daylight) example until ggtree is fixed
 
Package: PureCN
Commit: dec6c1e1109f366882d614f20880753a680d3dcf
Author: Markus Riester <markus.riester@novartis.com>
Date: 2021-05-11 18:10:29 -0400
Commit message:

 Documentation updates and minor issue fixed in IntervalFile.R.
 
Package: NetSAM
Commit: 4f381fdb2a614043ebc7b46a6a925dd76f152920
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2021-05-11 16:22:07 -0500
Commit message:

 update version
 
Package: NetSAM
Commit: 99bcc814178f3a6f29aaeabc1cca0c4ce3e8d2c2
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2021-05-11 16:19:09 -0500
Commit message:

 update version
 
Package: NetSAM
Commit: b62aadfbb6406fba2323a44a6aaa4b09b1f1c903
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2021-05-11 16:08:58 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: NetSAM
Commit: fb0313b800fd4c96beb06772310c30bfaf36bb5f
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2018-03-05 17:14:23 -0600
Commit message:

 release 2.0.5
 
Package: NetSAM
Commit: b4db8191dc66f0ba07199d34ee79e7710dd86f13
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2018-02-06 08:22:05 -0600
Commit message:

 In constructing consensus network, use "__" instead of "_" to connect edge genes, just
in case that gene names contain "_".
 
Package: NetSAM
Commit: 1cd9c62c32140406d50858b867f81fd8654bd12f
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2018-02-02 14:51:40 -0600
Commit message:

 Remove outputfile from consensusNet()
 
Package: NetSAM
Commit: fd270dcd71894e8dda5244c86ffaa535c135934a
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2018-02-02 14:26:33 -0600
Commit message:

 For consensusNet, there are two levels of parallelims.
(1) the number of concurrent MatNet processes
(2) for each MatNet procesess, how many threads can be used
These two numbers can be now be set separately.
 
Package: NetSAM
Commit: 88c42773cfe45b4f404101ed78c3917c7a7be4b0
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2017-10-02 08:50:21 -0500
Commit message:

 Add naPer parameter to consensusNet function
 
Package: NetSAM
Commit: b746eca4b0691b757e823f832567c4643f8e2181
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2017-08-16 09:42:48 -0500
Commit message:

 Remove dependency on snow, use parallel instead
 
Package: NetSAM
Commit: d683efc2738d9463be0f15abd92667df17f7abd6
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2017-08-08 15:34:33 -0500
Commit message:

 * rewrite vignettes with Rmarkdown
 
Package: NetSAM
Commit: 5540a9dca64c03645fb219f75a9c663ef22e3ca9
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2017-08-07 17:10:15 -0500
Commit message:

 ignore anything under inst/doc
 
Package: NetSAM
Commit: 2327b563e619e4e42875dd3bcba18f31e0c7637a
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2017-08-07 15:35:29 -0500
Commit message:

 * add consensusNet function
* replace parallel backend with doParallel
 
Package: NetSAM
Commit: f6f70311255154686985fc0bc4e77f050c718e29
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2017-08-07 11:47:22 -0500
Commit message:

 ignore build directory
 
Package: NetSAM
Commit: b0533bbdc9bb8e5938cd3824fe5a4283ef1abf2d
Author: Zhiao Shi <zhiao.shi@gmail.com>
Date: 2017-07-18 09:42:41 -0500
Commit message:

 initial commit
 
Package: hca
Commit: ec6978c32aabb38c58a73db6fe1073a44e1733b2
Author: MRMcD <49954418+reed-mcdaniel-716@users.noreply.github.com>
Date: 2021-05-11 17:14:54 -0400
Commit message:

 Merge pull request #15 from Bioconductor/0.99.7-format-validate

introduce .wrap_lines() to produce lines wrapped to console width 
Package: hca
Commit: 873c4bb8343c4c749e162b794f4ee9eebd4dace2
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-05-11 13:34:32 -0400
Commit message:

 introduce .wrap_lines() to produce lines wrapped to console width

- intended for messages, etc., seen by the user, e.g., facet_options() error
  that might span multiple lines
- adjusts to getOption("width") and hence to, for example RStudio console
  width
 
Package: epigraHMM
Commit: 64ca00a39ea82c9e6066de6245d9860d0eb4f762
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 23:10:22 +0200
Commit message:

 version bump
 
Package: epigraHMM
Commit: 3f1768f0791d6a592ef0306febf3be82adb16b13
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 23:09:52 +0200
Commit message:

 Speeding up examples and vignette
 
Package: dittoSeq
Commit: 0a04fff47f552991eef78def61a7edaefdc1032e
Author: Daniel Bunis <daniel.bunis@ucsf.edu>
Date: 2021-05-11 13:53:24 -0700
Commit message:

 Version Bump & NEWS Update

and roxygenize 
Package: dittoSeq
Commit: a2b33c730f6742d41961bd5728f34367064c3537
Author: dtm2451 <daniel.bunis@ucsf.edu>
Date: 2021-05-11 13:23:45 -0700
Commit message:

 Switch default for 'retain.factor.levels' to 'FALSE'

& add tests!
 
Package: dittoSeq
Commit: bd6aa4ca99610cb8a39e181a53f4fe3c14d50adc
Author: dtm2451 <daniel.bunis@ucsf.edu>
Date: 2021-05-11 12:30:26 -0700
Commit message:

 Adds 'retain.factor.levels' control to 'dittoFreqPlot()'
 
Package: BayesSpace
Commit: 3d75fbe0dc4009ab5ed98fd0aadd6afe73df3027
Author: Edward Zhao <zhaoe@uw.edu>
Date: 2021-05-06 09:17:00 -0700
Commit message:

 update to NEWS and version to 1.1.3
 
Package: BayesSpace
Commit: 0b4aacc34f309f4bb788fb3c1d9194062aa058ee
Author: Edward Zhao <zhaoe@uw.edu>
Date: 2021-05-04 14:59:52 -0700
Commit message:

 update URL for datasets
 
Package: BayesSpace
Commit: 9254efaa69958bf676e924e0369beca6e4aca993
Author: Edward Zhao <zhaoe@uw.edu>
Date: 2021-03-04 23:01:06 -0800
Commit message:

 generate documentation
 
Package: BayesSpace
Commit: 87bcca161ae818311967acc91b28766019c562ae
Author: Edward Zhao <zhaoe@uw.edu>
Date: 2021-03-04 22:42:46 -0800
Commit message:

 documentation
 
Package: BayesSpace
Commit: e38c95d26f29a356fe3d3f76150c328d44431e23
Author: Matt Stone <mstone@fredhutch.org>
Date: 2020-12-30 15:53:20 -0800
Commit message:

 Fix character/factor labels in clusterPlot()
 
Package: BayesSpace
Commit: 18d2997e60c5623d0ce823a67f8dcb920d8fc389
Author: Matt Stone <mstone@fredhutch.org>
Date: 2020-12-03 20:35:18 -0800
Commit message:

 Merge branch 'master' of github.com:edward130603/BayesSpace
 
Package: BayesSpace
Commit: e8a2739901dbc01ab1f498120a137f536ed17349
Author: Matt Stone <mstone@fredhutch.org>
Date: 2020-12-03 20:35:04 -0800
Commit message:

 bump version
 
Package: BayesSpace
Commit: 5e40f78df744af9ff213c959476d7efb4716991e
Author: Matt Stone <mstone@fredhutch.org>
Date: 2020-11-17 20:08:12 -0800
Commit message:

 Update README and remove bioc-check action

* Replace badge in README with bioconductor build status
* Add bioconductor to installation details
* bioc-check action was bugged and redundant with bioc build system
 
Package: BayesSpace
Commit: 84ec24dbc3985a5cb3f20b293543637a72b30857
Author: Matt Stone <mstone@fredhutch.org>
Date: 2020-11-17 14:19:34 -0800
Commit message:

 use exact PCA
 
Package: MouseGastrulationData
Commit: 78ffcdaa4e48618d4b4bfae21a4811a3a6adf6ee
Author: jonathangriffiths <7976085+jonathangriffiths@users.noreply.github.com>
Date: 2021-05-11 21:00:48 +0100
Commit message:

 Version bump + typo fix
 
Package: MouseGastrulationData
Commit: 93554a31915c4734b46c26e658b212846a139b59
Author: jonathangriffiths <7976085+jonathangriffiths@users.noreply.github.com>
Date: 2021-05-11 19:31:47 +0100
Commit message:

 Bugfix
 
Package: MouseGastrulationData
Commit: 1e6b33f1ef6b375daba5a7ad8d4a30066471204a
Author: jonathangriffiths <7976085+jonathangriffiths@users.noreply.github.com>
Date: 2021-05-11 19:11:26 +0100
Commit message:

 New approach for getData sce-making
 
Package: MouseGastrulationData
Commit: cde6ab61c3b155bfd8adc4f0f33c08b4c181ca9b
Author: jonathangriffiths <7976085+jonathangriffiths@users.noreply.github.com>
Date: 2021-05-11 17:52:09 +0100
Commit message:

 getData refactor
 
Package: systemPipeTools
Commit: 4c1e6e67ec53ffe571493dbcfbba0e61be392e55
Author: dcassol <danicassol@gmail.com>
Date: 2021-05-11 13:01:40 -0700
Commit message:

 version up
 
Package: scanMiR
Commit: 4efd15cb6eb9d1230d636f95386973f0097cfcb9
Author: fridoling <fridoling@hotmail.com>
Date: 2021-05-11 19:01:31 +0000
Commit message:

 version bump
 
Package: scanMiR
Commit: f670e1a3fb7f8295b678130212db827dd73be5e8
Author: fridoling <fridoling@hotmail.com>
Date: 2021-05-11 19:00:22 +0000
Commit message:

 update vignette
 
Package: scanMiR
Commit: de315a259ed058adceea65826242eefd42c3fce9
Author: fridoling <fridoling@hotmail.com>
Date: 2021-05-11 18:42:27 +0000
Commit message:

 a and c as log
 
Package: scanMiR
Commit: 7078fb02ad3422b73e1cee27e61be8e111eebc88
Author: plger <pl.germain@gmail.com>
Date: 2021-05-11 17:25:01 +0200
Commit message:

 updated aggregation formulas
 
Package: scanMiR
Commit: 40d668a484d95ef8faec352b36d8101481e750ff
Author: plger <pl.germain@gmail.com>
Date: 2021-05-09 10:48:14 +0200
Commit message:

 resolved merge
 
Package: scanMiR
Commit: 94895be920e884c55e1db31496a166c5dcf48d48
Author: plger <pl.germain@gmail.com>
Date: 2021-05-09 10:46:42 +0200
Commit message:

