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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: DropletUtils
Commit: 901a2f4c35c9279db44a522cb94ccb70bd808058
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-18 14:39:52 +0100
Commit message:

 Fixed CITATION info.
 
Package: DropletUtils
Commit: 1b70638a3cccc24e582ff846ea2682c46ae5d4ce
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-18 14:28:16 +0100
Commit message:

 Updated DESCRIPTION, NEWS.
 
Package: DropletUtils
Commit: 076bf39c8d46c01bd68dc0aae067ca1311d33d58
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-18 14:25:48 +0100
Commit message:

 Updated downsampleReads docs and tests, related to vector 'prop'.
 
Package: DropletUtils
Commit: 35f2ab2b62615e435d9702990904de00c5be2e01
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-18 14:24:08 +0100
Commit message:

 Refactored downsampleReads to use C++ cell/GEM ordering.
 
Package: DropletUtils
Commit: 20611c623e5482263dd319864cd82c3d587cb646
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-18 14:18:21 +0100
Commit message:

 Added docs for new function, updated NAMESPACE for export.
 
Package: DropletUtils
Commit: b165fd6d291cbe7483d8403053f4d5b405d11a82
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-18 14:17:02 +0100
Commit message:

 Added tests for new get10xMolInfoStats function.
 
Package: DropletUtils
Commit: 9f2583a6d672782f02af81fda9ecc2a02df04470
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-18 13:57:17 +0100
Commit message:

 Added helper function to compute basic mol info stats.
 
Package: DropletUtils
Commit: 232e6b0dd499e43faccaa2bf8a26ecd8c4e8dc1d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 20:07:30 +0100
Commit message:

 Added more file reading control to read10xMolInfo.
 
Package: iCARE
Commit: b44c6162f7369f84dd60dadcb2a1bb4d02dd31d6
Author: wheelerb <wheelerb@imsweb.com>
Date: 2018-08-17 16:22:34 -0400
Commit message:

 new man files and vignette
 
Package: RTN
Commit: 3b6470b3ceffaaf79c598cbde7d4c1e043fbe8f4
Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2018-08-17 16:36:24 -0300
Commit message:

 regular maintenance
 
Package: beachmat
Commit: 4ca1a2cec73416e900d634a1d4eb7244d972dc5d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 14:59:25 +0100
Commit message:

 Switched to get/setDefaultBlockSize in tests.
 
Package: beachmat
Commit: 1f9a677a6dd48af2edb13521abd518eb747d8106
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 14:49:28 +0100
Commit message:

 Cleaned up vignettes for updated HDF5/DelayedArray functions.
 
Package: beachmat
Commit: c9edd5a56251d2373966744ba592bfecd9fa7d45
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-08-17 12:42:56 +0100
Commit message:

 Merge pull request #13 from LTLA/external

Add support for external matrices 
Package: beachmat
Commit: f5121fefc9ad47fe4f998ebbbacea02cac8fa750
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 12:05:42 +0100
Commit message:

 Minor doc fix, bumped version and date, updated NEWS.
 
Package: beachmat
Commit: 788a888eea1c6db33e7d136e4ace02e92f064378
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 11:59:57 +0100
Commit message:

 Added extension test check to longtests.
 
Package: beachmat
Commit: ebd440863c1345c78e38a41fbe82df8e3d3efee7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 11:50:02 +0100
Commit message:

 Minor fixes to vignettes.
 
Package: beachmat
Commit: 11380b05fc8ca8f9a7dbd2bbb1a97b63bec26834
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 11:49:35 +0100
Commit message:

 Cleaned up output vignette.
 
Package: beachmat
Commit: 8abd7f97a17a7b17c49eea6df41cfc87062fb525
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 11:31:58 +0100
Commit message:

 Switched to size_t& for external get_dim().
 
Package: beachmat
Commit: ff331e2c6f210bd096ca1dc55594ce19bd3187fd
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 11:28:21 +0100
Commit message:

 Documented how to provide external matrix support.
 
Package: beachmat
Commit: b2973a7c52871ade469413115a2c68f372651bef
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 10:14:55 +0100
Commit message:

 Added multi-row/col extraction to input vignette.
 
Package: beachmat
Commit: 919d952c675323ca5ac07776a5c666bb23a06063
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 10:04:04 +0100
Commit message:

 Clean up to linking vignette.
 
Package: beachmat
Commit: 646822c36eff717d1d85f39df7d3550372bd9bfb
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-17 10:01:08 +0100
Commit message:

 Cleaned up input vignette.
 
Package: beachmat
Commit: d52674e1811eb93e04540e986694e1374f301b11
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 19:41:22 +0100
Commit message:

 Refine supportCppAccess function.
 
Package: beachmat
Commit: 780969688522da1b70b9bc74d2f39f89e0f25ddd
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 19:36:49 +0100
Commit message:

 Cleaned up morebeach tests for actual execution.
 
Package: beachmat
Commit: 5054092505ef2a0f3e2307431d531e84a505b5c4
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 19:34:12 +0100
Commit message:

 Switched to using references for external indexed getter.
 
Package: beachmat
Commit: 6ebe336d6ee9f5cbe37c1fa3766816fca041595c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 19:33:49 +0100
Commit message:

 Added test support for external special getters.
 
Package: beachmat
Commit: 6f36b41862d462947c5b0b8ad3a32dc7b235d200
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 19:03:14 +0100
Commit message:

 Use specialized access methods for external reader in realized matrices.
 
Package: beachmat
Commit: b2d899d5126814b13ead6ec390d79e8523bf32de
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 19:02:29 +0100
Commit message:

 Streamlined external reader to reduce redundancy.
 
Package: beachmat
Commit: 51e850f82132e7e9a93e1be82d66b44fa2adc88a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 10:34:23 +0100
Commit message:

 Added tests for character external matrix.
 
Package: beachmat
Commit: 982c1bd762bab8cd6b49bd2a45775360d4a61e74
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 10:32:40 +0100
Commit message:

 Added access functions for character matrices.
 
Package: beachmat
Commit: 8cffcf454eff40fc6a4fb64a4154ed149af53c91
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 10:32:22 +0100
Commit message:

 Split up registration from integer access functions.
 
Package: beachmat
Commit: 205335bd1628135cc47574a4873d99504f3b9e89
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 10:18:58 +0100
Commit message:

 Added external support for character matrices.
 
Package: beachmat
Commit: daa6855dec034821a21d344cb2049ca068cb023f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 10:00:32 +0100
Commit message:

 Added documentation for supportCppAccess.
 
Package: beachmat
Commit: fd17caeeaa56471ef3683453314c64be6970dc21
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 09:42:59 +0100
Commit message:

 Avoid impossible allocations for HDF5 character multirow/col getters.
 
Package: beachmat
Commit: 89ee754f0497ce122fee82b68113a70a6d67f1ff
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-16 09:41:31 +0100
Commit message:

 Cast Rcpp iterators to raw pointers for HDF5 reads.
 
Package: beachmat
Commit: 6b030f2db158edbf30ebaa46bbff37af1c500240
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 20:30:50 +0100
Commit message:

 Corrected iterator notation for get_rows() functions.
 
Package: beachmat
Commit: 1a548df51f4ec19c230d7f546c2107b7b6db5aae
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 20:14:16 +0100
Commit message:

 Added error tests for multi-row/col getters.
 
Package: beachmat
Commit: 25b9db332b59d8d31726ce44ceffef9b88115a0b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 19:51:58 +0100
Commit message:

 Limited exposure of h5selector members via const methods.
Switched to same-dimension dataspace for multirow/col getters
(avoid HDF5lib's performance penalty where possible).
 
Package: beachmat
Commit: 69f3ce5186a4f56ae6aed13efb1418cf1aa1772f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 19:17:30 +0100
Commit message:

 Streamlined unknown_reader's storage variables for clarity.
Added status check for whether cached storage is row- or column-based.
 
Package: beachmat
Commit: 8b9b933e4319c6a533180d6af0c2e1dd23e4d33b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 18:37:03 +0100
Commit message:

 Updated example package to use Rcpp::Vector::iterator functions.
Activated tests for input error checks.
 
Package: beachmat
Commit: ef5b2bcc834551f7619eb8d2c546ae54b4eabfd1
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 18:36:09 +0100
Commit message:

 Switched to Rcpp::Vector::iterator in external interface.
Added input checks to external reader.
 
Package: beachmat
Commit: cc401a8e62ae069930d1d6d7d129066fd4f2b755
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 18:08:28 +0100
Commit message:

 Added class check for external matrix inputs.
 
Package: beachmat
Commit: 6afb87039335b302ed20a8f7b50583334cbe0ace
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 18:07:53 +0100
Commit message:

 Exported external_reader header.
 
Package: beachmat
Commit: 7c4d3cba04984b6be8cb75ec3a2fe92abdd33a63
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 17:59:15 +0100
Commit message:

 Switch to size_t for external function calls.
 
Package: beachmat
Commit: bb1c0a8b6d556a11d71b2f8ccf08139c5f95af67
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 17:49:16 +0100
Commit message:

 Added tests for integer AaronMatrix access.
 
Package: beachmat
Commit: 0e6c35b443a19da319d57c968c8bbf8e81d546f2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 17:48:58 +0100
Commit message:

 Created as.matrix S3 method for correct dispatch.
 
Package: beachmat
Commit: 05bd674a08e606aad3535b7eab222d337d874423
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 17:28:26 +0100
Commit message:

 Added example matrix-like class with beachmat bindings.
 
Package: beachmat
Commit: 1261a68a80e8b4d75c85d415ecd8c3b73be59e07
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 17:26:18 +0100
Commit message:

 Get dimensions of external matrices via C++.
 
Package: beachmat
Commit: ad0edd231552aff062e8c7886083644fb980f616
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 15:24:40 +0100
Commit message:

 Add supportCppAccess generic and base method.
 
Package: beachmat
Commit: 9b66f31fb7af64b9cd1d4cb378f087d31d462b5b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 15:24:02 +0100
Commit message:

 Corrected external access function pointers.
 
Package: beachmat
Commit: feed5db65b9fc121fe4ffff5da452a5d0fa0b4d9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 15:23:03 +0100
Commit message:

 Add functions to support external_matrix LIN dispatch.
 
Package: beachmat
Commit: cc68eccdc6e44cbafc1cf6d403b9505852a31c7d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 14:32:28 +0100
Commit message:

 Added preliminary support for external LIN matrices.
 
Package: beachmat
Commit: 707b621684d06d4f86ba74b725f4bfcd526d27cc
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 11:37:47 +0100
Commit message:

 Moved beachtest linkage tests to longtests.
 
Package: statTarget
Commit: c6dc55d3ac581488fbbea03dbcb397ccae339f1d
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 18:10:29 +0800
Commit message:

 test
 
Package: statTarget
Commit: 6cb1360fc3af04720d0343a0982e7396cb73f4d4
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 17:32:39 +0800
Commit message:

 test
 
Package: M3C
Commit: 3e7defcd7d2ede9070d2a5282dad4dcceb0a3bd2
Author: crj32 <chris.r.john86@gmail.com>
Date: 2018-08-17 08:09:01 +0100
Commit message:

 changed version number
 
Package: M3C
Commit: 14c39716be0a8d462264accc652db0a37368b024
Author: crj32 <chris.r.john86@gmail.com>
Date: 2018-08-17 07:50:47 +0100
Commit message:

 added hc with ward and clinical analysis code
 
Package: Rsubread
Commit: 8cfb7c1366ee997efd9eb6792770c465f24b6d26
Author: Wei Shi <shi@wehi.edu.au>
Date: 2018-08-17 13:37:20 +1000
Commit message:

 featureCounts now counts multi-mapping reads by default.
 