 Merge branch 'master' of github.com:ETHZ-INS/scanMiR
 
Package: scanMiR
Commit: d441505bf71c9afe1fc213c4a9427c74202406fb
Author: plger <pl.germain@gmail.com>
Date: 2021-05-09 10:34:09 +0200
Commit message:

 version bump
 
Package: scanMiR
Commit: 6f0a9e347cbffc5b8991e1e6c8c5f047873b839c
Author: plger <pl.germain@gmail.com>
Date: 2021-05-09 10:33:23 +0200
Commit message:

 added lenght correction when aggregating separetely
 
Package: cosmosR
Commit: f4eb97c690950524ea4c2f87ce39c5b3de3c96f5
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-05-11 20:58:20 +0200
Commit message:

 Small fixes of R CMD check, BiocCheck and devtools::check
 
Package: cosmosR
Commit: 885cfe2d9cd7c50aeacce25db889a60b273547ed
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-05-11 18:20:04 +0200
Commit message:

 Vignette figure directory update
 
Package: cosmosR
Commit: 1e27a72e8bbf8eeb311b606d0ab61f86f4c182fa
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-05-11 11:42:14 +0200
Commit message:

 Merge branch 'master' of https://github.com/saezlab/COSMOS
 
Package: cosmosR
Commit: 77eac6dfa103d01da32d20aa1952c324fcf63bc1
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-05-11 11:42:07 +0200
Commit message:

 Small additional changes of data loading dependencies and code formatting
 
Package: cosmosR
Commit: c14b6105948845381a2870c83dc24f1528049232
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-11 10:11:25 +0200
Commit message:

 Merge branch 'master' of github.com:saezlab/cosmosR
 
Package: cosmosR
Commit: da0ac321153508c86d1cdf97c356c7ea60bb4eb1
Author: adugourd <adugourd@ukaachen.de>
Date: 2021-05-11 10:01:11 +0200
Commit message:

 Merge branch 'master' of https://github.com/saezlab/cosmosR
 
Package: cosmosR
Commit: f356d6bb79a1230b7647ebea48e8c15ecaa27555
Author: adugourd <adugourd@ukaachen.de>
Date: 2021-05-11 10:00:58 +0200
Commit message:

 fixed transforming sapply into vapply when possible
 
Package: cosmosR
Commit: 888cd0c05811359459ed4f4b8dd52ba766760173
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-11 09:47:08 +0200
Commit message:

 fixing warning
 
Package: cosmosR
Commit: 3cd4760314097a5f6bb5192f55a581484c5041d2
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-11 09:39:38 +0200
Commit message:

 Merge branch 'master' of github.com:saezlab/cosmosR
 
Package: cosmosR
Commit: 07a1d41feee5907be1a0035f6de209ef5aa2e7b7
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-11 09:27:49 +0200
Commit message:

 Merge pull request #10 from saezlab/christianholland-patch-1

Small fix with installation section 
Package: cosmosR
Commit: e7ff070daf70c104d28b232b4b41c1babdbc9a36
Author: Christian Holland <cholland2408@gmail.com>
Date: 2021-05-11 09:25:45 +0200
Commit message:

 Update tutorial.Rmd 
Package: cosmosR
Commit: 972e17ffaa55cc8dc1ea423c596b1e1a72e92ecc
Author: Christian Holland <cholland2408@gmail.com>
Date: 2021-05-11 09:23:19 +0200
Commit message:

 Update tutorial.Rmd 
Package: cosmosR
Commit: 7fe75e64ade786ebe695989627c7ef1535a2f355
Author: adugourd <adugourd@ukaachen.de>
Date: 2021-05-11 09:19:22 +0200
Commit message:

 removed paste from condition signaler
 
Package: cosmosR
Commit: 6cd9da33d653eed98effc291c3fe340464fee52c
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-11 08:45:35 +0200
Commit message:

 fix merge conflict on description lazyloading

Merge branch 'master' of github.com:saezlab/cosmosR

# Conflicts:
#	DESCRIPTION
 
Package: cosmosR
Commit: ebe6aaf55686e12868f60a31083accc5b7289957
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-05-10 19:07:24 +0200
Commit message:

 Merge branch 'master' of https://github.com/saezlab/COSMOS

# Conflicts:
#	NEWS.md
 
Package: cosmosR
Commit: 97dd37472be31fdc3c25f2fc55eb5d5ef6177c3c
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-05-10 18:48:50 +0200
Commit message:

 Required Change - Omited lazydata loading

Omitted the loading and changed data loading dependencies in the code
 
Package: cosmosR
Commit: 077e50941c78c3187aa7aa0a04e47f0dec87c72e
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-05-10 18:44:00 +0200
Commit message:

 Required Change - Updated News.md documentation format
 
Package: cosmosR
Commit: 6161686c7185975cbb70d170058aa2792057129b
Author: Christian Holland <cholland2408@gmail.com>
Date: 2021-05-10 18:10:38 +0200
Commit message:

 made proper installation section 
Package: cosmosR
Commit: e5aca3a97f548ee2f02c3c4b0ee2cfddbf3e16c9
Author: Christian Holland <cholland2408@gmail.com>
Date: 2021-05-10 18:09:00 +0200
Commit message:

 shift installation from vignette to main page 
Package: cosmosR
Commit: 5606c8529120f5c37b0a3f50c6b0731002991357
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-10 17:12:20 +0200
Commit message:

 removed lazy load from description - fixing bioconductor issue
 
Package: cosmosR
Commit: 7994560a2a10495bed04c240a44f12f849cb034a
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-10 17:11:16 +0200
Commit message:

 remove docs folder - github io page will be fixed later
 
Package: cosmosR
Commit: 181e39329d74f1922d8508e0a1f8bca4e0cb4392
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-10 17:10:25 +0200
Commit message:

 removed figures from the manual folder
 
Package: cosmosR
Commit: 7904980d505d419f1ff798b2a5c669cd95f0f325
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-10 17:10:09 +0200
Commit message:

 updated readme and relocated figures to inst folder
 
Package: cosmosR
Commit: 598612d6c92be2de32561ceaad85c729849b76e1
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-10 17:03:49 +0200
Commit message:

 license stated in description only
 
Package: cosmosR
Commit: 6a34eeca8886c6e33476c5647851b6ad96d0401d
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-10 11:49:54 +0200
Commit message:

 fix formatiing of news
 
Package: cosmosR
Commit: 8b293963dc2206d407b64d64d4c43c469fbe37e9
Author: Attila Gabor <gabor.attila87@gmail.com>
Date: 2021-05-10 11:49:44 +0200
Commit message:

 add installation and ToC to vignette
 
Package: cosmosR
Commit: 5fc03c924226c8ab1dcf17483b9578cc29ca9ebe
Author: adugourd <adugourd@ukaachen.de>
Date: 2021-05-10 10:42:52 +0200
Commit message:

 updated landing page with pkgdown
 
Package: MAST
Commit: dd3aeff60f6270b1dc5a76da9aa074af364a6c27
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-05-11 14:24:42 -0400
Commit message:

 Add a exprs_values slot to the ZlmFit class.

Needed to maintain state in lrTest and bootstrapping.
 
Package: trio
Commit: f67c958931c3cc837cf295fc15c7e5f4e7ee14c1
Author: holgerschw <holgerschw@users.noreply.github.com>
Date: 2021-05-11 20:03:52 +0200
Commit message:

 Corrected a stupid mistake.
 
Package: ASpli
Commit: c7d879dd3e7c069f157bbf1bd85ea4d08f17b712
Author: andresrabinovich <andresrabinovich@gmail.com>
Date: 2021-05-11 13:14:42 -0300
Commit message:

 Resuelve el issue #8, DESCRIPTION incluia erroneamente graphic en lugar de graphics
 
Package: ASpli
Commit: 062e5dfe8dcf70d4f2a108c29ce290beb5f1921e
Author: andresrabinovich <andresrabinovich@gmail.com>
Date: 2021-05-11 12:34:54 -0300
Commit message:

 Resuelve el issue #7, agrega progress bar a binGenome
 
Package: ASpli
Commit: d5faa8f4382c674abf4d1137d29b091419a17f14
Author: andy <cursos@a2b2c.org>
Date: 2021-05-10 21:52:12 -0300
Commit message:

 Changes CITATION destination and fixes some problems with man
 
Package: BloodGen3Module
Commit: e13e3fd3759fb93a1df54e9c0658a57efc79d57a
Author: Drinchai <drinchai@gmail.com>
Date: 2021-05-11 21:21:08 +0400
Commit message:

 Update version
 
Package: BloodGen3Module
Commit: 50f36cc84f330dd30827a4d6cd1ca9dad87c1561
Author: Drinchai <drinchai@gmail.com>
Date: 2021-05-11 21:13:30 +0400
Commit message:

 updated scripts
 
Package: AHWikipathwaysDbs
Commit: 04edc62328d2a94c8b345bac188df41a8f04c199
Author: Kozo Nishida <kozo.nishida@gmail.com>
Date: 2021-05-12 02:08:10 +0900
Commit message:

 Add rmarkdown to Suggests 
Package: methylclockData
Commit: 39767192a6061c1560a490fd4477a96362aea2e0
Author: dpelegri <dpelegri@gmail.com>
Date: 2021-05-11 19:04:27 +0200
Commit message:

 added new data
 
Package: epigraHMM
Commit: 4b88bb4615f859ea259a68d77e37473147e5875d
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 18:33:25 +0200
Commit message:

 Speeding up tests
 
Package: epigraHMM
Commit: 9a8899e29e5dcb7d84cc2893ab765dcc813ffb3e
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 18:33:08 +0200
Commit message:

 Version bump
 
Package: ReactomeGraph4R
Commit: 5e7913b806d6066df626fd8fd7013f7e70c8d5c0
Author: chilampoon <clpoon807@gmail.com>
Date: 2021-05-11 12:28:36 -0400
Commit message:

 version bump again...
 
Package: GSVA
Commit: 32aee6be6b30fbfb5192ef400b123fc9a3fa97bb
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2021-05-11 18:25:49 +0200
Commit message:

 bump version
 
Package: ReactomeGraph4R
Commit: c1aadc37c079a5fb6c752e5d3e03c7d223b78987
Author: chilampoon <clpoon807@gmail.com>
Date: 2021-05-11 12:17:15 -0400
Commit message:

 minor changes
 
Package: BloodGen3Module
Commit: be54ac70b7b5a5ef5b8cbf64bb960a95ca030e9a
Author: Drinchai <drinchai@gmail.com>
Date: 2021-05-11 20:14:34 +0400
Commit message:

 Update version
 
Package: BloodGen3Module
Commit: 16b206057ee7e729d9be78f13c6467966f1ba607
Author: Drinchai <drinchai@gmail.com>
Date: 2021-05-11 18:57:47 +0300
Commit message:

 Delete .DS_Store 
Package: BloodGen3Module
Commit: c5805e3bc9186648dba3445385061494d91644f0
Author: Drinchai <drinchai@gmail.com>
Date: 2021-05-11 18:56:14 +0300
Commit message:

 Delete .DS_Store 
Package: BloodGen3Module
Commit: 74d5626038e74679aab5e0b29137df0f1b824dc1
Author: Drinchai <drinchai@gmail.com>
Date: 2021-05-11 19:53:05 +0400
Commit message:

 Update README.md
 
Package: BloodGen3Module
Commit: 422f776b40463a447ac2dd54270d62b4cf04ea2f
Author: Drinchai <drinchai@gmail.com>
Date: 2021-05-11 19:43:17 +0400
Commit message:

 updated scripts
 
Package: ReactomeGraph4R
Commit: fb8c61f55f941193f48c78b12657fc588d2929a9
Author: chilampoon <clpoon807@gmail.com>
Date: 2021-05-11 12:04:44 -0400
Commit message:

 bump
 
Package: ReactomeGraph4R
Commit: 4fbeee91fdc0320be9d4ba92188051034732a50a
Author: chilampoon <clpoon807@gmail.com>
Date: 2021-05-11 11:59:18 -0400
Commit message:

 Address some biocCheck notes
 
Package: BUSseq
Commit: 49b2bea14c4fea398a413a5219830535cc4caf7a
Author: BUSseq <sfd1994895@gmai.com>
Date: 2021-05-12 00:04:17 +0800
Commit message:

 Continue to fix warnings and errors

 
Package: InterCellar
Commit: 9c789dacdb334f1f88cfa9c5fdd9cd08aa15939d
Author: martaint <marta.interlandi01@gmail.com>
Date: 2021-05-11 17:36:23 +0200
Commit message:

 fix scsr and custom
 
Package: scone
Commit: f12d5e6ed66ae578a4d5ed35b7b4615aa97b2ac0
Author: Davide Risso <risso.davide@gmail.com>
Date: 2021-05-07 10:26:12 +0200
Commit message:

 Bump version
 
Package: scone
Commit: 6492c88dba320649bc66b8fe4faebfa06dabb1af
Author: Davide Risso <risso.davide@gmail.com>
Date: 2021-05-07 10:25:41 +0200
Commit message:

 Rescale PsiNorm normalized data in wrapper
 
Package: scone
Commit: 3feef5fee7be745902cf22371c7bf9e99d8a99bc
Author: Davide Risso <risso.davide@gmail.com>
Date: 2021-05-07 10:16:43 +0200
Commit message:

 Add PsiNorm wrapper
 
Package: scone
Commit: 8aeeec54443c471bacffb4e5e33007b0c1871b29
Author: Davide Risso <risso.davide@gmail.com>
Date: 2021-05-07 10:16:21 +0200
Commit message:

 Avoid inverse
 
Package: decoupleR
Commit: 1fb389b29b5a03e7a52c98896bd1ebe9a3ee6d13
Author: Jesús Vélez <jvelezmagic@gmail.com>
Date: 2021-05-11 10:19:26 -0500
Commit message:

 Bump version to 0.99.8
 
Package: decoupleR
Commit: 8caaeefd1c7af96ca92eab05860072067259f38d
Author: Jesús Vélez <jvelezmagic@gmail.com>
Date: 2021-05-11 10:17:17 -0500
Commit message:

 Remove LICENSE and .travis.yml
 
Package: celda
Commit: 3a9bde76dce733e1a97fb14c8fae354f5c20bfd7
Author: zhewa <zhe@bu.edu>
Date: 2021-05-11 11:10:13 -0400
Commit message:

 add displayName to featureModuleTable. Remove stringi
 
Package: celda
Commit: 5b961faeb72fa7b05b501e5b4d8d936844f2b9a5
Author: zhewa <zhe@bu.edu>
Date: 2021-05-11 09:43:13 -0400
Commit message:

 version bump
 
Package: celda
Commit: 2f5b22e4afe0f87e2ec4bd0a8794697822a9fc1c
Author: zhewa <zhe@bu.edu>
Date: 2021-05-11 09:41:58 -0400
Commit message:

 fix plotDimReduceFeature label bug
 
Package: singleCellTK
Commit: d2d4d0c71e2ff58300e3faf7918ea18538602371
Author: Yichen Wang <wangych@bu.edu>
Date: 2021-05-11 10:54:34 -0400
Commit message:

 Bumping to 2.1.1
 
Package: singleCellTK
Commit: e208c9ea01875b03ff606c561221829489aba512
Author: Yichen Wang <wangych@bu.edu>
Date: 2021-05-10 23:43:26 -0400
Commit message:

 Remove cache files
 
Package: singleCellTK
Commit: d2da70c304a101d6dd10419e66122f749be0cb8d
Author: Yichen Wang <wangych@bu.edu>
Date: 2021-05-10 23:30:48 -0400
Commit message:

 Try bumping to release v2.0.2
 
Package: proActiv
Commit: 84ad7d6ee3fea576b058a7a9652628fe8490d4ea
Author: Joseph Lee <joseph.lee@u.nus.edu>
Date: 2021-05-11 22:48:44 +0800
Commit message:

 update for Bioc 3.13
 
Package: epigraHMM
Commit: 0601455a69954971d9977c326c4d9cedac757a7d
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:46:54 +0200
Commit message:

 Improving identation, function length, and using auxiliary functions to facilitate testing
 
Package: epigraHMM
Commit: 68013dc4e48369da68fb3ae1ac14a86c98153389
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:45:31 +0200
Commit message:

 Cleaning up old base.R. Functions now are split by their role in base-*.R files
 
Package: epigraHMM
Commit: 76dcb7cd0479e512293f930434d235ea988f193f
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:45:02 +0200
Commit message:

 Adding exporters to base-writers.R
 
Package: epigraHMM
Commit: a5c48c505c30cc6ab59146fdc5fe2adac459a3fc
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:44:47 +0200
Commit message:

 Adding wrapper functions to base-wrappers.R
 
Package: epigraHMM
Commit: c414cb04208ede8a9fa5e717e9ed2987ffd1760c
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:44:29 +0200
Commit message:

 Adding general utility functions to base-utils.R
 
Package: epigraHMM
Commit: 9ddffd15052fa5869063d9b133f03a42646c8332
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:44:13 +0200
Commit message:

 Adding optimizers to base-optim.R
 
Package: epigraHMM
Commit: 8c797f99a57bd0a724a422825a9ebe1861ec4448
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:44:01 +0200
Commit message:

 Adding scripts with log-likelihood functions utilized by epigraHMM in base-loglikelihood.R
 
Package: epigraHMM
Commit: 7e3c0fea81eb342185c85128fb627a231494fe63
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:43:28 +0200
Commit message:

 Adding core scripts from epigraHMM (initializer, consensus, and differential peak caller) to base-core.R
 
Package: epigraHMM
Commit: ed441d7152642491dff8d852e4d8b872d3173359
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:42:50 +0200
Commit message:

 Adding scripts with code checkers in base-checkers.R
 
Package: epigraHMM
Commit: 13ad900c9a06be9a16881e8cc77ad2f80625810c
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:42:22 +0200
Commit message:

 Adding scripts with EM loops in base-EM.R
 
Package: epigraHMM
Commit: 15d4c128e97d6caecf9b17db565fe8d2427dba6c
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2021-05-11 16:41:59 +0200
Commit message:

 Version up
 
Package: rtracklayer
Commit: 2c4936861f62f62173097d6eeddb92936c570134
Author: Michael Lawrence <michafla@gene.com>
Date: 2021-05-11 07:38:01 -0700
Commit message:

 Merge pull request #49 from sanchit-saini/parseURI-fix

.parseUri() fix 
Package: rtracklayer
Commit: 245e6cc9914985d6d6eb4ede8371443dcfa30c06
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2021-05-11 09:11:37 +0530
Commit message:

 Update code according to updated .parseURI() implementation

- Update normURI() to checkURI()
 
Package: rtracklayer
Commit: 72f981da71f8106ea37c98bd237bfa21343d0372
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2021-05-10 22:34:30 +0530
Commit message:

 Remove duplicate code already present in BiocIO
 
Package: RnBeads
Commit: 33c6fdb9fa0da559d8ac8c06d6a536f4aa2077f2
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2021-05-11 16:34:43 +0200
Commit message:

 bumped version
 
Package: RnBeads
Commit: cf76f5bd41856fa929b8c759dc097dcb513b76c8
Author: Fabian Müller <fmueller@mpi-inf.mpg.de>
Date: 2021-05-11 16:32:59 +0200
Commit message:

 Merge branch 'feature/MouseMethylationBeadChip' of https://github.com/epigen/RnBeads
 