Package: statTarget
Commit: e6804bbd922eca8120bff5ae5bcf6ad91568392e
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:59:16 +0800
Commit message:

 test
 
Package: statTarget
Commit: fc9373779a0c41db5d72334d12df552c9c3dc6c9
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:51:17 +0800
Commit message:

 test
 
Package: statTarget
Commit: 053abe7bdec656043f5cfa52abe75f9948267227
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:38:03 +0800
Commit message:

 test
 
Package: statTarget
Commit: 2541017048f0753336bdd842253154fa4412a392
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:37:02 +0800
Commit message:

 test
 
Package: statTarget
Commit: b64e4a2cbe69251c5f9edb72e711a58282d1fae0
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:35:43 +0800
Commit message:

 test
 
Package: statTarget
Commit: f0d9831f821823ec36cfe821a778431a7d0071ca
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:33:46 +0800
Commit message:

 test
 
Package: statTarget
Commit: 7fe501f8bffff495ce7aa37f773b83ae0f30994b
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:33:01 +0800
Commit message:

 test
 
Package: statTarget
Commit: a569fdd5303333f7eb3d20efa5c3d90dd99ec1ae
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:31:49 +0800
Commit message:

 test
 
Package: statTarget
Commit: e5cb352309b4ee02d5c4819d41d60d2637511a63
Author: 13479776 <hemi.luan@gmail.com>
Date: 2018-08-17 10:28:48 +0800
Commit message:

 test
 
Package: HMP16SData
Commit: 4fc142bade3f5f2ac6a29da4688f5cc8ef336732
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2018-08-17 01:00:06 +0000
Commit message:

 additional analysis add to vignette
 
Package: HMP16SData
Commit: 16a2f2ada588e9342f9973d3def802efdc6959ad
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2018-08-16 14:24:59 +0000
Commit message:

 minor grammar correction in vignette
 
Package: HMP16SData
Commit: 4f15baf6d3b04501645c171230843b7957413abc
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2018-08-16 14:16:03 +0000
Commit message:

 update readme to reflect BiocManager install
 
Package: HMP16SData
Commit: 1e0f56016071b04970d29e8d274091dcef785772
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2018-08-16 14:09:14 +0000
Commit message:

 correct grammar in the vignette
 
Package: HMP16SData
Commit: cce11060f7580b0d096ec7b8bc7ea07695a659e5
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2018-08-16 14:02:48 +0000
Commit message:

 add an acknowledgement of phyloseq to the vignette
 
Package: HMP16SData
Commit: ec291d48a99aa4f348046e221fe7e9e0b9456f16
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2018-08-16 13:45:52 +0000
Commit message:

 vignette section demonstrating export to other formats
 
Package: HMP16SData
Commit: cace6a3aac41a1c5db44920c357cebdc249b804a
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2018-08-16 12:31:55 +0000
Commit message:

 update vignette to reflect install using BiocManager
 
Package: HMP16SData
Commit: 2309f392c3783624c4c08744df9ebc31f5dd7627
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2018-08-07 13:24:56 +0000
Commit message:

 additional vignette detail
 
Package: DelayedArray
Commit: a4b9da0081cd645c2f58983d0c8dfb1be546fe5b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-16 16:11:06 -0700
Commit message:

 Make simple_abind() work on arrays of type "list"
 
Package: DelayedArray
Commit: 70fd89afceaef3b07556c662f1d4b50ae86875ec
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-16 14:43:23 -0700
Commit message:

 Add early sanity check on some delayed operations

This sanity check will trigger an error in situations like:
  M <- DelayedArray(matrix(character(12), ncol=3))
  M2 <- log(M)  # error!
Before this change, the above code was working and the error was delayed
until the user would display or realize M2. The check is cheap so better
fail early than late!
 
Package: tRNAscanImport
Commit: c62345accd5ac3acb9f403c4e597e5bd8d3b7a0f
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2018-08-16 23:01:11 +0200
Commit message:

 version bump
 
Package: tRNAscanImport
Commit: 34db6899005616213fa28227ed3196a8f8bc3e6f
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2018-08-16 22:53:33 +0200
Commit message:

 version bump
 
Package: tRNAscanImport
Commit: a8f1a249f895834890d985c4d96d3b184bc88ac1
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2018-08-16 21:14:21 +0200
Commit message:

 added tests for gettRNAstructureRanges and gettRNAstructureSeqs
 
Package: tRNAscanImport
Commit: 9b5158dc9f26ef3af4d56bb1bc19f8234baff478
Author: FelixErnst <felix.ernst@ulb.ac.be>
Date: 2018-08-16 17:09:58 +0200
Commit message:

 added more options to gettRNAstructureSeqs

additional options allow for more fine tuned results in terms of padding and sequence joining
 
Package: tRNAscanImport
Commit: 4b66672fe74f0128aa713cc680e447f7850b15ee
Author: FelixErnst <felix.ernst@ulb.ac.be>
Date: 2018-08-16 09:47:56 +0200
Commit message:

 bugfix pseudogene recognition
 
Package: tRNAscanImport
Commit: 0272b5f5e4685e85a5d2d2a6db533cc3880073ed
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2018-08-15 23:20:33 +0200
Commit message:

 updated version number and vignette
 
Package: tRNAscanImport
Commit: eb73b01f299e3b4929108d8f0b1f1d1780b0375c
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2018-08-15 23:07:10 +0200
Commit message:

 Merge branch 'master' of https://github.com/FelixErnst/tRNAscanImport
 
Package: tRNAscanImport
Commit: fda6074d701ad5ca8a73b559acb2851e7418d2b9
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2018-08-15 23:07:08 +0200
Commit message:

 added gettRNAstructureSeq

gettRNAstructureSeq retuns the subset of sequences for the individual tRNA structure elements
 
Package: tRNAscanImport
Commit: d3c12b2bac556cd70b82f1091a5d8fe52ef0df1d
Author: FelixErnst <felix.ernst@ulb.ac.be>
Date: 2018-06-14 17:28:27 +0200
Commit message:

 vignette changes
 
Package: DelayedArray
Commit: ecddbd72001cd7d73fe720a2840b66f9fb2ab544
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-16 13:44:57 -0700
Commit message:

 Internal helper get_type_size() now accept the "list" type
 
Package: iPAC
Commit: 5de4b5acb092554ed11ae1e4e8789e87f0707514
Author: Greg Ryslik <greg@mindstronghealth.com>
Date: 2018-08-16 13:03:43 -0700
Commit message:

 All examples now use https for FASTA pulls. Should fix a redirect error when compiling on windows machines.
 
Package: flowDensity
Commit: 4efeddf3d20e77d40aee680bb868fbfdcdb8e048
Author: mehrnoushmalek <mmalekes@bccrc.ca>
Date: 2018-08-16 11:02:21 -0700
Commit message:

 Mehrnoush Malek
 
Package: flowDensity
Commit: fb38854708d389d334ad6e522a893a9d337c6fec
Author: mehrnoushmalek <mmalekes@bccrc.ca>
Date: 2018-08-16 11:00:48 -0700
Commit message:

 Mehrnoush Malek
 
Package: EnrichmentBrowser
Commit: 6c7d4108a67b033633c0aedb97a93de828efe3e9
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2018-08-16 13:36:02 -0400
Commit message:

 consistent entrez-based gs from KEGG
 
Package: HDF5Array
Commit: dbc8d4287da083ab5976289e896bd38381984aad
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-16 09:40:02 -0700
Commit message:

 Small tweak to "write_block" method for HDF5RealizationSink objects

The method now uses the more natural h5read( , start= , count= ) interface
instead of the h5read( , index= ) interface to write the data to disk.

Also added a "type" method for HDF5RealizationSink objects.
 
Package: bioCancer
Commit: 47896e412e4f3e3bf7da8dac4829a4fa26a8a92f
Author: kmezhoud
Date: 2018-08-16 15:36:28 +0100
Commit message:

 updates related to changes of radiant.data 1.9.2

Merge branch 'master' of git.bioconductor.org:packages/bioCancer

# Conflicts:
#	DESCRIPTION
 
</div>
Package: bioCancer
Commit: 9f4cf734c6a150ba7937db847c9028e502fbddcf
Author: kmezhoud
Date: 2018-08-16 15:32:56 +0100
Commit message:

 updates related to changes in radiant.data
 
</div>
Package: HDF5Array
Commit: 2dd73e17c78662a4730aeb24c38568eae74663c1
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-15 19:14:49 -0700
Commit message:

 Rename extractNonZeroValuesByCol() -> extractNonZeroDataByCol()

Also make it a lot faster on TENxMatrix objects (between 5x and 30x
faster, depending on the number of columns to extract).
 
Package: splatter
Commit: a2360a1c7ff4bc627d3ba7c490bb8e6d0dad5b74
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2018-08-16 11:24:52 +1000
Commit message:

 Bump version number
 
Package: splatter
Commit: fab0bf2166e70328d40272bf934217486b56e095
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2018-08-16 11:17:20 +1000
Commit message:

 Add suggested package checks to tests

Fixes #56
 
Package: splatter
Commit: c77ddc9ac25859a81e3e942d0218153df292e018
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2018-08-16 10:49:03 +1000
Commit message:

 Fix variable name to be compatible with scater
 
Package: splatter
Commit: 8207a353f649462a4210a5955db92d61f1a879b0
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2018-08-16 10:10:10 +1000
Commit message:

 Update Roxygen version
 
Package: splatter
Commit: e24b206298ff30bd6919e8e971e27e7d5a1d7288
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2018-06-27 11:29:15 +1000
Commit message:

 Merge branch 'master' of github.com:Oshlack/splatter

* 'master' of github.com:Oshlack/splatter:
  Fix bug in reversing directions for factors less than one
 
Package: splatter
Commit: 382e22e6b22f32f2bb86a4152af369eda19aaba3
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2018-06-27 11:28:38 +1000
Commit message:

 Merge pull request #51 from Irrationone/master

Fix bug in reversing directions for factors less than one 
Package: splatter
Commit: 92c2194a98551abab21b42ea21b7eb02cdd85951
Author: Allen Zhang <alzhang@bccrc.ca>
Date: 2018-06-20 23:51:10 -0700
Commit message:

 Fix bug in reversing directions for factors less than one
 
Package: HDF5Array
Commit: e795bdef4aba0d040185496f05a83a20bf6d658c
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-15 16:27:14 -0700
Commit message:

 Some minor code polish
 
Package: GlobalAncova
Commit: 645d66d1015a5d36291e31f64b5902fdd27bc1e2
Author: Hummel <hummelma@ad.dkfz-heidelberg.de>
Date: 2018-08-15 10:44:18 +0200
Commit message:

 fixed DESCRIPTION
 
Package: ontoProc
Commit: 2f53fb3868429ce2b6f139f60f9789bc2345c3e9
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-15 16:48:14 -0400
Commit message:

 adding in HCA ontology
 
Package: rhdf5client
Commit: 5193f488ec08d6de6c32d4d723cfee6c7cea3f86
Author: User-Zero <User-Zero@user-zeros-air.dfci.harvard.edu>
Date: 2018-08-15 15:17:52 -0400
Commit message:

 fix example for getDims, reformat error messages
 
Package: rhdf5client
Commit: 2a1e37026cec5508ccfe2664b03cc898791052e8
Author: sampoll <sampoll@users.noreply.github.com>
Date: 2018-08-15 14:40:36 -0400
Commit message:

 Merge pull request #18 from shwetagopaul92/master

making changes to code, adding line feed, version bump 1.3.8 
Package: rhdf5client
Commit: 004b95f785cd8f798f17dce2d8bd5710950504f7
Author: Shweta Gopaulakrishnan <shwetagopaul92@gmail.com>
Date: 2018-08-15 11:47:34 -0400
Commit message:

 Merge branch 'master' into master 
Package: rhdf5client
Commit: 43bc73535ffc106c97e355f096a9d997e6538bd3
Author: shwetagopaul <mail@shwetagopaul92.com>
Date: 2018-08-15 11:44:20 -0400
Commit message:

 making changes to code, adding line feed, version bump 1.3.8
 
Package: rhdf5client
Commit: b61e223aa4da4a92565251ccfb1b747190060c80
Author: Samuela Pollack <sampoll@users.noreply.github.com>
Date: 2018-08-14 09:28:33 -0400
Commit message:

 Merge branch 'master' of https://github.com/sampoll/rhdf5client
 
Package: rhdf5client
Commit: 597da6ce9a14196fe1f509fe8d9b939ff7b93b6c
Author: Samuela Pollack <sampoll@users.noreply.github.com>
Date: 2018-08-14 09:28:20 -0400
Commit message:

 tiny roxygen fix
 
Package: BiocStyle
Commit: 0e194fd6ca4c593d3bf28c1594256fa1191fae6d
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-08-15 07:14:56 -0400
Commit message:

 Biocpkg() only italicizes packages

- see https://github.com/Bioconductor/BiocStyle/commit/5d73110c52c440af881855e226e386d9c04e59d1#commitcomment-30084377
 
Package: diffcyt
Commit: 5cbec8881bd70006449d232bf9b79e4d38edd18d
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-08-15 12:41:03 +0200
Commit message:

 documentation
 
Package: HDF5Array
Commit: 0880157eebde016d8bead082412e3ee25ea0ae6a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-15 03:23:02 -0700
Commit message:

 Various fixes and optimizations to TENxMatrix objects

The "extract_array" method for TENxMatrixSeed objects had several bugs
leading to the wrong data ending up in memory. Its implementation has been
revisited, fixed, and tested. It has also been optimized for the common
use cases. Depending on the size of the data that needs to be loaded, the
speedup can vary between 2x and 10x.

Also the examples in ?TENxMatrix have been expanded significantly.
 
Package: simpleSingleCell
Commit: b00978dc1e2bc8474334d59eed50de3b6f24a0d8
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 10:08:24 +0100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/simpleSingleCell
 
Package: simpleSingleCell
Commit: d0975802ead5d5ab5c85a6df8686296d65e0d9cd
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 09:57:12 +0100
Commit message:

 Bumped version number.
 
Package: simpleSingleCell
Commit: 634b60b581942255ef5df8dcb16efa7ff9aa02f0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 09:54:48 +0100
Commit message:

 Corrected some comments about DE for marker gene discovery.
 
Package: simpleSingleCell
Commit: 3f7746f47836834d73ecbe2ec6e9c54e3741a63d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-15 09:43:03 +0100
Commit message:

 Upgraded cross-workflow links to use new Biocpkg() vignette linking.
 
Package: BiocStyle
Commit: 155a2153e1d00e8350c24ab489ff5e5cb2222d8e
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-08-14 18:20:37 -0400
Commit message:

 Merge branch 'LTLA-master'

- closes #51, add vignette = argument to Biocpkg()
 
Package: BiocStyle
Commit: 6f8dcfaae6394872178f6fc6cccf6348ef704274
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-08-14 18:20:11 -0400
Commit message:

 version bump
 
Package: BiocStyle
Commit: 5d73110c52c440af881855e226e386d9c04e59d1
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2018-08-14 18:12:28 -0400
Commit message:

 add 'label' to Biocpkg()

- Also, use BiocManager::version() rather than (internal hack) on BiocVersion
  per se
- minor white-space (line wrap, remove trailing whitespace)
 
Package: BiocStyle
Commit: 7c11e8022bcc1ea8eea2c50bbfcb57232d745d51
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-14 13:52:42 +0100
Commit message:

 Reoxygenated docs and NAMESPACE.
 
Package: BiocStyle
Commit: 74a2c885547c2b1292681b46fa6ea956ddf57b8b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-14 13:51:16 +0100
Commit message:

 Update Biocpkg() for more convenient Bioc website redirects.
Provide direct support vignette= in Biocpkg().
Remove Biocworkpg(), and switch other macros to use Biocpkg().
 
Package: BiocStyle
Commit: 8a0f5ca97e0a9bcafb6508641a79c12bc71bfee8
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-15 11:53:41 +0100
Commit message:

 Removed return statement in Biocworkpkg.
 
Package: BiocStyle
Commit: 38c203592371c07da797947fd8a7eadb6e0a65d7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-14 15:02:37 +0100
Commit message:

 Renamed internal function for greater clarity.
 
Package: BiocStyle
Commit: d5a7a5e03cdd028fd42e7c6a377b2a77ea762cce
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-13 12:00:41 +0100
Commit message:

 Use BiocVersion to obtain release/devel versioning information.
 
Package: BiocStyle
Commit: f801eb62d7a622c60748889532d8f615866a20ed
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-07-13 11:44:57 +0100
Commit message:

 Removed unnecessary section= argument in Biocworkpkg.
 
Package: BiocStyle
Commit: 252d115160d29c9fbe409f9c9b39d471e429f8ce
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-06-07 10:14:31 +0100
Commit message:

 Support release/devel switch in other Bioc*pkg functions.
Switched to HTTPS for Biocworkpkg links.
 
Package: BiocStyle
Commit: 9a447c8ffcdf50e2e3a7368e6677fd72e85434f3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-06-07 10:02:34 +0100
Commit message:

 Added Biocworkpkg function to link to workflow packages.
 
Package: DelayedArray
Commit: c9de522cfb80e022a07769b4fa8b49bf2eec18c2
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-14 14:42:58 -0700
Commit message:

 Fix another performance regression introduced at commit e1cee763

Commit e1cee763 introduced another severe preformance regression to the
"show" method for DelayedArray objects. This time the regression was
occuring in the context of displaying objects of 3 dimensions or more.
In order to display 2D slices of the object, the slices were fully loaded
into memory.
This fix uses [ instead of extract_array() to obtain the 2D slices so the
slices are no more loaded in memory ([ is delayed). As a result only the
elements of the 2D slices that need to be displayed get loaded into memory.
 
Package: GDSArray
Commit: f8fa27c1dabc168720a3312ba057b0ad68164244
Author: Qian Liu <qliu7@buffalo.edu>
Date: 2018-08-14 17:12:04 -0400
Commit message:

 Merge remote-tracking branch 'origin/master'
 
Package: GDSArray
Commit: 4167a2128fd4f534114060d5a91b84bfe27edb58
Author: Qian Liu <qliu7@buffalo.edu>
Date: 2018-08-14 17:11:57 -0400
Commit message:

 merged upstream/master
 
Package: GDSArray
Commit: c466b3d86207c88f281a0b9e3d0fa354407f2d10
Author: Qian Liu <qliu7@buffalo.edu>
Date: 2018-08-14 17:10:40 -0400
Commit message:

 tweaks in authors and BiocViews
 
Package: GDSArray
Commit: 7a36b49d48a8132d992d3a3bcf558c2a4c2ffe2f
Author: Qian Liu <qliu7@buffalo.edu>
Date: 2018-08-14 17:07:54 -0400
Commit message:

 tweaks for authors and biocViews
 
Package: EnrichmentBrowser
Commit: 3b6951b8addd4a53739fae18c2f24f8a619d75c0
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2018-08-14 16:44:17 -0400
Commit message:

 sync sbea/nbea result format
 
Package: COMPASS
Commit: 542705e96fbe389eac3be63f8451a003b684ff4b
Author: Greg Finak <greg.finak@gmail.com>
Date: 2018-06-06 11:12:55 -0700
Commit message:

 codecov badge 
Package: COMPASS
Commit: 90fb8440752f7c2581b65faad8f5b27effed5b2f
Author: Greg Finak <greg.finak@gmail.com>
Date: 2018-05-11 14:11:38 -0700
Commit message:

 add ggplot2 to travis build 
Package: EnrichmentBrowser
Commit: f5e4b23f7d29df10843443da2294184c59857f8d
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2018-08-14 14:41:17 -0400
Commit message:

 resolve conflicted select
 
Package: RVS
Commit: 4ed125b0b7b5a2cf015ae473462e4624d0289bd5
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2018-08-14 13:39:17 -0400
Commit message:

 pulled new version from BioC and merged
 
Package: RVS
Commit: b0b79fc5a217ea878f1b0242fe240d0a3d5c80be
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2018-08-14 13:38:28 -0400
Commit message:

 fixed NA values when probabilities are near zero
 
Package: DMRcaller
Commit: 48c4072bed1ac8304859367fea24f374a7d18cd2
Author: nrzabet <n.r.zabet@gen.cam.ac.uk>
Date: 2018-08-14 18:07:32 +0100
Commit message:

 bug fix
 
Package: trackViewer
Commit: ca143d9576ed087bc9148665a85482bb3336fb29
Author: Jianhong Ou <jianhongou@riboimager.research.duhs.duke.edu>
Date: 2018-08-14 11:01:47 -0400
Commit message:

 add flag type in lollipop plot
 
Package: diffcyt
Commit: 27c37bcb7ff9481eccc12b1e3b5625225939d9c1
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-08-14 16:51:04 +0200
Commit message:

 version
 
Package: diffcyt
Commit: 6f857296455ecb103f2cf64a87d38a0b086219bb
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-08-14 16:45:01 +0200
Commit message:

 expose eBayes option 'trend = TRUE' for testDS_limma
 
Package: DAPAR
Commit: bb1d6c0ed747def6e52cc1edf2f8856db8e7ac5d
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-14 14:05:04 +0200
Commit message:

 changes to BiocManager
 
Package: DAPAR
Commit: 510bcbea69cf2ddb7768dbd22ff0685fab41e307
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-14 14:04:22 +0200
Commit message:

 changes to BiocManager
 
Package: DAPAR
Commit: fbcbfbca7763d4420f2dd2e3a6354777c37a2453
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-13 04:57:33 +0200
Commit message:

 Add files via upload 
Package: DAPAR
Commit: 033c65b9539078dadbf64a7ccaed232f5705415e
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-13 04:48:37 +0200
Commit message:

 Add files via upload 
Package: DAPAR
Commit: 5106932952d0dba1b7ba6d1cfe2db66dc8c9919a
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-12 11:09:18 +0200
Commit message:

 Add files via upload 
Package: DAPAR
Commit: 4f73f0dfddbc2230a8192ce053785bfc161808a1
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-12 11:08:56 +0200
Commit message:

 Add files via upload 
Package: DAPAR
Commit: ef2d8045bd7f25439cc9d9803b996f6cc7cf6c19
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-10 09:40:50 +0200
Commit message:

 version 1.13.1
 
Package: pRolocdata
Commit: 4eae6e91416d47542b30ab572656de99df583d27
Author: lmsimp <lisa.m.simp@gmail.com>
Date: 2018-08-14 10:28:02 +0100
Commit message:

 Dan's yeast data
 
Package: pRolocdata
Commit: 1bdd0fe144c54a3b02d1465473c665d3586eb8d7
Author: Laurent <lg390@cam.ac.uk>
Date: 2018-07-27 00:03:10 +0100
Commit message:

 new gh devel version
 
Package: karyoploteR
Commit: 5016a1f37cdc092fa219ca561a147b7f07c5d66d
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-14 12:55:09 +0200
Commit message:

 Added toGRanges to zoom to allow UCSC style zoom region definition

 
Package: regioneR
Commit: d64d658c5f5a1fbdf8b606174d4a1f268d2e4403
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-14 11:23:51 +0200
Commit message:

 Updated vignette

 
Package: regioneR
Commit: 61225806ae295d8c4b07e8b7f5bdc142df958688
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-14 10:44:09 +0200
Commit message:

 Cleaned up imports and depends

 
Package: regioneR
Commit: babdf7d839abfdbc18b50ddd901466a68598913c
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-13 16:31:16 +0200
Commit message:

 Updated docs and email i DESCRIPTION

 
Package: regioneR
Commit: c42444c7f2c8be3b7bac83047aecce31d4ebfce5
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-13 16:08:26 +0200
Commit message:

 Removed Latex Vignette

 
Package: regioneR
Commit: d39107832be035d810efe381feeed48282e0b897
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-13 16:07:11 +0200
Commit message:

 Updated Latex Vignette

 
Package: regioneR
Commit: 15987041b81c3ee3ec95842ab8f1d81b961e0f7c
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-13 16:06:28 +0200
Commit message:

 Added an HTML vignette

 
Package: regioneR
Commit: 799afd5b5c8031ba805891813bda8c26fedf82db
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-13 15:25:00 +0200
Commit message:

 Added new options to parse location strings and new genome param

 
Package: regioneR
Commit: 3a58891905e5fcf6b3ede8b0f43c4135384a5a7c
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-13 15:24:13 +0200
Commit message:

 Warning to message if the masked version was not available

 
Package: MAGeCKFlute
Commit: 2b866c79347bfd2e7916ba4abd420a2c1e5be824
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-08-14 13:55:54 +0800
Commit message:

 1.1.6
 
Package: LRBaseDbi
Commit: 8ee61f0c828a24372dc880b2c95d4ebc8a616ab4
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2018-08-10 15:15:11 +0900
Commit message:

 v-0.99.19
 
Package: MAGeCKFlute
Commit: e84783823893cd1e31a16a22100269986f22d8b0
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-08-14 11:21:52 +0800
Commit message:

 1-1-5
 
Package: GENESIS
Commit: 77c4ba56db66177363bfd7b22ed92e32d9e39f07
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2018-08-13 16:10:45 -0700
Commit message:

 bug fix for user-specified weights

If assocTestAggregate is called with user-specified weights and
the alleles of the selected variants do not match all the
requested variants, need to subset the weight vector to the
variants with matching alleles.
 
Package: GenomicFeatures
Commit: ff4e0dc3cad4c39e09bc93b08d67961a274b8162
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-13 11:36:15 -0700
Commit message:

 makeTxDb() now accepts missing CDS phases
 
Package: twoddpcr
Commit: 6991407574270d46368a929c6a1f5e5672ce0106
Author: Anthony Chiu <anthony.chiu@bbc.co.uk>
Date: 2018-08-13 19:26:58 +0100
Commit message:

 Call BiocStyle functions explicitly in vignette
 
Package: rhdf5client
Commit: 4b1c39c439821b5a412aca78c03cd4ecb8ef846c
Author: User-Zero <User-Zero@user-zeros-air.dfci.harvard.edu>
Date: 2018-08-13 13:31:45 -0400
Commit message:

 Incremented version number
 
Package: rhdf5client
Commit: 4d3ebfae35c066263bb85c4cb732fd29f289ab33
Author: Samuela Pollack <sampoll@users.noreply.github.com>
Date: 2018-08-13 13:30:19 -0400
Commit message:

 Modifications to vignette and examples to pass checks with current server state
 
Package: BiocCheck
Commit: 1598a0bf16032749017053b730c064d45827b4ed
Author: lshep <shepherl@gmail.com>
Date: 2018-08-13 13:04:33 -0400
Commit message:

 Fix BiocCheckGitClone

  - checks raw clone, do not install or created build product files
 
Package: twoddpcr
Commit: 776da760777794450d058a502678ee8dded28e16
Author: Anthony Chiu <anthony.chiu@bbc.co.uk>
Date: 2018-08-13 18:02:24 +0100
Commit message:

 Update for BiocManager
 
Package: EnrichmentBrowser
Commit: f67bc3fb5499c21602f8a5c4e2ee15be44c204e6
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2018-08-13 12:44:17 -0400
Commit message:

 replace biocLite by BiocManager
 
Package: TPP
Commit: edd10bceea3d337aba738764fb158a7524d52995
Author: Dorothee Childs <dorothee.childs@embl.de>
Date: 2018-08-07 14:43:46 +0200
Commit message:

 Merge branch 'master' of https://github.com/DoroChilds/TPP
 
Package: TPP
Commit: e617511c89895a1fb78d9e0c94d579378e401fd2
Author: Dorothee Childs <dorothee.childs@embl.de>
Date: 2018-08-07 14:20:28 +0200
Commit message:

 Fix error produced by R CMD check on Windows.
 
Package: TPP
Commit: 7a60279e6497d1372e8dfd2178aec4e5b0db21a2
Author: Dorothee Childs <dorothee.childs@embl.de>
Date: 2018-08-07 14:20:28 +0200
Commit message:

 Fix error produced by R CMD check on Windows.
 
Package: TPP
Commit: d6c0516544fabde804fc76b0e60dffbdd38431a6
Author: Dorothee Childs <dorothee.childs@embl.de>
Date: 2018-08-07 13:43:59 +0200
Commit message:

 replace biocLite with BiocManager::install
 
Package: RITAN
Commit: ae7642b56a849783d5c39224804e0a4745e6b8ba
Author: Michael Zimmermann 2017-10-18 <mtzimmermann@mcw.edu>
Date: 2018-08-13 08:31:20 -0500
Commit message:

 bugfix to finish removing ProNet
 
Package: iSEE
Commit: 7960fcf17158c7f1fb307d280f5cdba54ca683bf
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-13 13:44:37 +0100
Commit message:

 Merge pull request #227 from csoneson/alt_custom

More generalized support for custom panels 
Package: iSEE
Commit: 4ac4718129efe5fd246e16126b95532d55876395
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-08-13 14:21:46 +0200
Commit message:

 Mention Display panel settings in vignette
 
Package: iSEE
Commit: 49b9745d53e7a8d6d26dfac87b819a1023262dd6
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 20:16:39 +0100
Commit message:

 fix
 
Package: iSEE
Commit: c43269e6ea2467f22426e77d4fc1d938ed78a789
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 15:42:28 +0100
Commit message:

 resolved orphaned sections, and grouped references to help pages
 
Package: iSEE
Commit: 3dd36652149028d372f0f6a43341c20ae5d6da3c
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 15:33:48 +0100
Commit message:

 fix X axis row stat table linked selection
 
Package: iSEE
Commit: 1053eacd21fdb772957aabb3e29697a3f584896b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 15:29:23 +0100
Commit message:

 introduce Assay as character value until the integer/character section
 
Package: iSEE
Commit: 9ba739f9b7ae2c0073f40c8f9307b9ac341809c7
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 15:26:30 +0100
Commit message:

 space
 
Package: iSEE
Commit: fc35a2474392c9f90d07911b73754b74763da737
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 15:26:03 +0100
Commit message:

 1 to 3
 
Package: iSEE
Commit: fbc576ddf04676618e861a0c65d1f3a0d3c2b42b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 15:23:01 +0100
Commit message:

 examples of integer and character values
 
Package: iSEE
Commit: 4977cd110b1dd5e68964f487a45083a08b37ab2e
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 14:49:54 +0100
Commit message:

 split brush and lasso
 
Package: iSEE
Commit: f3dbd49c1ef86c74efd53207182b0960822b3db2
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 14:48:55 +0100
Commit message:

 demo shiny brush and lasso
 
Package: iSEE
Commit: 582425e9a9a9790efe9d5499e18dd20a16ac4153
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 14:40:13 +0100
Commit message:

 point selection parameters
 
Package: iSEE
Commit: d81cd54c38e8dd977c4352bdd049ecd4f3c1d7f1
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 14:12:51 +0100
Commit message:

 demo faceting
 
Package: iSEE
Commit: 122641a31635945768f11b0ec779dce47f02f352
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 13:56:04 +0100
Commit message:

 more examples of default params
 
Package: iSEE
Commit: de257c529dc10dde514a02edbb5e2939f7238802
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 13:03:55 +0100
Commit message:

 link color to a variable
 
Package: iSEE
Commit: d7b018c07576a45260d2eb8d722c23d9f69690d2
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 12:46:11 +0100
Commit message:

 rename section, fix eponymous
 
Package: iSEE
Commit: d29bc4f33d2c83068397c298499701fb37d9b6fa
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 12:31:10 +0100
Commit message:

 chocolate3
 
Package: iSEE
Commit: c92cdf65f0fdaf802dcf8bd67c037d6522414fb1
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 12:19:39 +0100
Commit message:

 numbered examples; demonstrate assay data
 
Package: iSEE
Commit: 8edfd368d22ae975fdc3aca80a6b2a31b8ef5264
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 11:59:13 +0100
Commit message:

 open collapsible data box in examples
 
Package: iSEE
Commit: 8afcb4ae434240efb7233bcdb44e6aa0be30fb9a
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 11:53:20 +0100
Commit message:

 trim white line
 
Package: iSEE
Commit: d08c7b13ae1e3a9c54f3742ee9d47571812880c1
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 11:53:13 +0100
Commit message:

 RStudio cleanup
 
Package: iSEE
Commit: c5d892eb6feb1e53eaa7fc275e99f99d0751abcd
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 11:53:04 +0100
Commit message:

 remove debug print statement
 
Package: iSEE
Commit: 1eab591c0c5184b8bd6a0a7e30e368fd972462ff
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 11:50:50 +0100
Commit message:

 example of Xaxis configuration
 
Package: iSEE
Commit: 511de82f16ffd35a049edb790b680712357fed3a
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-12 11:50:38 +0100
Commit message:

 RStudio cleanup
 
Package: iSEE
Commit: 4fdeefc63c0b8671956173a203f5e4387addd960
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 22:50:59 +0100
Commit message:

 first details about configuration
 
Package: iSEE
Commit: ba0ba81a0fd0a6062078c1412a03023d49fe0c93
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 20:17:08 +0100
Commit message:

 document the sample assay plot in basic vignette
 
Package: iSEE
Commit: 80d30d323fc99e89f1de677b32c7882d1f763b02
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 20:11:54 +0100
Commit message:

 minor edits to configure vignette
 
Package: iSEE
Commit: de395de9ef5712a5d5ff1a588b44683017284f2b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 20:11:38 +0100
Commit message:

 start updating NEWS
 
Package: iSEE
Commit: 36f5a7214e8e4e23955111c48d4b32841b8a7731
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 20:11:20 +0100
Commit message:

 update internal man page
 
Package: iSEE
Commit: 690d564475adb121d0fbbfd059e6bd6952bcd59f
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 19:16:41 +0100
Commit message:

 clearer label for point selection source selectizes
 
Package: iSEE
Commit: 84b7bec3c73ba101883e28663e34f9fe1f453107
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 19:03:10 +0100
Commit message:

 extract "configure app" section from "advanced features" vignette into a separate vignette
 
Package: iSEE
Commit: dd82c67363e0d8c2548016199c052d2a9b5a96c5
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 18:08:36 +0100
Commit message:

 fix reference
 
Package: iSEE
Commit: cd56b879871115d34bb8ee6c8b788607ae4b6102
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-11 16:48:23 +0100
Commit message:

 Removed unnecessary internal function.
 