Package: RnBeads
Commit: 7f7fb554ba761a8b643b6c8704d19d3c506896d9
Author: lutsik <pavlo.lutsik@gmail.com>
Date: 2021-05-11 16:08:59 +0200
Commit message:

 added low bead coverage masking for array data 
Package: RnBeads
Commit: ecafa53b325cccfe8c7d589c2ec7264c67d5f99c
Author: lutsik <pavlo.lutsik@gmail.com>
Date: 2021-05-11 16:08:00 +0200
Commit message:

 added a possibilty to use bead coverage in greedycut 
Package: RnBeads
Commit: 335cee848264e5f93d691c259f044c6d001e5864
Author: lutsik <pavlo.lutsik@gmail.com>
Date: 2021-05-01 00:59:30 +0200
Commit message:

 modified greedycut to work with both p-value and coverage threshold 
Package: RnBeads
Commit: 80fe2b695629f6d38a0b03057326421e539492af
Author: lutsik <pavlo.lutsik@gmail.com>
Date: 2021-05-01 00:56:56 +0200
Commit message:

 added implementations of basic normalization methods 
Package: RnBeads
Commit: 30739e11360f90d3c88fa3773f004742440a84f4
Author: lutsik <lutsik@dkfz-vpn37.inet.dkfz-heidelberg.de>
Date: 2021-03-14 14:50:23 +0100
Commit message:

 updated the DESCRIPTION file to include normalizationMethods.R 
Package: RnBeads
Commit: ceda26c18220af96ce3d78a30c0ed5934fe63fdb
Author: lutsik <lutsik@dkfz-vpn21.inet.dkfz-heidelberg.de>
Date: 2021-02-23 23:45:52 +0100
Commit message:

 updated a platform support message in CNV analysis 
Package: RnBeads
Commit: ab71f4dcdab7f7214b0481200f91b429b572a2e6
Author: lutsik <lutsik@dkfz-vpn21.inet.dkfz-heidelberg.de>
Date: 2021-02-23 22:39:48 +0100
Commit message:

 added simple dye bias and background correction methods 
Package: RnBeads
Commit: b0e891c48a7a39139bb94e78ba2a52dcd1b1ff36
Author: lutsik <lutsik@dkfz-vpn21.inet.dkfz-heidelberg.de>
Date: 2021-02-06 23:45:13 +0100
Commit message:

 fixed enmix.oob for MMBC 
Package: RnBeads
Commit: 62ebd9592b80e4424c28a6a5596772df529bb790
Author: lutsik <lutsik@dkfz-vpn21.inet.dkfz-heidelberg.de>
Date: 2021-02-06 19:24:11 +0100
Commit message:

 fixed QC probe-based batch effect detection 
Package: RnBeads
Commit: 969e4b1e7efbee1c2dbae6228b1e830cdab259a0
Author: lutsik <lutsik@dkfz-vpn21.inet.dkfz-heidelberg.de>
Date: 2021-02-06 19:23:04 +0100
Commit message:

 added more normalization methods to options 
Package: RnBeads
Commit: 76233cef3ad437913e762544fd60ee1a04fcde19
Author: lutsik <lutsik@dkfz-vpn21.inet.dkfz-heidelberg.de>
Date: 2021-02-06 12:03:09 +0100
Commit message:

 -- QC for MMBC array

-- re-implemented normalization by scaling to conrols and negative
control-based background subtraction methods 
Package: RnBeads
Commit: 6e28585476fa0291a66b91921c10658dbec8bfc3
Author: lutsik <lutsik@dkfz-vpn21.inet.dkfz-heidelberg.de>
Date: 2021-02-03 00:24:04 +0100
Commit message:

 first version of the QC module for MMBC 
Package: RnBeads
Commit: 911a95ba9b5050ddb2cde2a78db30f5b721e2593
Author: lutsik <lutsik@b370-mb01.inet.dkfz-heidelberg.de>
Date: 2021-01-26 18:23:40 +0100
Commit message:

 fixed the annotation token 
Package: RnBeads
Commit: b6cc067628e0c03bb244a59ccde953e5ab85f020
Author: lutsik <lutsik@b370-mb01.inet.dkfz-heidelberg.de>
Date: 2021-01-26 18:08:57 +0100
Commit message:

 first version of the MMBC support 
Package: splatter
Commit: c8de6598477f1324d4dded43d3b5db62ee492523
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-05-11 16:17:56 +0200
Commit message:

 Fix DESCRIPTION date
 
Package: splatter
Commit: 7a4c13a2d89c133a22511d9ebe22441bd31e1d7d
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-05-11 16:16:59 +0200
Commit message:

 Merge pull request #113 from azodichr/splatPop_updates

Alright, I think this is ready to merge 🎉. Thanks for addressing all my comments. There might be some small changes to make later on but let's see if it passes the Bioconductor checks first 🤞🏻. 
Package: splatter
Commit: 6396e1650d888b846e96abcca41081087ed18dd8
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-05-11 16:14:51 +0200
Commit message:

 Update DESCRIPTION and NEWS
 
Package: splatter
Commit: d4937499ff75bb74ea4b421c16097e9fc8ceabf7
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-05-11 16:07:05 +0200
Commit message:

 Minor changes to tests to avoid #114
 
Package: splatter
Commit: accdf187137025a479969f93b02567aa79dc6ce0
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-05-11 13:50:02 +1000
Commit message:

 minor fixes suggested by luke
 
Package: splatter
Commit: 99db327a844ca56ca84f79237372199286a90a0a
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-05-06 16:26:53 +0200
Commit message:

 Fix vector argument name in expandParams() docs
 
Package: splatter
Commit: 3e111130a69f9aefe565c733fa9f4a5d08a932e1
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-05-04 17:09:38 +1000
Commit message:

 fix issue with examples taking too long
 
Package: splatter
Commit: dbc16b718dd3916b2b33e798385d7df664e12155
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-05-04 16:28:08 +1000
Commit message:

 fixed merge conflicts
 
Package: splatter
Commit: f2dba49a7ccb9124c665b2b9e0523c2a38df774a
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-05-04 15:21:43 +1000
Commit message:

 Address first half of comments from Luke
 
Package: splatter
Commit: 3e931edcfe5f855dc30bc68c37b6ff1a0a2a64fc
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-04-23 10:36:44 +0200
Commit message:

 Add missing package prefix
 
Package: splatter
Commit: d5b06275f2455ed8889f7f702ca84c14f9b98fbe
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-04-23 10:34:24 +0200
Commit message:

 Move parameter expansion to a function called by methods
 
Package: splatter
Commit: 3bd418fcaf389430cabec59bbce599a553d59fad
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-04-15 11:21:49 +1000
Commit message:

 minor bug fix: splatPop batches was not able to take in different effect size distribution parameters for different batches.
 
Package: splatter
Commit: 994fea0db1115559f67df0867f296147320c3d08
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-04-15 10:51:34 +1000
Commit message:

 minor bug fix: splatPop batches was not able to take in different effect size distribution parameters for different batches.
 
Package: splatter
Commit: b25606527dd0d40c132296881ffce0e31a8af7b4
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-03-29 16:29:07 +1100
Commit message:

 Added conditional effect feature
 
Package: splatter
Commit: 712393eb65a5fadcb8dda8c2534cf638ad9c6730
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-03-03 10:55:56 +1100
Commit message:

 Sample n cells per sample from user provided distribution
 
Package: splatter
Commit: 387d700124445a452fffa8d2dbe6d84f90a6ee5a
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-02-15 13:03:08 +1100
Commit message:

 Update batch effect function for splatPop to simulate multiplexing
 
Package: splatter
Commit: 5e13209731524e589f9308af12319fe6e7e9f3a0
Author: cazodi <cazodi@svi.edu.au>
Date: 2021-01-14 17:12:35 +1100
Commit message:

 update default eQTL effect size parameters to include only GTEx thyroid eQTL with MAF greater than 10 percent
 
Package: splatter
Commit: 38c11a5284a182fcb0cd2513ab3d668653d11a07
Author: cazodi <cazodi@svi.edu.au>
Date: 2020-12-21 17:03:18 +1100
Commit message:

 Bug Fix: Gene outlier factors were being assigned to each individual separately. Fixed by assigning gene outlier factors during splatPopSimulateMeans instead of during splatPopSimulateSC. The outlier factor is now saved in the splatPop key.
 
Package: splatter
Commit: 0371168e8df6917b8a1b46a1d1a865b78ff5d35d
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2020-12-01 10:49:39 +0100
Commit message:

 Update NEWS again
 
Package: transcriptogramer
Commit: ab3a7c2c73d53eb6d82bf9bb3b5b65ffd1d40cc3
Author: Diego Morais <arthur.vinx@gmail.com>
Date: 2021-05-11 10:24:19 -0300
Commit message:

 Typo 
Package: ISAnalytics
Commit: f70029dbb24ae460f3ff3c1c3ea8dd46da4551b9
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-05-11 14:50:41 +0200
Commit message:

 [UPDATE] Upgrade to v 1.1.11
 
Package: ISAnalytics
Commit: b37a80c5465828560d19c99c2ef64914ea578cbe
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-04-08 14:39:42 +0200
Commit message:

 Update pkgdown.yaml 
Package: ISAnalytics
Commit: f2f54591cf71be661b8f080861798217866586dd
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-04-08 14:33:52 +0200
Commit message:

 Update pkgdown.yaml 
Package: UMI4Cats
Commit: dc8fab93c73774558e406ef99bc36f2dcfff2d14
Author: mireia-bioinfo <mireiarr9@gmail.com>
Date: 2021-05-11 14:25:08 +0200
Commit message:

 Merge branch 'master' of github.com:Pasquali-lab/UMI4Cats
 
Package: UMI4Cats
Commit: 4585617bed63d5dcec5785cfe9afa1ac5885a106
Author: mireia-bioinfo <mireiarr9@gmail.com>
Date: 2021-05-11 14:23:26 +0200
Commit message:

 Minor typo
 
Package: UMI4Cats
Commit: 25362b4a74f851b0615f7c2be563b802cb070ed8
Author: mireia-bioinfo <mireiarr9@gmail.com>
Date: 2021-05-11 14:23:26 +0200
Commit message:

 mend
 
Package: structToolbox
Commit: 3ee3b4a2024b5b20dfb96e4eb39e6f860bda8b66
Author: Gavin Rhys Lloyd <g.r.lloyd@bham.ac.uk>
Date: 2021-05-11 12:46:41 +0100
Commit message:

 update news and version bump

ready for v1.4.0 bioc 3.13 release
 
Package: structToolbox
Commit: e4e79a3666b2f7286eb37c8c0c267f41fea700ae
Author: Gavin Rhys Lloyd <g.r.lloyd@bham.ac.uk>
Date: 2021-05-11 11:28:24 +0100
Commit message:

 add vip_summary chart
 
Package: GSVA
Commit: 80ded0b1aad1b1bcef68d4f124ea6bedcff0aac7
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2021-05-11 13:42:56 +0200
Commit message:

 Merge branch 'pablo-rodr-bio2-shinyDashboard'
 
Package: GSVA
Commit: a3216e79e33918d5a8a06d8920e3a8dbede8c65a
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2021-05-11 13:20:49 +0200
Commit message:

 Merge branch 'shinyDashboard' of https://github.com/pablo-rodr-bio2/GSVA into pablo-rodr-bio2-shinyDashboard
 