Package: iSEE
Commit: 95d9e6113e49ebff376ae2e0d5d05fd6ea6709f7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-11 16:35:12 +0100
Commit message:

 Fixed links to/from internal documentation.
 
Package: iSEE
Commit: 5101bbaa0b21406538c576389b3e8ee5abe94f39
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-11 16:25:54 +0100
Commit message:

 Renamed and rebuilt doc files for common parameter defaults.
 
Package: iSEE
Commit: 10a10196ae85c2655e0c695417ac2df4f2c08280
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-11 16:24:06 +0100
Commit message:

 Rebuilt documentation for each separate defaults function.
 
Package: iSEE
Commit: bdd45690ee6b5dcf2401f6fc327dd54b1529977d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-11 16:23:05 +0100
Commit message:

 Split up monolithic defaults documentation to several files.
 
Package: iSEE
Commit: 17d96c7dd33725d8fe67bdbb667a74e8c482f4b5
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-11 15:18:28 +0100
Commit message:

 Minor rewording of custom vignette.
 
Package: iSEE
Commit: d96a640d62fb46493d431259748b0ad41eca8f45
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 12:58:24 +0100
Commit message:

 version bump 1.1.4
 
Package: iSEE
Commit: 575282a22e1a47e070ef5f2124e57ef0fbfa10b0
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 11:48:33 +0100
Commit message:

 example of Arguments for custom table
 
Package: iSEE
Commit: 46cb144de142a3ae427f2ca215e2dce97b99b506
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 11:43:44 +0100
Commit message:

 preserve dimensions when subsetting assay
 
Package: iSEE
Commit: 102f2f47ce365986fcea0e0aee6420c2060b5f2f
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 11:43:12 +0100
Commit message:

 RStudio autoclean (space)
 
Package: iSEE
Commit: c74b73583a7ad89b4b1faa5dbf31e1b4ec7cf873
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 11:24:52 +0100
Commit message:

 added documentation of custom plot and table parameters
 
Package: iSEE
Commit: 5f87dab1430063626c37dfc9f56e734d4c427ea9
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 11:08:21 +0100
Commit message:

 add custom args defaults to the examples
 
Package: iSEE
Commit: d735140c53b24be62cf8636c46f94c83c56f0720
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 10:57:50 +0100
Commit message:

 forgot to save file
 
Package: iSEE
Commit: 38579f547f81f7f88a8c83d1a137b17ab51cf526
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-11 10:57:14 +0100
Commit message:

 add example of custom_stat_fun
 
Package: iSEE
Commit: d9967c3ab19f167d6c94b0a735dd5ffbfcec1615
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 17:40:04 +0100
Commit message:

 Cleaned up CITATION.
 
Package: iSEE
Commit: d4e10c28b8268300f576545401e8ffdf48e8ce95
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 17:33:38 +0100
Commit message:

 Rebuilt NAMESPACE.
 
Package: iSEE
Commit: c30bf6b350dacdceec725e71eb7b106a159fbe36
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 17:32:59 +0100
Commit message:

 Take advantage of exported SCE internal getters.
 
Package: iSEE
Commit: c29d4a5683c58a19b15b287cefbd609a1c4cde6f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 17:27:43 +0100
Commit message:

 Updated internal documentation to match code.
 
Package: iSEE
Commit: e60093868d576e4d0f67b4d934e1d34e6ad248b9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 17:21:10 +0100
Commit message:

 Updated code tracker tests for new behaviour.
 
Package: iSEE
Commit: 04d71d5eb336f230113ff6f52c402295143cb6ad
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 17:20:16 +0100
Commit message:

 Refined selection-only code tracker to report only relevant panels.
 
Package: iSEE
Commit: 445f509520be0a30f74416edcdac7119d694ef81
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 16:57:04 +0100
Commit message:

 Added tests for selection-only code tracker.
 
Package: iSEE
Commit: a84ffdfb27fb9d5ba26c5d97b6013d508941f19b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 16:41:39 +0100
Commit message:

 Added options for tracking only the selection-related code.
 
Package: iSEE
Commit: d561e585a25bd2da9531b6f294196d1ab43180a0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-08 18:20:52 +0100
Commit message:

 Switch code tracker functions to use panel groupings.
 
Package: iSEE
Commit: 669e9e3c10407e93cb74b9b38d5abca47c7d3e43
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-08 18:15:57 +0100
Commit message:

 Added tests for the code tracker functions.
 
Package: iSEE
Commit: beed3ff9e359a62331d998296baa61c68c4fa31e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-08 18:15:28 +0100
Commit message:

 Removed reporting order test from selection links test file.
 
Package: iSEE
Commit: 756d219738ec99c202c5397da368e2678c3a2832
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-08 17:41:23 +0100
Commit message:

 Tested proper selection graph setup for custom panels.
 
Package: iSEE
Commit: cedbba40d527744b6c6fd973b505749db353a82c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-08 17:38:10 +0100
Commit message:

 Fixed bug with selection graph spawning for custom panels.
 
Package: iSEE
Commit: 7563d15e9539c9005d5cba580de23b8ba0422b7f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-08 17:09:08 +0100
Commit message:

 Added tests for .text2args().
Tested row selection transmission to a custom panel.
Removed obsolete tests for discarded custom functionality.
 
Package: iSEE
Commit: 13576a208aa0b4fb0c810b04bd8a700e99e2a7ce
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-08 16:58:28 +0100
Commit message:

 Merge branch 'alt_custom' of https://github.com/csoneson/iSEE into alt_custom
 
Package: iSEE
Commit: 74efa1fcb26ed65e69e00f72eaff8df28acaa9f0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-08 16:58:19 +0100
Commit message:

 Refined regexes to protect against silly custom user inputs.
 
Package: iSEE
Commit: 777640955742bc9dc396e0cf2f2acb9318d097c3
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-08-08 16:53:02 +0100
Commit message:

 Merge branch 'master' into alt_custom 
Package: iSEE
Commit: 9b67d378047bb4ed1787450c20086a8c1e4301e0
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 23:12:01 +0100
Commit message:

 new custom names in test_selection_links
 
Package: iSEE
Commit: ecebaf0580d0c5f0fcff63ac0ea9986acd2bfdbc
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 23:01:24 +0100
Commit message:

 new custom names in test_ui
 
Package: iSEE
Commit: 744704669035c17c718c3d79679dbe84ea53de2a
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 22:54:37 +0100
Commit message:

 rename customArgs in tests
 
Package: iSEE
Commit: 008e81a59ab51f640c48be12d63119748aeb6841
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 22:44:46 +0100
Commit message:

 fixed test_plotting
 
Package: iSEE
Commit: f350f941638da842bbd650a3a7899c1d046fbd03
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 22:41:58 +0100
Commit message:

 stat_fun missing
 
Package: iSEE
Commit: ab8e69456e678f2b477491e5e3c40ebe9b4a539d
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 22:35:20 +0100
Commit message:

 stat_fun missing
 
Package: iSEE
Commit: a1dae0a9757e39ed9732e0cc39066b294b436db5
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 22:13:46 +0100
Commit message:

 stat_fun missing
 
Package: iSEE
Commit: 41f2c7be9e3fdcfad94c20a06159587cb549019d
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 22:13:00 +0100
Commit message:

 missing stat_fun
 
Package: iSEE
Commit: 86fcdf9bdd015b31d45e3a5cbbaa9f8019e52846
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-07 22:10:52 +0100
Commit message:

 no selection leads to empty plot
 
Package: iSEE
Commit: a067c1f35d9f61e4b403eb554f7c0aa3083cdaa4
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 10:06:13 +0100
Commit message:

 Further bugfix to grouping constants.
 
Package: iSEE
Commit: 07fb7ef68f43e176de9d8ec1425a48e1dc9835c1
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 10:05:29 +0100
Commit message:

 Bugfix to grouping constants.
 
Package: iSEE
Commit: 659c25eef3ad5a99f2f0cc41b486d4f6de3403f0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 10:03:23 +0100
Commit message:

 Further streamlining of code using the grouping constants.
 
Package: iSEE
Commit: a87f34c017a0eb0b1660fc6de2e27951b798c619
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 09:49:17 +0100
Commit message:

 Bugfix for link updates upon deletion of custom panels.
Created central constants describing panel groupings.
 
Package: iSEE
Commit: 9322b6f9b2bf9fe3d537d93d4f3dd1ceb9254702
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-06 22:52:44 +0100
Commit message:

 renamed last few occurences of customColPlot to customDataPlot
 
Package: iSEE
Commit: 06be9d94b5249efeeccb2fcb7ee4bfa32a72e9e9
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-06 22:48:26 +0100
Commit message:

 there is no more cache
 
Package: iSEE
Commit: ae3224f34f508ae6fc3bc68f20bcf6a2c4ee5633
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-06 22:47:46 +0100
Commit message:

 fixed test_custom
 
Package: iSEE
Commit: 38fbdf8cb5bc3633cba89f96b1fa9d8d0da18641
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 19:01:51 +0100
Commit message:

 Corrected name of scaling argument to plotPCA in vignette.
 
Package: iSEE
Commit: 74a36b97a15ea67593ecab918a909ad219aaffb4
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 18:57:07 +0100
Commit message:

 Modularized code tracker, support custom plots.
 
Package: iSEE
Commit: 66b2c57950013419e6d40cefcce17ffa3de6579f
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 22:55:58 +0100
Commit message:

 added a dummy custom_stat function; doesn't break anything
 
Package: iSEE
Commit: f959c1f9dfd5a1f0b90bf91089d29e456204b196
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:44:49 +0100
Commit message:

 custom plots do not respond to downsampling anymore
 
Package: iSEE
Commit: 8f9d1d7152303db47873e1fc00b1f8cdb451c60d
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:40:01 +0100
Commit message:

 removed deprecated outputs, but test not fixed
 
Package: iSEE
Commit: e26485cc3269d50717243e586abfdb776e72c631
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:36:10 +0100
Commit message:

 removed unused arguments: ecm, cached
 
Package: iSEE
Commit: c5305fb6dd9fa52783be4179d6405f600d30486c
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:32:23 +0100
Commit message:

 renamed .make_customColPlot to .make_customDataPlot; matched PC2 to cmd_list
 
Package: iSEE
Commit: 2861733191dd3b65eb00dbc6cb5ab48f1f8ef012
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:27:48 +0100
Commit message:

 another test passed
 
Package: iSEE
Commit: 11ebc31e735f33880c15b5b55b4f4ac3f53d8994
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:08:33 +0100
Commit message:

 getting a test to pass
 
Package: iSEE
Commit: f0b4d3f79cb6fc35c45696d58352a6a89b17fd43
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:06:57 +0100
Commit message:

 rename custom_col_fun to custom_data_fun
 
Package: iSEE
Commit: 7404948251d6370f6eace43d4eca74c21b30ab09
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:06:18 +0100
Commit message:

 bring in example from new custom vignette, and update arguments to custom function
 
Package: iSEE
Commit: 4c220d9abb28572ff6496a7d335e47ebc96133b7
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:05:40 +0100
Commit message:

 renamed customColPlotDefaults to customDataPlotDefaults
 
Package: iSEE
Commit: 23d671deb90d96225f40dbd8d51ebc048389e0e9
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:04:49 +0100
Commit message:

 renamed customColPlotDefaults to customDataPlotDefaults
 
Package: iSEE
Commit: dbb4154d5b9b056c7d957c7dc3106368e0532244
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 19:01:47 +0100
Commit message:

 remove debug print
 
Package: iSEE
Commit: 6c9632b2640cacad16420f9f48b0dbf9f1cbec37
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 16:12:38 +0100
Commit message:

 minor fix
 
Package: iSEE
Commit: 214f60216224d61728d3a5612032b170bd5cf215
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-05 15:48:37 +0100
Commit message:

 Removed custom plot doc page.
 
Package: iSEE
Commit: 5ce3b8a4558f74b8d1a60533691461cb554aa421
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-05 15:46:14 +0100
Commit message:

 Reoxygenated.
 
Package: iSEE
Commit: 0816078a14f33982bccc1d01c05b141306b2404a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-05 15:45:28 +0100
Commit message:

 Control vignette ordering on landing page.
 
Package: iSEE
Commit: 30277be46a19e1f7e8545375c1b1ba5a737283fe
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-05 15:43:21 +0100
Commit message:

 Promoted description of custom panels to a vignette.
 
Package: iSEE
Commit: 9f2112c0d243bfe21988a23eda822e3d1afb0139
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-05 15:42:06 +0100
Commit message:

 Added support for custom statistics tables.
Streamlined observers, other infrastructure for all custom panels.
 
Package: iSEE
Commit: 3024e886a152b6156093fa22613ce41a21017233
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-04 19:59:57 +0100
Commit message:

 Reoxygenated docs, NAMESPACE.
 
Package: iSEE
Commit: 00970da356c38debd04c6c1f44233013e6b9cfbd
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-04 19:58:07 +0100
Commit message:

 Generalized custom plots to any user-defined plotting function.
Renamed customColPlots to customDataPlots.
Reduced redundancy in code for processing row/column data.
 
Package: iSEE
Commit: 13336e47234023b856dda740d52eb0f25a902456
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-05 15:52:27 +0100
Commit message:

 Merge pull request #226 from csoneson/biocmanager

replace BiocInstaller by biocLite in travis YML 
Package: iSEE
Commit: c46ea0decdfc9c398bd99965b0f36c4c9366da89
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2018-08-04 14:17:19 +0100
Commit message:

 replace BiocInstaller by biocLite in travis YML
 
Package: iSEE
Commit: 414167430b7dbedd3d096d2f985595968fd63ce1
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-07-31 15:20:59 -0400
Commit message:

 Merge pull request #224 from csoneson/contourfix

Contourfix 
Package: iSEE
Commit: ba18bd9f686fc017682d687466254e9bc590bfe7
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-07-31 18:40:07 +0200
Commit message:

 Change name of contour color variable
 
Package: iSEE
Commit: a3aadafdc437c0d0d18492acd7ae4bb3a14e9b19
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-07-31 18:25:44 +0200
Commit message:

 Use .conditional_on_check_solo
 
Package: iSEE
Commit: 5d3ffbe7480f065e3db65c0c023f1852a980e43e
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-07-31 12:13:44 -0400
Commit message:

 Merge pull request #223 from csoneson/contours

Contours 
Package: iSEE
Commit: 439a9ee1b98890c8477655a16bb81278e15b8bfe
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-07-28 22:47:01 +0200
Commit message:

 Add options to color contour lines.
 
Package: iSEE
Commit: a96929fd125ea36991a1ae6c7edc2e357ea7cc37
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-07-28 21:26:30 +0200
Commit message:

 Option to add contour lines to scatter plots
 
Package: DelayedMatrixStats
Commit: f63d55c9929d9ca60eaa6465c6ac9f8749a8bf22
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-13 21:02:55 +1000
Commit message:

 Re-enable unit tests

Fixed bug in rowblock_APPLY() 
Package: DelayedMatrixStats
Commit: 3dd0b128fd915be279dc4f6988ff6271c0be1355
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-13 20:07:45 +1000
Commit message:

 Temporarily limit unit tests

Need to investigate why unit tests for colsum() and rowsum() break when using a small block size 
Package: DelayedMatrixStats
Commit: c4957390b337c0a2380de518615861c1779b319b
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-13 16:09:28 +1000
Commit message:

 More tweaks to colsum() and rowsum() 
Package: DelayedMatrixStats
Commit: 22c123135d9ce3487d0b7813672f4ecfbe619bbf
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-13 15:08:59 +1000
Commit message:

 Reactivate all tests 
Package: DelayedMatrixStats
Commit: 57d198b42e56005deeb18af42d45da1cc44a41c8
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-13 15:07:06 +1000
Commit message:

 Roxygenise

 
Package: DelayedMatrixStats
Commit: 82c175cbb59d81d18be65a8475f888ac149c2f57
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-13 15:06:21 +1000
Commit message:

 Merge upstream and master 
Package: DelayedMatrixStats
Commit: 6de19f2a0693ecbee63819f407d20a193c7d3449
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-13 15:03:58 +1000
Commit message:

 Tweaks to colsum() and rowsum() 
Package: DelayedMatrixStats
Commit: 4ee7ece247f0e5fa9f83331825a092cce0575a9f
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-05 15:02:03 +1000
Commit message:

 Update NEWS.md 
Package: DelayedMatrixStats
Commit: 0badc5b3cc27ad811e984545593fd363f30c68f9
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-05 14:52:22 +1000
Commit message:

 Add colsum,HDF5Matrix-method and rowsum,HDF5Matrix-method

- These both return an HDF5Matrix rather than a matrix
- Move 'HDF5Array' from Suggests to Imports 
Package: DelayedMatrixStats
Commit: 28c27202418fab84ed45124b6cb0e28bff09c014
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-01 18:11:43 +1000
Commit message:

 Tidy up roxygen comments and re-roxygenise 
Package: DelayedMatrixStats
Commit: efb93b86719564dd0b2e840d1a86133602370fa2
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-08-01 18:03:01 +1000
Commit message:

 Add rowsum() and colsum() 
Package: BiocOncoTK
Commit: 5ee0ef1857ff9142d0585dd3c0f5f1e0b5ed2e80
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-13 06:50:21 -0400
Commit message:

 squelching tests for now owing to authentication issues
a new protocol is needed
 
Package: chroGPS
Commit: 225ff69b7ac8f9271746b6ecaf97402fa13eae5c
Author: oreina <oreina@biocf06.irb.pcb.ub.es>
Date: 2018-08-13 12:42:09 +0200
Commit message:

 Updated vignette
 
Package: restfulSE
Commit: 96942d93114642fc2b2df08468dfc9ce034c3cd5
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-12 22:51:55 -0400
Commit message:

 updating for BiocOncoTK
 
Package: restfulSE
Commit: 686d18dad54a90346545a50d6a902f6a3f7de1d1
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-12 22:49:10 -0400
Commit message:

 needed updates to allow BiocOncoTK to proceed
 
Package: tenXplore
Commit: 419bb7f7084653aa90a51eacb228703a5a950a1f
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-12 22:42:35 -0400
Commit message:

 updating for simple maintenance in inst/app
 
Package: BiocOncoTK
Commit: 5100d2245d1c073f43e4cb481f4d122849ef6a6d
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-12 21:24:05 -0400
Commit message:

 incrementing version of restfulSE required
 
Package: BiocOncoTK
Commit: c9f26259efedb3473027ce9dae2b8dae7641a5ee
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-12 21:23:33 -0400
Commit message:

 updating tests
 
Package: CNPBayes
Commit: 6f3ffdab4da32959dd627ea5e5e72f600362d20a
Author: Robert Scharpf <rscharpf@Roberts-MacBook-Pro-2.local>
Date: 2018-08-12 20:36:37 -0400
Commit message:

 update documentation
 
Package: CNPBayes
Commit: 2ac26468063f27563395c3d13d929b09ca16832d
Author: Robert Scharpf <rscharpf@Roberts-MacBook-Pro-2.local>
Date: 2018-08-12 20:34:39 -0400
Commit message:

 update documentation and add parentheses in miscfunctions.cpp
 
Package: BiocOncoTK
Commit: f052f6464a074791cee0562b91e9ade1c208a62a
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-12 17:53:15 -0400
Commit message:

 updating darmGBMcls.rda to use HDFgroup kitalab /shared/bioconductor/
 
Package: REMP
Commit: 5ec36ea61273e0caefe79fc43d3708796e96581f
Author: Yinan Zheng <y-zheng@northwestern.edu>
Date: 2018-08-12 15:09:52 -0500
Commit message:

 Updates v1.4.1: bug fixes in grooMethy and remprofile
 
Package: BiocOncoTK
Commit: 6bdad306122cd87ad69dc6b7035bf1146dfca49d
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2018-08-12 12:42:28 -0400
Commit message:

 add tests for buildPancanSE
 
Package: MAGeCKFlute
Commit: 0138f30f834c2e2670ae956d87d7ea151af751cd
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-08-12 16:20:18 +0800
Commit message:

 1.1.4
 
Package: MAGeCKFlute
Commit: 11275a3a07704beb8794a4c1fa30db6c359afca7
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-08-11 18:42:19 +0800
Commit message:

 rm unknown files
 
Package: MAGeCKFlute
Commit: 45beb477f487e72f22499dd3a332fbe7db5413d6
Author: WubingZhang <Watson5bZhang@gmail.com>
Date: 2018-08-11 18:40:33 +0800
Commit message:

 1.1.3
 
Package: CellTrails
Commit: ce6ad195dbde256f2b79dc2b1260e203f641c7bb
Author: dcellwanger <dc.ellwanger.dev@gmail.com>
Date: 2018-08-10 17:09:12 -0700
Commit message:

 updated readme [ci skip]
 
Package: RCy3
Commit: 7405ef09a68581b7a3775a47d314fc4cefdf38f5
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-08-10 16:38:39 -0700
Commit message:

 version bump
 
Package: RCy3
Commit: 021c3d01cdc23caf9747dc59dd93d3aa3acb024b
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-08-10 16:32:32 -0700
Commit message:

 docfix: add lib for new tests
 
Package: RCy3
Commit: 5227131b9a35bb4983b048e5ed48fcaa4bf4b43b
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-08-10 16:29:32 -0700
Commit message:

 bugfix: fixes #37
 
Package: SNPRelate
Commit: db7d1cf239e973692e396803bc93c108984fa7cb
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2018-08-10 16:28:01 -0700
Commit message:

 snpgdsIndInb() fixes missing sample and SNP IDs
 
Package: EnrichmentBrowser
Commit: d9b5c08308117a44f77427ed4543035dd45b9bd7
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2018-08-10 17:47:42 -0400
Commit message:

 doc enhancement: ebrowser
 
Package: GenomicFeatures
Commit: a1d517337ac447ed6d26fb1110e5da5a0bf9908a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-10 14:39:25 -0700
Commit message:

 makeTxDbFromGRanges() now accepts missing/invalid CDS phases

makeTxDbFromGRanges() now issues a warning instead of an error if any
CDS phase is missing or not between 0 and 2. This change also affects
makeTxDbFromGFF() which uses makeTxDbFromGRanges() internally.
 