Package: GSVA
Commit: 8f6a756d9ba11e1b0177da36aba5946b5bbaa1fe
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-05-11 12:25:57 +0200
Commit message:

 added css ad shinydashboard
 
Package: GSVA
Commit: c49457078c9c70b830682e7582c7abaa8dc92a64
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-05-07 04:18:33 -0400
Commit message:

 added css to cls and dwn btn
 
Package: GSVA
Commit: 8874e35d95dfdd68e7ecc9da4474b2638191c882
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-05-06 19:51:11 +0200
Commit message:

 still bad buttons
 
Package: GSVA
Commit: b7783fd5f607a86e23be243b840c1aef12d31bac
Author: pablo-rodr-bio2 <pablo.rodriguez.bio2@gmail.com>
Date: 2021-05-05 08:01:52 +0200
Commit message:

 proving dashboards
 
Package: GSEABase
Commit: 2128cd75d791b4dacb783ae70afedaf707809cee
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-05-11 07:29:44 -0400
Commit message:

 Version bump for removing Unigene
 
Package: GSEABase
Commit: 74beabbe1abb9843abdc84947838713205b27070
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-05-11 07:23:01 -0400
Commit message:

 Remove unigene support
 
Package: UMI4Cats
Commit: 67bfc099841b9fb2629622eac86f562e1b077514
Author: mireia-bioinfo <mireiarr9@gmail.com>
Date: 2021-05-11 12:51:46 +0200
Commit message:

 Update maintainers
 
Package: Spaniel
Commit: 0303dbc879c455d4d82e6b9822ba4d7830cdb8ae
Author: Rachel Queen <rachel.queen@newcastle.ac.uk>
Date: 2021-05-11 11:53:35 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: Spaniel
Commit: 7704933037ff30913a6c4ec5f260f9490bb80747
Author: RachelQueen1 <rachel.queen@ncl.ac.uk>
Date: 2020-11-24 09:25:27 +0000
Commit message:

 Update README.md 
Package: Spaniel
Commit: d2a3c7f87f2ae5dff3e07a45581dfb112966bc9a
Author: RachelQueen1 <rachel.queen@ncl.ac.uk>
Date: 2020-11-24 09:25:06 +0000
Commit message:

 Update README.md

Correct developmental installation 
Package: Spaniel
Commit: f757f227d04411824d383353937bdd3ba22b3802
Author: RachelQueen1 <rachel.queen@ncl.ac.uk>
Date: 2019-10-04 09:40:35 +0100
Commit message:

 Update README.md 
Package: XNAString
Commit: 34f55e00c05da47d5be09f642e926bcf4eb770f9
Author: Marianna Plucinska <marianna.plucinska@roche.com>
Date: 2021-05-11 12:04:57 +0200
Commit message:

 Removed vapply from the code
 
Package: BgeeCall
Commit: 491d97b45b5b4e59ecaea3ea4f8da991537519e9
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-05-11 11:14:46 +0200
Commit message:

 dump version
 
Package: BgeeCall
Commit: 8ead965e45f82c1919e20449a0a312d7c130587a
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-05-11 11:14:15 +0200
Commit message:

 solve warnings and notes
 
Package: CNVgears
Commit: 8c1cd4fcf60c516562bd6fa14edd94db624f98a7
Author: Simone <sm@Simones-MacBook-Pro.local>
Date: 2021-05-11 10:11:31 +0200
Commit message:

 -mVersion bump
 
Package: CNVgears
Commit: cfc149c4c26d5a592456b3b965af3d2a41fd7862
Author: Simone <sm@Simones-MacBook-Pro.local>
Date: 2021-05-11 10:00:48 +0200
Commit message:

 -mUpdated CNVRs computation
 
Package: CNVgears
Commit: 11075d1b1a2358383768e878bb22da69d3b55a33
Author: Simone Montalbano <48947872+SinomeM@users.noreply.github.com>
Date: 2021-04-28 16:26:56 +0200
Commit message:

 Update CNVRs_creation.R 
Package: CNVgears
Commit: ea2f2d2295dca45857e8c5ec5de267fbd6135cbb
Author: Simone Montalbano <48947872+SinomeM@users.noreply.github.com>
Date: 2021-04-15 11:17:50 +0200
Commit message:

 Update README.md 
Package: scran
Commit: 2c32b7a9c9c433834a63862367851274d2bfd74b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-11 01:01:15 -0700
Commit message:

 Realize file-backed matrices prior to the PCA steps.
 
Package: ggtree
Commit: 384cc42a2cf5b6200756fc607b00a00598c65a25
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-05-11 15:24:10 +0800
Commit message:

 bump version up
 
Package: fishpond
Commit: fe9c275aed707d411d279d5df347e56d59acd344
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-05-11 09:23:17 +0200
Commit message:

 fix vignette
 
Package: apeglm
Commit: 5827c3d9198410cbf3762d363c81fd02c9cdbe3f
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-05-11 09:21:38 +0200
Commit message:

 remove test
 
Package: apeglm
Commit: d87a1599693aa330ff1e4374ffd1b71d3c10e466
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-05-11 09:10:05 +0200
Commit message:

 updating to fix vignette error
 
Package: beachmat
Commit: 99d970013bc972bdb5485f7bf502b5fe0c73b2cb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-10 23:51:37 -0700
Commit message:

 Testfix, added missing import.
 
Package: beachmat
Commit: 16b4ca9699bca87a5f3fea4a7e4d0ae4d11065c8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-10 23:41:03 -0700
Commit message:

 Coerce SparseArraySeeds to dgCMatrices by default.
 
Package: beachmat
Commit: a8e07745c7ccaa961ea316bba352c3d32aece7c9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-05-10 22:30:18 -0700
Commit message:

 Added a realizeFileBackedMatrix utility for downstream use.
 
Package: cellmigRation
Commit: 32419f4a9b8814d4f69f881b7aa5adb0ef47114d
Author: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: 2021-05-11 06:59:31 +0200
Commit message:

 Updated NEWS file
 
Package: SeqArray
Commit: cdec7d16b091245ba0f684ebcfbb7040c0a9bb32
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2021-05-11 01:07:16 -0500
Commit message:

 update NEWS
 
Package: gdsfmt
Commit: ee1cd280da15a3f0aef3cb6b0fd80893013869f3
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2021-05-11 01:01:10 -0500
Commit message:

 update NEWS
 
Package: SAIGEgds
Commit: 6e561331e0e80b8722c2c7194f0655a6baa816d5
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2021-05-11 00:55:34 -0500
Commit message:

 fix
 
Package: dittoSeq
Commit: 08cadf1a3146e35b40c5208a87d887c8aa6e94d3
Author: dtm2451 <daniel.bunis@ucsf.edu>
Date: 2021-05-10 22:37:25 -0700
Commit message:

 Revert "Update ComplexHeatmap tests"

This reverts commit a4f7ec449f0cf13a3a63424f61dba898550cfa50.
 
Package: dittoSeq
Commit: d9b60c2cd0b3331b922a82d78452eaf50e15331a
Author: Daniel Bunis <daniel.bunis@ucsf.edu>
Date: 2021-05-10 22:34:42 -0700
Commit message:

 Merge branch 'master' of https://github.com/dtm2451/dittoSeq
 
Package: dittoSeq
Commit: 80cb30449448a09e1a5d11e8b619b83a63a85a9f
Author: Daniel Bunis <daniel.bunis@ucsf.edu>
Date: 2021-05-07 13:34:03 -0700
Commit message:

 Version Bump & NEWS Update
 
Package: HIBAG
Commit: b8f58914fb76010d994f6e9f2379b0cf97067c44
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2021-05-11 00:28:04 -0500
Commit message:

 fix
 
Package: systemPipeTools
Commit: b29e0c6be51eb4c206ddbb60521e8245a8ddd860
Author: dcassol <danicassol@gmail.com>
Date: 2021-05-10 21:56:52 -0700
Commit message:

 version up
 
Package: ribor
Commit: 1edbdc9fd880125a776f6853d2f86d312d706ad8
Author: mjgeng <michael.j.geng@gmail.com>
Date: 2021-05-10 23:07:21 -0500
Commit message:

 added in new annotation functions
 
Package: ribor
Commit: 9c7c219a6a72e2cad90ea6bc59b3d92deb7b373e
Author: Michael Geng <michael.j.geng@gmail.com>
Date: 2021-05-10 17:36:45 -0500
Commit message:

 Merge pull request #18 from mjgeng/master

added in additional annotation functions for issue #16 
Package: ribor
Commit: a07faacf6e3dae371de12339387400dbf93a4bf4
Author: Michael Geng <michael.j.geng@gmail.com>
Date: 2021-05-05 17:33:01 -0500
Commit message:

 added in additional annotation functions
 
Package: ribor
Commit: 794b98e0e03dde41bc74427f52021ca61d28ca5b
Author: Michael Geng <michael.j.geng@gmail.com>
Date: 2021-02-09 10:47:00 -0600
Commit message:

 Merge pull request #15 from mjgeng/master

Add multiple ribo file section in vignette 
Package: ribor
Commit: e7b920b886095522d5fc55499ef03fe70fd18e18
Author: Michael Geng <michael.j.geng@gmail.com>
Date: 2021-02-09 10:45:25 -0600
Commit message:

 Add multiple ribo file section in vignette
 
Package: ribor
Commit: 268d01bafcc457db659c5bd1ca12e50f42f4b7dc
Author: Hakan Ozadam <hakanozadam@users.noreply.github.com>
Date: 2020-12-04 12:50:35 -0600
Commit message:

 Update README.md 
Package: ribor
Commit: bf5ef068f12dcd75ef2eb35adbd73122f26beef3
Author: Michael Geng <michael.j.geng@gmail.com>
Date: 2020-03-24 11:58:04 -0500
Commit message:

 Update README.md 
Package: PureCN
Commit: 076d2ed53a93acc2a350d777c4b31e0947dc0a2c
Author: Markus Riester <markus.riester@novartis.com>
Date: 2021-05-10 21:42:29 -0400
Commit message:

 Added tests for previous commit.
 
Package: PureCN
Commit: 77601e248f1b803383f0a2067bbc754442c9b661
Author: Markus Riester <markus.riester@novartis.com>
Date: 2021-05-10 20:11:18 -0400
Commit message:

 Fix breakpoints in baits.
 
Package: PureCN
Commit: de1dc16557442d758bd27fb0a535673ee52c3646
Author: Markus Riester <markus.riester@novartis.com>
Date: 2021-05-09 22:03:56 -0400
Commit message:

 More documentation updates regarding optional GC-normalization.
 
Package: RCy3
Commit: e9cbd09fec22b48405b60ed1febac70e2d64e64e
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2021-05-10 18:14:46 -0700
Commit message:

 version bump
 
Package: RCy3
Commit: 3348c653a0167420e0dc7354c927520719868183
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2021-05-10 18:07:30 -0700
Commit message:

 fixed logic now that .edgeNameToEdgeSUID has been fixed
 
Package: RCy3
Commit: eee9a404511e731c1c73ee179ea61e27c4b7794e
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2021-05-10 17:44:03 -0700
Commit message:

 fixing check and BioC check errors and warnings
 
Package: RCy3
Commit: 5b5f96fcf75c0df8d4f2836ad8ab9995cb0c4452
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2021-05-10 17:43:09 -0700
Commit message:

 Adding functions and tests for Annotations
 
Package: RCy3
Commit: 4d1e1994333d6b10955385a72f7e965fa621f1ee
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2021-05-10 16:16:36 -0700
Commit message:

 doc fix #103: names or suids
 
Package: RCy3
Commit: dd4a9359039b08f757c410e298aee48f7c1a06a6
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2021-05-10 15:35:30 -0700
Commit message:

 clean up
 
Package: RCy3
Commit: a73fbdd00068236588cbe4ebc5a658e7a2de91f3
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2021-05-10 15:34:42 -0700
Commit message:

 bug fix #133: alt to IRkernel
 
Package: ASpli
Commit: cdfdce1a2afbba7695f35e5623d29141675e8bdf
Author: estepi <soyestepi@gmail.com>
Date: 2021-05-10 19:02:23 +0200
Commit message:

 changes in description and news
 
Package: ASpli
Commit: 5ab3febf38d04759a678014f566ff2114ea5e927
Author: estepi <soyestepi@gmail.com>
Date: 2021-05-10 18:41:33 +0200
Commit message:

 add citation
 
Package: ASpli
Commit: e92b4bf79f274e6ccec42a5bf6502658c2554e52
Author: Andrés Rabinovich <andresrabinovich@gmail.com>
Date: 2021-04-23 17:59:35 -0300
Commit message:

 Adds an NA check for junctions when sumarizing reads. Removes NA junctions with a warning, solving issue #5
 
Package: ASpli
Commit: 844c8f90b3dbcbcf921e67518e4d67938f72726f
Author: Andrés Rabinovich <andresrabinovich@gmail.com>
Date: 2021-04-16 17:46:11 -0300
Commit message:

 Resuelve issue #3 comentando el codigo de busqueda del string "NA" en nombres de junturas. Pueden aparecer cromosomas con, por ejemplo, nombres tipo rDNA con lo cual no era un buen metodo para encontrar junturas NA. Ademas, el comportamiento que tenia era de debuguing y solo servia para colgar la ejecucion
 
Package: ASpli
Commit: bebaed4b4cca15715d16b85e0423beab3a41e1c7
Author: Ariel Chernomoretz <ariel@df.uba.ar>
Date: 2021-03-10 14:25:22 -0300
Commit message:

 Merge branch 'main' of https://github.com/chernolab/ASpli-labo into main
 
Package: ASpli
Commit: dd99c96a6d5da6467651792f371e876f4d62146b
Author: Ariel Chernomoretz <ariel@df.uba.ar>
Date: 2021-03-10 14:06:39 -0300
Commit message:

 update Readme.md
 
Package: ASpli
Commit: d3c58c3d6364ff51ecad2d66b78f6102d12b2114
Author: Ariel Chernomoretz <ariel@df.uba.ar>
Date: 2021-03-10 14:01:09 -0300
Commit message:

 udate Readme.md with workin quick start example.

Add citation paragraph and github ASpli
 
Package: EnrichmentBrowser
Commit: 26e4e9cc4d36fd7dab6739686133bf97086cb540
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2021-05-10 20:13:49 -0400
Commit message:

 postpone new features to next release
 
Package: BiocGenerics
Commit: c4afd4e74b2e6ea9f9b49416ecc4061407f63747
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-10 16:33:14 -0700
Commit message:

 code formatting
 
Package: BiocGenerics
Commit: 75a31a7bccfbb6dd25b36de78b10c015a4ccd6b6
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-05-10 16:31:49 -0700
Commit message:

 Revisit my previous fix to long standing bug in updateObject() on a factor
 
Package: AnnotationDbi
Commit: 257f83161dc27f5523c6bd64abc3aa2e4ea77bbc
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-10 15:24:51 -0700
Commit message:

 Fix to a unit test.
 
Package: AnnotationDbi
Commit: 427c7d1124e7773748c2de22ca6faa607c7f0bfb
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-10 15:01:24 -0700
Commit message:

 Changes to tests and help pages to acccommodate loss of UniGene tables.
 
Package: AnnotationDbi
Commit: e1196ea4ee7300991d7cb994dca72901233f1aa8
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-10 14:12:00 -0700
Commit message:

 This is a version bump after merging the anno_3_13 branch back into master. The branch was created
as part of the build for the April 2021 Bioconductor 3.13 release. Several things were changed

UniGene tables were removed from the OrgDb packages
Added Gene type table to OrgDb packages
Created new Orthology.eg.db package to map between species

This includes all the changes required to the AnnotationDbi package to accommodate the changes.
 
Package: AnnotationDbi
Commit: 8cccf3d301b754833a936abd44bf6c5f2877465b
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-10 14:10:15 -0700
Commit message:

 Merge branch 'anno_3_13'
 
Package: AnnotationDbi
Commit: 7a7614bbdab69e973eb9763fe326af21f0975fa7
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 15:33:16 -0700
Commit message:

 Small bugfix in select method for OrthologyDb.
 
Package: AnnotationDbi
Commit: 7bbd8a89b9879de82360244d278d0d87ba218504
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 15:21:57 -0700
Commit message:

 Small bugfix in select method for OrthologyDb.
 
Package: AnnotationDbi
Commit: e253e57734ffa7edb99e1baa9362434fb75d9b75
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 11:48:04 -0700
Commit message:

 Fix to creatAnnObjs to ignore Orthology.eg.db package, which has no BiMap objects.
 
Package: AnnotationDbi
Commit: 2188e5f666df70766013ec9859ce71360446b1b5
Author: Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal>
Date: 2021-05-06 17:55:20 +0000
Commit message:

 Added Orthology methods to collate field in DESCRIPTION
 
Package: AnnotationDbi
Commit: 7cd53cf5e6a5353b48a1776ee13d2fb0c4e0d439
Author: Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal>
Date: 2021-05-06 17:30:28 +0000
Commit message:

 Added keys, columns, keytypes and updated man pages for OrthologyDb.
 
Package: AnnotationDbi
Commit: 661bb6cf4f5646fb2f0e62f5eccfe0a3f29f1a7f
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-04 08:10:04 -0700
Commit message:

 Added OrthologyDb class
 
Package: AnnotationDbi
Commit: cc27707119a064ae40f37dc0001673f1caa863a8
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-28 08:03:33 -0700
Commit message:

 Added GENETYPE back to X laevis...
 
Package: AnnotationDbi
Commit: 37a03e1fe5f5276344fdf459015edb14e7486da8
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-28 06:33:23 -0700
Commit message:

 Fixed GENETYPE exclusion for C elegans.
 
Package: AnnotationDbi
Commit: 2103897edc66fc91e1188f2243f93172985131dc
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-27 16:59:12 -0700
Commit message:

 Back out removal of GENETYPE BiMap from other species.
 
Package: AnnotationDbi
Commit: 3794956dca415dda7f553b40edd25b0cf977d5f9
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-27 13:57:38 -0700
Commit message:

 Back out removal of GENETYPE BiMap from Rhesus.
 
Package: AnnotationDbi
Commit: a0187aa84920dd895a4bec33bd580cafd8b7ddab
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-23 13:11:27 -0700
Commit message:

 Replaced calls to dbGetQuery that modify the DB with calls to dbExecute.
 
Package: AnnotationDbi
Commit: fda9fd4b14ceba7ea41df803453911ae2aed7069
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-23 07:13:39 -0700
Commit message:

 Addded BiMap for gene type table.
 
Package: AnnotationDbi
Commit: 8e015d561f3009fec71cce56262f8b75f7e17cb3
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-22 10:06:10 -0700
Commit message:

 Added missing parenthesis in createAnnObjs-utils.R.
 
Package: AnnotationDbi
Commit: df0fddd4005182ff5467de3799d6abe74bd66ec4
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-19 13:57:49 -0700
Commit message:

 Removed UniGene queries and BiMap objects. Swapped much of the existing UniGene stuff to query the new gene type table.
 
Package: AnnotationDbi
Commit: aedc644792ef7a7d2852710cd308426b7ba2f3f5
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-16 09:03:23 -0700
Commit message:

 Initial commit of changes for removal of UniGene tables and introduction of gene type tables.
 
Package: AnnotationForge
Commit: 635c9bad4167f81af1d0097c23e47668194a2efd
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-10 15:43:59 -0700
Commit message:

 Changes to vignettes and ChipDb builder to accommodate loss of UniGene table.
 
Package: AnnotationForge
Commit: a173ca1ba1b4c66bdfc3c5f9d039c7ae547001f2
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-10 14:32:26 -0700
Commit message:

 Version bump after merging anno_3_13 branch
 
Package: AnnotationForge
Commit: 2f40df0c4e1f3475a5306b223b1caa45f722f956
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-10 14:28:54 -0700
Commit message:

 Merge branch 'anno_3_13'

This branch included all the changes to AnnotationForge required by the following updates
that were made as part of building the annotation packages for the April 2021 Bioconductor 3.13 release:

Removed UniGene table from OrgDb packages
Added Gene type table to OrgDb packages
Created new Orthology.eg.db package to map NCBI Gene IDs between species
 
Package: AnnotationForge
Commit: b12ccaac07518a5e9bac04d3cc2bfbb1599012ea
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 15:02:15 -0700
Commit message:

 Fix for .onload where it was trying to make the BiMaps.
 
Package: AnnotationForge
Commit: c2b9c22609a0a4d455a3739fcc2bbcbe05c131e4
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 14:55:45 -0700
Commit message:

 More changes to ANNDBPKG-INDEX to accommodate building OrthologyDb package.
 
Package: AnnotationForge
Commit: 7d977e6aac9aa8e3d499ce9c4251a8146ad7fcdd
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 14:38:42 -0700
Commit message:

 Removed organism from DESCRIPTION file for OrthologyDb.
 
Package: AnnotationForge
Commit: 2e59953fda3a3433448dc882c3afdd19a543af4f
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 14:05:14 -0700
Commit message:

 Removed organism from DESCRIPTION file for OrthologyDb.
 