Package: RCy3
Commit: 02619aec761239c700de726254787b50898f154b
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2018-08-09 22:23:11 -0700
Commit message:

 docfix: tests, readme and man pages
 
Package: diffcyt
Commit: 9de85606c2bc3f63af95fc5efaca5f8ccfb1e0bd
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-08-10 22:12:33 +0200
Commit message:

 simplify normalization
 
Package: CellTrails
Commit: 50a9b0dc46a735d253c86ada9584a9d3c9fbda18
Author: dcellwanger <dc.ellwanger.dev@gmail.com>
Date: 2018-08-10 12:51:21 -0700
Commit message:

 updated readme [ci skip]
 
Package: CellTrails
Commit: 694b2ff34bb5934a718bfb232c2c6c08ed9d8247
Author: dcellwanger <dc.ellwanger.dev@gmail.com>
Date: 2018-08-10 12:49:00 -0700
Commit message:

 updated readme [ci skip]
 
Package: rtracklayer
Commit: cafa0a44f8900a2942a005b6d722edda60beeb55
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-10 12:48:37 -0700
Commit message:

 Issue warning when writting GFF/GTF file with missing CDS phase
 
Package: CellTrails
Commit: 5fb59600eec98e601928460c721ba3c874cc4bdf
Author: dcellwanger <dc.ellwanger.dev@gmail.com>
Date: 2018-08-10 12:47:40 -0700
Commit message:

 updated readme [ci skip]
 
Package: CellTrails
Commit: 89ffe06332e74bbb452aa97cf6149ab254be4ecd
Author: dcellwanger <dc.ellwanger.dev@gmail.com>
Date: 2018-08-10 12:45:30 -0700
Commit message:

 readme update [ci skip]
 
Package: diffcyt
Commit: 595c8fca14d511babb8902d88b6111cea14f1ca4
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2018-08-10 21:18:07 +0200
Commit message:

 option to disable transformation
 
Package: minfi
Commit: 2234f43445bf043846039146495a23512dd0db23
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-10 10:00:25 -0700
Commit message:

 Resync with recent change to DelayedArray

Use getDefaultBlockLength(type(x)) instead of
DelayedArray:::get_default_block_maxlength(type(x)).
 
Package: DelayedArray
Commit: 408c1ca9abd7996766820e4403db4736a2e9861e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-10 10:13:12 -0700
Commit message:

 Suppress some annoying and not-so-useful load-time messages
 
Package: iCARE
Commit: d424c1becbc0eb46dcee76249acefd3272e6e757
Author: wheelerb <wheelerb@imsweb.com>
Date: 2018-08-10 13:00:18 -0400
Commit message:

 update man files
 
Package: DelayedArray
Commit: 91b8e59cc9c4352b0631027c227addc9a4a0b4bc
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-10 09:54:41 -0700
Commit message:

 Check user input in getDefaultBlockLength()
 
Package: RTCGAToolbox
Commit: 05519b0b30e1d07ae19f68edc5f9f2e308384182
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-08-10 12:40:17 -0400
Commit message:

 update biocLite calls in vignette
 
Package: DelayedMatrixStats
Commit: 65bfe7751de218ac73e9ebf05c59242a6a81d508
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-10 09:01:51 -0700
Commit message:

 Import getDefaultBlockLength from the DelayedArray package
 
Package: DelayedMatrixStats
Commit: 0ec4bd8777a567f9b2d7a92d476b376f556cb733
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-08-10 08:50:12 -0700
Commit message:

 Resync with some recent changes to DelayedArray

- Use getDefaultBlockSize() instead of getOption("DelayedArray.block.size").
- Use getDefaultBlockLength(type(x)) instead of
  DelayedArray:::get_default_block_maxlength(type(x)).
- Arg 'viewport_maxlen' in makeRegularArrayGridOfCappedLengthViewports()
  was renamed 'viewport_len'.
 
Package: CellTrails
Commit: fccc7fb63da5d300d1036fdc313399595210324f
Author: dcellwanger <dc.ellwanger.dev@gmail.com>
Date: 2018-08-10 08:54:10 -0700
Commit message:

 updated Travis CI
 
Package: Prostar
Commit: de93fc82eebb17ba6a939ed5f394c83af9aa4f62
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-08-10 16:18:14 +0200
Commit message:

 new Version
 
Package: Prostar
Commit: 431ff411b592449c6d30abfd3717e11b4f234db8
Author: ThomasBurger <thomas.burger@cea.fr>
Date: 2018-07-31 17:46:48 +0200
Commit message:

 Update ui_FAQ.R 
Package: Prostar
Commit: eb198b49e2d3ba3094fc04077a82bb7e5997d366
Author: ThomasBurger <thomas.burger@cea.fr>
Date: 2018-07-31 17:41:52 +0200
Commit message:

 Update srv_BuildDesign.R 
Package: Prostar
Commit: 293df6852f4e521d7680604f5604782983eadb26
Author: ThomasBurger <thomas.burger@cea.fr>
Date: 2018-07-31 17:39:09 +0200
Commit message:

 Update srv_FAQ.R 
Package: Prostar
Commit: f39c0c01b3aae34a8c3b9049d766fbec6ec1505a
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-30 05:41:29 +0200
Commit message:

 Cleaning of imputation srv code
 
Package: Prostar
Commit: 4819c61b4edf4097aabe4fa3ae84567450f7a7da
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-29 05:46:39 +0200
Commit message:

 Update FAQ
 
Package: Prostar
Commit: 9332d02ebc4a09e2cc67022ea437cd22d3d0a63e
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-28 16:12:16 +0200
Commit message:

 add actionLinks
 
Package: Prostar
Commit: 393cd70fb541b430b64d0459a6833d783b463ba9
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-28 10:01:46 +0200
Commit message:

 Add imports
 
Package: Prostar
Commit: 5345e85d5365ca9128f2ef967519f0563bb31809
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-28 09:32:58 +0200
Commit message:

 Same
 
Package: Prostar
Commit: dc1f4af337d51573d4fb40432bae165083db597a
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-28 09:31:35 +0200
Commit message:

 Version 1.13.2 : add Bug report tool
 
Package: Prostar
Commit: 8b5c5b7f31c8f0b58f915b4c924eac1ceb8671ad
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-27 17:14:10 +0200
Commit message:

 Several updates
 
Package: Prostar
Commit: cd18a6e93567780d87cd9621eaf3fd884d5f75f3
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-27 09:35:02 +0200
Commit message:

 Update in manage UI
 
Package: Prostar
Commit: 5b22f5b1d2d1cc1b5803e27a7fd2c15181f67cb6
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-26 16:20:15 +0200
Commit message:

 Contextuals menus updates
 
Package: Prostar
Commit: 01e8e454151a07a5355352e2bb2750ab9ee5b401
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-26 09:50:48 +0200
Commit message:

 toto
 
Package: Prostar
Commit: 366175ddf6ce8df87f94203ab45ae9d6134c2130
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-25 06:26:30 +0200
Commit message:

 Update in boxplot options
 
Package: Prostar
Commit: 1db3f48ce37b945fc8e35c6b49edd953be8afb53
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-24 05:32:43 +0200
Commit message:

 Change colnames in pData (Sample.name, Condition)
 
Package: Prostar
Commit: 98e8ffca8bb7326e746772118e19a485f78aa63b
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-23 07:40:13 +0200
Commit message:

 Replace FC by logFC
 
Package: Prostar
Commit: f5328227b858d128ef1ce78ed9e2a4aaa42b1909
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-23 05:39:29 +0200
Commit message:

 Clean up of source files
 
Package: Prostar
Commit: 8e9b5fd6f0491f1fb9b026d85f7c9ab5b662d377
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-22 05:54:13 +0200
Commit message:

 new master
 
Package: Prostar
Commit: d67ef93601bfc26f9d0b1af60a6dc06ebc8f24ff
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-04 07:26:42 +0200
Commit message:

 Add files via upload 
Package: Prostar
Commit: c9c4ccc9e91e98c2a545bb7919421828fa15fa7a
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2018-06-04 07:26:21 +0200
Commit message:

 Add files via upload 
Package: variants
Commit: 28ff8eabd667e7bf2269696b39cfe4eb61c4c9dd
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:50:27 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: flowAI
Commit: 4919fd49bd3c0df8316d49977a1a048fd813d071
Author: Gianni <mongianni1@gmail.com>
Date: 2018-08-10 15:49:22 +0200
Commit message:

 bump
 
Package: TCGAWorkflow
Commit: 7148363aaf09a0889844ffb309b4917c5d8ccfa5
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:49:11 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: simpleSingleCell
Commit: 29a4134b38d246324dfb17884809f7926c992350
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:46:49 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: sequencing
Commit: aa316c9ca2e1a79138548ef8d58d218a288ff424
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:45:20 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: RnaSeqGeneEdgeRQL
Commit: 163009b58dfbe783b7ca13820471ea2047c0f7b5
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:44:29 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: rnaseqGene
Commit: 9cb20419a0400bea7fe59c2335b9bf027ca4c523
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:42:34 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: rnaseqDTU
Commit: 1b760051293d28ed53d32d887ad8014b6de0b16a
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:41:22 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: RNAseq123
Commit: 2f1285a06c1494cca969404c1b9bedb7e2f52fe2
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:39:49 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: recountWorkflow
Commit: eeda70658d8bad00727a82463a9f8978b1860b9a
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:38:57 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: proteomics
Commit: 006758f50e61a555d139361cb10cc27759ca2260
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:36:52 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: methylationArrayAnalysis
Commit: d2f7495883d9f5e2bd8f8b7cdc69d15b2181d2b3
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:33:36 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: eQTL
Commit: 32b70afbaca769e22c10ab2ee526b30894a759ce
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:32:30 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: maEndToEnd
Commit: 135704a1ad01025bef96766631f5bbf87d874f99
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:31:45 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: liftOver
Commit: 9198562c8645d3ab4ac471c1ce29d652dd889cf2
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:28:54 -0400
Commit message:

 Update BiocInstaller for BiocManager
 
Package: highthroughputassays
Commit: 7b38c5643f192526511e369e30e3c0bd4a33fa80
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:27:55 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: generegulation
Commit: 32f296f21ce014b52192ef97b50c416eeb897c53
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:26:25 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: ExpressionNormalizationWorkflow
Commit: 245b7fe8215622ee53bf53d5c03a32aded8815e0
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:23:31 -0400
Commit message:

 Update BiocInstaller for BiocManager
 
Package: EGSEA123
Commit: fb7c59a68a93f7c0d796dc9e7f59e8df4fa42664
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:17:41 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: chipseqDB
Commit: 1a12ea2d1d10eaa369592671d39eaebf7736b93f
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:11:54 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: BiocMetaWorkflow
Commit: 29e714a06e9e4c9393185cec20e590333efb0042
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:09:55 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: arrays
Commit: b9e4e751964512c445abc5371350af1783eca6ab
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:07:00 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: annotation
Commit: 3779acbbaa1f4f636c62ab313097420592aecca0
Author: lshep <shepherl@gmail.com>
Date: 2018-08-10 09:06:01 -0400
Commit message:

 Update BiocInstaller to BiocManager
 
Package: karyoploteR
Commit: d286096c5ba4f264ce09c38114689596669e06e1
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-10 14:36:25 +0200
Commit message:

 Added new kpPlotBAMCoverage function

 
Package: karyoploteR
Commit: f349eea7dfa95416d106f05503aa1c1bf712dc77
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-10 14:35:41 +0200
Commit message:

 readded comment with TODO

 
Package: karyoploteR
Commit: 4696ea6448e5cc2aee3b4c1a47a50f3cc1932d98
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-10 14:35:15 +0200
Commit message:

 Added explicit scoping to a call to Seqinfo

 
Package: karyoploteR
Commit: f978749ac91d23b755f26efcd362da746b591fef
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-10 13:58:16 +0200
Commit message:

 Fixed a bug in kpAxis: no visible axis when in zoom

 
Package: karyoploteR
Commit: 4ebdc0fba0e4acb63bd444a1c4772fa1bbc6b9eb
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-09 15:16:45 +0200
Commit message:

 Improved efficiency of kpPlotBAMDensity when zoomed

 
Package: karyoploteR
Commit: 2993ff29b5265c0b881bcdb8f04f5db74d20431a
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-08-09 15:15:11 +0200
Commit message:

 Updated News file

 
Package: karyoploteR
Commit: 7f8f5d5230a53c653cecc89d0c423f74312f787b
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2018-06-14 11:44:04 +0200
Commit message:

 Added a digits parameter to kpAddBaseNumbers

Added a new digits parameter to kpAddBaseNumbers to control the number of digits after the decimal point in genome position labels 
Package: DropletUtils
Commit: bd5ec8df0e02ae5f466e4ce4fccc786d76f5f6ac
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 12:59:26 +0100
Commit message:

 Bumped version number, date for beachmat update.
 