Package: AnnotationForge
Commit: 6616f87fac20c6a2a26a4fd7f44eb75933a64215
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 13:46:53 -0700
Commit message:

 More changes to accommodate building OrthologyDb packages.
 
Package: AnnotationForge
Commit: b6942b71c19749b78fc7d305820e823931b5a09a
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 12:54:15 -0700
Commit message:

 Missed a closing curly brace.
 
Package: AnnotationForge
Commit: afca4a1ec88967de52b8bff2358a84d4162b1a7f
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 12:48:38 -0700
Commit message:

 Edits so makeAnnDbPkg does not try to get map_metadata from OrthologyDb.
 
Package: AnnotationForge
Commit: e2eb4a0098781120c74ac507976ab0a53e16c21e
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 12:28:09 -0700
Commit message:

 Merge branch 'anno_3_13' of github.com:jmacdon/AnnotationForge into anno_3_13
 
Package: AnnotationForge
Commit: 23e3cdb21957e579667601b51832bf369e95e3ed
Author: James W. MacDonald <jmacdon@uw.edu>
Date: 2021-05-06 12:25:36 -0700
Commit message:

 Changed to ORTHOLOGY.DB template so the build hopefully does not go through the BiMap building process.
 
Package: AnnotationForge
Commit: 795edf86340bd58991254331508d221e92bd85c8
Author: Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal>
Date: 2021-05-06 18:29:01 +0000
Commit message:

 Typo in Orthology package name.
 
Package: AnnotationForge
Commit: 58b23ae6d21fdcebb8326e2584f36954f359a320
Author: James W. MacDonald <jmacdon@uw.edu>
Date: 2021-05-06 11:22:50 -0700
Commit message:

 Put Orthology schema back in ANNDBPKG-INDEX.txt
 
Package: AnnotationForge
Commit: 20cbcd9956e264cadca28d9ba508bd1152346ebb
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-06 10:49:30 -0700
Commit message:

 Merge branch 'anno_3_13' of github.com:jmacdon/AnnotationForge into anno_3_13
 
Package: AnnotationForge
Commit: 01ab200c2ae6270e4dd410bc0c2cfb152cfecfef
Author: Ubuntu <ubuntu@ip-172-30-0-226.ec2.internal>
Date: 2021-05-06 17:47:36 +0000
Commit message:

 Updated Orthology help page with examples.
 
Package: AnnotationForge
Commit: 7128a67d26bdf69691fecb9f43002caa4d2a8a68
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-03 15:35:58 -0700
Commit message:

 Backing out changes - the Orthology package will be easier if it does not follow the usual paradigm.
 
Package: AnnotationForge
Commit: 19f6861dc0e66e8d7fb2d771c32559621e9f682c
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-03 13:27:24 -0700
Commit message:

 Changed orthology to Orthology
 
Package: AnnotationForge
Commit: 6100cd3ec1c223bb9e8bbacf957fcfe04dbb55ad
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-05-03 13:15:35 -0700
Commit message:

 Added orthology db to ANNDBPKG-INDEX
 
Package: AnnotationForge
Commit: d60a3c91ee36f94d89e98c3978e5b69930578d6c
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-27 09:27:39 -0700
Commit message:

 More changes to the GENETYPE man page so it gets found.
 
Package: AnnotationForge
Commit: c06d76a3fffe9ba873b162113f9499f7eb48006e
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-23 13:10:03 -0700
Commit message:

 Added GENETYPE.Rd file to NCBIORG.DB template.
 
Package: AnnotationForge
Commit: 60018c4e55bfc9a4bd96bee3791d2cb881d3dbc2
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-23 09:05:14 -0700
Commit message:

 Removed GENETYPE2EG because there is no point in having that.
 
Package: AnnotationForge
Commit: 35381e284da933e586682e2154014036fde7becd
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-22 13:18:38 -0700
Commit message:

 Changed all dbGetQuery calls that are actually executable statements to dbExecute.
 
Package: AnnotationForge
Commit: 43cd1f8f9a9c43415364f6227ae0a46084ef14c5
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-22 12:46:32 -0700
Commit message:

 Additional bugfix.
 
Package: AnnotationForge
Commit: f15bdaea3ea83780054ff79df9615c6add681eba
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-22 11:44:26 -0700
Commit message:

 Additional bugfix.
 
Package: AnnotationForge
Commit: 0f77be781cbcafb8e1bb3e874402c72a172729bc
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-22 11:23:46 -0700
Commit message:

 Additional bugfix missed in last two commits.
 
Package: AnnotationForge
Commit: 77475e7aacfdae517a28e5079eacf4f8ce3547fd
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-22 11:20:23 -0700
Commit message:

 Additional bugfix missed in last commit.
 
Package: AnnotationForge
Commit: e4d1ac13fe51d055235cce6c74b2d01756f36a43
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-22 11:14:34 -0700
Commit message:

 Bugfix to SQL code to generate genetype tables.
 
Package: AnnotationForge
Commit: fd901ade6fd6858e66d563f31e49dfdf66140b2d
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-22 10:55:09 -0700
Commit message:

 Added appendGenetype function to all the popXXX functions.
 
Package: AnnotationForge
Commit: e2dd4de7ad2c703ed924a5eee08f435d6bfadd7c
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-21 12:59:27 -0700
Commit message:

 First pass at an orthology DB skeleton.
 
Package: AnnotationForge
Commit: 385d7fed3021ac04102b5127b13d3dd587251563
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-04-16 08:54:41 -0700
Commit message:

 Initial changes for the removal of UniGene tables and introduction of gene type tables.
 
Package: ChIPpeakAnno
Commit: 3316e4714f19b20071c5a5ba6383c63a8cbf5f68
Author: jianhong <jianhong.ou@gmail.com>
Date: 2021-05-10 18:43:34 -0400
Commit message:

 add lazyDataCompression to DESCRIPTION.
 
Package: systemPipeR
Commit: 79bbba4dea8bf64b241fdf8bf85d619b6239982b
Author: dcassol <danicassol@gmail.com>
Date: 2021-05-06 10:12:14 -0700
Commit message:

 build_check
 
Package: systemPipeR
Commit: 7de3d247a2ada55cc92b800e84155a1d76b711df
Author: dcassol <danicassol@gmail.com>
Date: 2021-05-06 10:11:25 -0700
Commit message:

 update
 
Package: CNViz
Commit: a41d8bd406396eff389daeb438de04ab93f9bcdf
Author: Rebecca Greenblatt <rebecca.greenblatt@gmail.com>
Date: 2021-05-10 17:50:28 -0400
Commit message:

 added sex chromosome segments and changed all snv nomenclature to variants to encompass short indels
 
Package: marr
Commit: 665d458bbd7d53af61c9da73f8744c345a3758c7
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-05-10 14:52:26 -0600
Commit message:

 NEWS updated 
Package: marr
Commit: 0e153fc39b2ff04427b7e2462670adb478d3ee08
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-05-10 14:51:54 -0600
Commit message:

 updated DESCRIPTION 
Package: marr
Commit: efdb0fd93d0f599cd5aa83b42a8417cfa2a98e4b
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-05-10 14:09:03 -0600
Commit message:

 Update NEWS.md 
Package: marr
Commit: a45e3cb90041ebc2f121c6a30191f17cb62ad792
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-05-10 14:07:12 -0600
Commit message:

 Update DESCRIPTION 
Package: marr
Commit: a59d7713ea99dcd4fd965c8c9182feb87a804cf5
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 19:18:02 -0600
Commit message:

 Merge pull request #18 from Ghoshlab/feature-label-output

Merge pull request #17 from Ghoshlab/master 
Package: marr
Commit: 41a23572cca6a882558c1e2dbd2c30954389259e
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 19:06:38 -0600
Commit message:

 Merge pull request #17 from Ghoshlab/master

Merge pull request #16 from Ghoshlab/feature-label-output 
Package: marr
Commit: d7561e68bfa26f5f400a8cb42fa82f5f8829abd1
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 19:00:33 -0600
Commit message:

 Merge pull request #16 from Ghoshlab/feature-label-output

Feature label output 
Package: marr
Commit: f8b559a222ede12a6b46b75680fb072fcb4d541c
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 18:59:21 -0600
Commit message:

 Merge pull request #15 from Ghoshlab/master

Updated vignette 
Package: marr
Commit: a425f16ca07d511e4318550d672c15393b30313a
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 18:57:47 -0600
Commit message:

 Updated vignette 
Package: marr
Commit: 66eb763832c89b352df87a233d24186fe47715b3
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 18:55:40 -0600
Commit message:

 Merge pull request #14 from Ghoshlab/master

Merge pull request #13 from Ghoshlab/feature-label-output 
Package: marr
Commit: 6d644d59071318ec9caee1898eef26e43106c8e8
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 18:54:40 -0600
Commit message:

 Merge pull request #13 from Ghoshlab/feature-label-output

Feature label output 
Package: marr
Commit: e42b06d1d174251121b2aa5ee53887e1fc688170
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 18:54:15 -0600
Commit message:

 Merge pull request #12 from Ghoshlab/master

Merge pull request #10 from Ghoshlab/feature-label-output 
Package: marr
Commit: 1734acd3df23b3f4bfa8f519f70bdd4ab127b2aa
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 18:05:09 -0600
Commit message:

 Merge pull request #11 from Ghoshlab/RELEASE_3_12

updated documentation 
Package: marr
Commit: aeeb343ca79f29def1b77458fbf16ce1f0328c95
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 17:49:26 -0600
Commit message:

 Merge pull request #10 from Ghoshlab/feature-label-output

Merge pull request #9 from Ghoshlab/master 
Package: marr
Commit: 576e47ad48f8b5af1be4e3296f2c58b2e80a3415
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 17:49:04 -0600
Commit message:

 Merge pull request #9 from Ghoshlab/master

updated 
Package: marr
Commit: 5c9d095570385a47dac13990bfc1844df3590e58
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 17:46:01 -0600
Commit message:

 updated documentation 
Package: marr
Commit: 5d1a30396d1fc6ce2ed3d8e88381569bc553b854
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 17:44:32 -0600
Commit message:

 updated 
Package: marr
Commit: ce9941ea7748dc6a6b37d382358c8b404777a5fc
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 17:04:21 -0600
Commit message:

 Merge pull request #7 from Ghoshlab/RELEASE_3_12

Merge pull request #6 from Ghoshlab/master 
Package: marr
Commit: afad8f519d378661e6114255a373e7a8890422c9
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 16:44:55 -0600
Commit message:

 Merge pull request #6 from Ghoshlab/master

merged 
Package: marr
Commit: 034eb13426823e5ec7988d479231e5e2b60e4dfd
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 16:34:11 -0600
Commit message:

 updated vignette 
Package: marr
Commit: 62abb70f2086e8d780b63c36a95761e47bf46dda
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 16:14:54 -0600
Commit message:

 Merge pull request #5 from Ghoshlab/feature-label-output

Feature label output 
Package: marr
Commit: 8433f4946cf716e16a2c18e4156ab6475407adae
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 16:08:05 -0600
Commit message:

 updated DESCRIPTION 
Package: marr
Commit: 1a09cc08a06eaea0bbc806eab57f62cc3fdc9374
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 16:04:22 -0600
Commit message:

 updated vignette 
Package: marr
Commit: d2ce6ee0db2bd18bc8d5c4cd0d53f0f906e6f2d7
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-04-27 15:47:30 -0600
Commit message:

 updated description 
Package: marr
Commit: 2e498016fac999b92d77bc4b355058fc90ea1eaf
Author: Max McGrath <max.a.mcgrath@gmail.com>
Date: 2021-04-27 15:24:00 -0600
Commit message:

 Adds slot accessors for new slots
 
Package: marr
Commit: bfa9b27d2ecf45ab79336b69e1d2996b93ef7bbb
Author: Max McGrath <max.a.mcgrath@gmail.com>
Date: 2021-04-16 13:24:19 -0600
Commit message:

 Updates documentation
 
Package: marr
Commit: 07b0c16af007f6900e14b8a6715dde941a05fee3
Author: Max McGrath <max.a.mcgrath@gmail.com>
Date: 2021-04-05 17:27:59 -0600
Commit message:

 Updates filterData
 
Package: marr
Commit: 80de5a5d06d22646f46741816a3a611bcfed56ad
Author: Max McGrath <max.a.mcgrath@gmail.com>
Date: 2021-04-01 15:03:59 -0600
Commit message:

 Updates MarrFilter

Now returns removed feature/samples
 
Package: marr
Commit: 945af380cd0b0144f3a3b00aba694db2a6924bdd
Author: Max McGrath <max.a.mcgrath@gmail.com>
Date: 2021-03-31 15:28:01 -0600
Commit message:

 Updates documentation
 
Package: marr
Commit: 4070d2720ae49c95d4c3d7ace4b267907fe75270
Author: Max McGrath <max.a.mcgrath@gmail.com>
Date: 2021-03-29 06:53:51 -0600
Commit message:

 Merge changes to Master
 
Package: marr
Commit: 3b82143b9173b312a90c65061433ac9a0212ff97
Author: Max McGrath <max.a.mcgrath@gmail.com>
Date: 2021-03-27 14:37:01 -0600
Commit message:

 Adds MarrFilterData

Adds function to filter data from Marr object based on reproducibility and updates documentation, tests, and class slots accordingly
 
Package: marr
Commit: d041d4e25c8907420c38849b6d8096191dcd32b5
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-03-06 13:58:19 -0700
Commit message:

 cutoff added 
Package: marr
Commit: e138b74bd5a2c33bddcea0876734be4d4ba06b74
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-03-06 13:56:25 -0700
Commit message:

 version bumped 
Package: marr
Commit: 1c3b86d1b98fa00c9da5931ea2c83d1074ed1618
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2021-03-06 13:32:20 -0700
Commit message:

 cutoff added 
Package: marr
Commit: 48ab3d78773f810c7afa37cb3daedfd6debc22be
Author: Max McGrath <max.a.mcgrath@gmail.com>
Date: 2021-03-05 14:50:09 -0700
Commit message:

 Adds labels to Marr output
 
Package: marr
Commit: 02952221696a1a5733066872572da88d3f4a938f
Author: Tusharkanti Ghosh <44294394+tghosh30@users.noreply.github.com>
Date: 2020-12-24 15:27:48 -0700
Commit message:

 Merge pull request #4 from Ghoshlab/RELEASE_3_12

Update version bump 
Package: marr
Commit: de2c11dd0e0482550f55b5cd5c5be34bc59438f6
Author: Tushar <ghosh.tushar@yahoo.co.in>
Date: 2020-12-24 14:40:05 -0700
Commit message:

 Update version bump
 
Package: fobitools
Commit: 432cba6701a335b61daa997d86832f9bf563256f
Author: Pol Castellano Escuder <polcaes@gmail.com>
Date: 2021-05-10 22:34:33 +0200
Commit message:

 working on new dietary text annotation vignette
 
Package: celda
Commit: 0b336ffe7106d752d206a7162f5b148cfb09327e
Author: zhewa <zhe@bu.edu>
Date: 2021-05-10 16:32:23 -0400
Commit message:

 fix perplexity altExpName bug
 
Package: multiGSEA
Commit: abe829e56c7600dc562c5df782d06699071d5b08
Author: canzler <sebastian.canzler@ufz.de>
Date: 2021-05-10 22:06:10 +0200
Commit message:

 Update NEWS, Version bump.
 
Package: multiGSEA
Commit: 518631e13434c6c4b2d39e571c0633da3d685ddc
Author: canzler <sebastian.canzler@ufz.de>
Date: 2021-05-10 22:03:23 +0200
Commit message:

 Bug fix: Remove Biocarta from databases used in vignette - its no longer supported by graphite.
 
Package: multiGSEA
Commit: ada69a6c41a0ba5ac435e8dfa4e8e515b2e1d299
Author: canzler <sebastian.canzler@ufz.de>
Date: 2021-05-10 22:02:24 +0200
Commit message:

 Print available databases when wrong database is selected
 
Package: SynExtend
Commit: f4655b1a69426fb85a56cac85db7d9c67ac1f674
Author: npcooley <npcooley@gmail.com>
Date: 2021-05-10 15:10:48 -0400
Commit message:

 Added DisjointSet and ExtractBy functions
 
Package: RCy3
Commit: 3118550f2e4eac7b901ced51960de2789d49e4c5
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-08 01:49:23 -0700
Commit message:

 remove DS_Store
 
Package: RCy3
Commit: be320a830ab063b27413852294653e0b930636d4
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-07 13:56:19 -0700
Commit message:

 remove DS_Store
 
Package: RCy3
Commit: b4e7fe0054ff0e90b26e7b4d87dd9421766bf3a6
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-07 00:21:17 -0700
Commit message:

 Fix cytoscapeFreeMemory
 
Package: RCy3
Commit: f3a534fca50cbdee948935f66233ce74068eb3b9
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-07 00:15:42 -0700
Commit message:

 Fix cytoscapeFreeMemory
 
Package: RCy3
Commit: 8ebb7ba168b046a0fd477b668135425bd4b1e3b3
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-07 00:14:06 -0700
Commit message:

 Fix cytoscapeFreeMemory
 
Package: RCy3
Commit: e55e4364c5a4668cb5e39846f97de236af690497
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-06 23:58:43 -0700
Commit message:

 Fix cytoscapeFreeMemory
 
Package: RCy3
Commit: 91338e044d0f6f49b541ff1f599dad4241282544
Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2021-05-06 13:21:46 -0700
Commit message:

 adding line to allow warnings in Travis 
Package: RCy3
Commit: a76447e9c5e3e0b2f46f7fc2e541de7745e57fa1
Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2021-05-06 12:51:43 -0700
Commit message:

 rmarkdown is now longer imported automatically by knitr 
Package: RCy3
Commit: c84a9544b790008f3f03618b7c208eaee3f440f2
Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2021-05-06 12:20:27 -0700
Commit message:

 added build buttons 
Package: RCy3
Commit: 88f50cefdd60f44438a5cce2c57e0744fe63a9be
Author: Alexander Pico <alex.pico@gladstone.ucsf.edu>
Date: 2021-05-06 10:36:29 -0700
Commit message:

 added dev badge 
Package: RCy3
Commit: 19b93add40d511f0b9ab8cabb412e827fa1a6b86
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-05 21:55:04 -0700
Commit message:

 Fix default url
 
Package: RCy3
Commit: 6b8d4f796894c15eb9eb60fa46e3b431944de19a
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-05 21:18:35 -0700
Commit message:

 Fix default url
 
Package: RCy3
Commit: 1af5759e5eb1d2ac5e0a8feefc6781dd0af2f5ba
Author: Yihang Xin <46608109+yihangx@users.noreply.github.com>
Date: 2021-05-04 21:56:04 -0700
Commit message:

 Merge pull request #132 from cytoscape/sandbox

Sandbox 
Package: RCy3
Commit: 25a4b557a4451f5f450f1289d11c637cd3b1943a
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-04 13:56:02 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 270e975fc91dc8e042bd5a97a57f2fd0951e6465
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-04 03:40:44 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: a70abfece0f111acdb42f51b12b615ab198f0370
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-04 03:23:52 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 30c11d99f02d885c3402cff8434459699dc66155
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-04 03:20:58 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 7fda2bda7b925a20fa0e854fb179cd7cbfc2b54b
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-04 03:20:42 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 5e90f28a861aec3fd797745caf07fbb17363fb14
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-04 03:18:20 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 2b54556664849fcc630c7928d3ff400f7f722bd4
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-04 02:44:10 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 3ebeac1ac9916886e16a78dca6fb94d825311db7
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-02 22:22:59 -0700
Commit message:

 Fix image bug
 
Package: RCy3
Commit: de6008bbf59a0d4debcf84f75c01af77a5b04b2f
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-02 22:22:47 -0700
Commit message:

 Fix image bug
 
Package: RCy3
Commit: a0a55e2b8b020f3cc306406dccdfc1014059a450
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-02 21:04:25 -0700
Commit message:

 Fix image bug
 
Package: RCy3
Commit: 0d09b88b88571c75d9f7bb937be02812ea0dff1a
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-02 21:04:10 -0700
Commit message:

 Fix image bug
 
Package: RCy3
Commit: dcd30f8d03cbb7cfbeb1bed538ca187579f390c9
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-02 02:42:17 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: b9f2ed78fbed732ce62540bb69f24f966bb1bd11
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-02 02:20:10 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 543153addf150537127a12b3d6e4fea0dbf16b19
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-02 02:05:41 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 69872195ad9e580e0cc23a83ef9875f711ae3b54
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-05-02 01:36:49 -0700
Commit message:

 wrap up
 
Package: RCy3
Commit: 5442aa614173244144f6d220f7efe22e4d6cb21c
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-04-29 01:06:24 -0700
Commit message:

 implement sandbox
 

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