Package: scater
Commit: 7fa77e354da829910061cd85ea95c64a71bd3a42
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 12:51:00 +0100
Commit message:

 Bumped version number for beachmat updates.
 
Package: debrowser
Commit: 0b973f7069606fa32323a42c30762cc941e50d65
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2018-08-10 13:02:51 +0200
Commit message:

 Warning fixes
 
Package: debrowser
Commit: aa2e8eeb25a4d92b017e346a09f0f1d9a3308185
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2018-08-10 12:45:53 +0200
Commit message:

 Merge branch 'master' of https://github.com/UMMS-Biocore/debrowser
 
Package: debrowser
Commit: ac2c4cdfa129fa2fc7d981444308c52139e90697
Author: onuryukselen <33356633+onuryukselen@users.noreply.github.com>
Date: 2018-08-07 16:11:53 -0400
Commit message:

 Readme and documentation updates. (#183)

 
Package: debrowser
Commit: ab7616736e988a67b573574385ab2b3e4fb00f1b
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2018-08-07 16:11:36 -0400
Commit message:

 startHeatmap (#184)

* Added startHeatmap functionality

* startHeatmap functionality

* version increase
 
Package: debrowser
Commit: b396d938b30b112ea4a008f781a096228b7ecd97
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2018-08-07 13:55:25 -0400
Commit message:

 Version increase (#182)

* Added startHeatmap functionality

* startHeatmap functionality

* version increase
 
Package: debrowser
Commit: 88b557d8585da49de287aee349f17e241fdda909
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2018-08-07 13:53:48 -0400
Commit message:

 startHeatmap functionality (#181)

* Added startHeatmap functionality

* startHeatmap functionality
 
Package: beachmat
Commit: 9890e63792ba249cc21a87621a24fc897afc5d81
Author: Aaron Lun <LTLA@users.noreply.github.com>
Date: 2018-08-10 12:07:23 +0100
Commit message:

 Merge pull request #11 from LTLA/refactor

Refactored beachmat 
Package: beachmat
Commit: bd0019176ef0e20c83d970629bd832cd0baf2a4b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 12:00:22 +0100
Commit message:

 Added ignore files, added missing Imports in DESCRIPTION.
 
Package: beachmat
Commit: 31e5cdefc166db9d32c43b403295b8cb3b049b5f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 11:38:30 +0100
Commit message:

 Rebuilt top-level NAMESPACE, bumped version and date.
 
Package: beachmat
Commit: 52a61a1546aafe0f40d4a38c0244bff04b7e2037
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 11:37:30 +0100
Commit message:

 Split tests for new delayed/unknown helper R functions.
 
Package: beachmat
Commit: 4a20a3cc6a253213f7bd77ce2b49baa6faf06fc1
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 11:21:06 +0100
Commit message:

 Streamlined CITATION.
 
Package: beachmat
Commit: 4b2ba8d2f7085d7622fee4715723b1c43a370f0e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 11:13:31 +0100
Commit message:

 Rebuilt NAMESPACE for test package.
 
Package: beachmat
Commit: 895faa328dbf3150e97289df8b0fc22255025772
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 11:12:02 +0100
Commit message:

 Centralized test matrix generating functions to setup script.
Removed unnecessary RLE output tests, as class tests are present.
Minor reformatting of test scripts, changes to seeds.
 
Package: beachmat
Commit: e1916461b3fdc9f2887082386814ed438a932113
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:39:08 +0100
Commit message:

 Updated test scripts for renamed functions.
Ensure DelayedArray::tolower is used in character output tests.
 
Package: beachmat
Commit: 17cc2e8ff976980079e8f673e57f2bdfdc4ba25c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:35:44 +0100
Commit message:

 Added missing file for testing input matrix class.
Renamed test function for checking the output matrix class.
 
Package: beachmat
Commit: 2add6c14294bf28aec9b60d1f81be4bbb06fa1b6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:28:13 +0100
Commit message:

 Reoxygenated, rebuilt NAMESPACE.
 
Package: beachmat
Commit: 14f4c4c5f5aee9c868dd999767a915a9ad578851
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:26:35 +0100
Commit message:

 Removed old R functions in the test package.
 
Package: beachmat
Commit: fa99349d83bd1e55fdb9865e50965cc844f07470
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:25:13 +0100
Commit message:

 Updated error checks for input matrix representation instantiation.
 
Package: beachmat
Commit: ae7bcb48fb7bf9c359a6f7e2b0d1a78dc3466103
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:20:16 +0100
Commit message:

 Added error catching macros to test C++ code.
 
Package: beachmat
Commit: 907fe32126bb61c2519a62785c8163c680ace245
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:17:02 +0100
Commit message:

 Removed old C++ files in the test package.
 
Package: beachmat
Commit: 26c8141ab3a07c7a80176bf648d9c9c6d1f7f903
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:13:52 +0100
Commit message:

 Removed old test scripts.
 
Package: beachmat
Commit: ae0131c5a726661c46400c0a65c6cc39dabef571
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:09:06 +0100
Commit message:

 Added input class checks to all input test scripts.
 
Package: beachmat
Commit: 2338a1d6719ac1a8735010e5dd277da7660fe249
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 10:07:25 +0100
Commit message:

 Generalized class checking test code for input matrices.
 
Package: beachmat
Commit: 6727e35b31823d054ab151a3b1c48be1d368921a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 09:50:09 +0100
Commit message:

 Updated write type checks, filled in missing sparse zero-dim tests.
 
Package: beachmat
Commit: f05e6a97ec87020e9def9d2e41e4ffb6bd35dd40
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 09:48:16 +0100
Commit message:

 Changed write type tests to a 'passaging' method.
 
Package: beachmat
Commit: ac6f730c51126501266d0b29f56c150dc4c9b9d9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-10 09:30:21 +0100
Commit message:

 Added tests for zero-dimension output matrices.
 
Package: beachmat
Commit: 3f526e4d657b7bc8b9d56f6a0edc656835465779
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 20:50:15 +0100
Commit message:

 Added sanity tests for zero-dimensional input matrices.
 
Package: beachmat
Commit: 11a692492f969c760634f55610751eb338ca7a72
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 19:10:15 +0100
Commit message:

 Tweaks to internal test methods to be robust to zero-dimensions.
 
Package: beachmat
Commit: 901d323be9b80e0aa9a9b902ad11fae50df12580
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 19:07:51 +0100
Commit message:

 Avoid crash due to chunk dims of zero in unknown reader.
 
Package: beachmat
Commit: 7e1ac5d1d61f2865368d3e089b5a0850a3324d65
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 18:56:52 +0100
Commit message:

 Bugfix for varslice col reader.
 
Package: beachmat
Commit: 5afe07fe19f8dfa64587f05f06aef147064dd193
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 18:48:39 +0100
Commit message:

 Added tests for correct choice of output class for each data type.
 
Package: beachmat
Commit: eb37c9c9308a992d36294e4c21ed9b9811318e4e
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 18:47:52 +0100
Commit message:

 Added functions to test correct choice of output class.
 
Package: beachmat
Commit: 8a55c05ec6afeac82d4a19c59d6ad15245ccbce8
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 18:45:19 +0100
Commit message:

 Standardized output_param constructor behaviour for choosing class.
 
Package: beachmat
Commit: 1d212e30af9b38e0bbd5e291245703800a6ba9bb
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 15:08:33 +0100
Commit message:

 Minor fix to set* error checks.
 
Package: beachmat
Commit: 5e0856c4624b404287b44460629cd8a426f01154
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 15:07:39 +0100
Commit message:

 Minor cleanup -  added missing returns.
 
Package: beachmat
Commit: 9b8bc90d1c74f347d4484e45038d8c5014e4e3a2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 15:07:13 +0100
Commit message:

 Minor fixes to output test scripts.
 
Package: beachmat
Commit: 659d9df2e8e97371b31f66c414a519a2a23e259c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 15:06:15 +0100
Commit message:

 Added tests for character output matrices.
 
Package: beachmat
Commit: aed7512137b64ee9448442637e73c54a2930ef4c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 14:52:23 +0100
Commit message:

 Added tests for logical output matrices.
 
Package: beachmat
Commit: 9c5db3a31265221a8cd203793f5a2d02b39c66fc
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 14:50:37 +0100
Commit message:

 Added tests for numeric output matrices.
 
Package: beachmat
Commit: b7e6287896a65da9dcc5cbabfb0288391ae57a61
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 14:50:23 +0100
Commit message:

 Allow limiting of tested conversion types.
 
Package: beachmat
Commit: e90b8fc8a297c6f51fa5dfb57e0a0b06edfd4277
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 14:42:46 +0100
Commit message:

 Cleared dimnames for reference matrix.
 
Package: beachmat
Commit: 05294d4535e705ab470548c6850fd508514c2cd0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 14:37:35 +0100
Commit message:

 Added integer output tests.
 
Package: beachmat
Commit: 88ea12f8ce4f4b6ce5a167e1042bd7b23ce3063f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 14:37:13 +0100
Commit message:

 Added special test for HDF5 write safety.
 
Package: beachmat
Commit: 38dcec90714e4758d940ebd37b123ccd394f1533
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 14:27:30 +0100
Commit message:

 Switched output_param construction method in write tests.
 
Package: beachmat
Commit: 70ba7013849eba563b73fe498b94e4be4b023bd2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 13:49:55 +0100
Commit message:

 Switched all write checkers to use expect_matrix() function.
Manually specify expected class in each function if out.class=NULL.
 
Package: beachmat
Commit: 6ce792cda26675cdb7a8cfb71e63f137be086662
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 13:35:11 +0100
Commit message:

 Added R/C++ functions to test write type conversions.
 
Package: beachmat
Commit: 6e73f8d5bcccd416b6e4592b563814c569c4866f
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 13:34:04 +0100
Commit message:

 Added centralized function to check matrix output.
 
Package: beachmat
Commit: ec3c7f55929d10abcc4ab7bfb6a1c872ffa2d9da
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 13:18:02 +0100
Commit message:

 Added tests to check errors in getters/setters for output classes.
 
Package: beachmat
Commit: 75765a2169cc07a3257b57f1fc5849ce55bca3e4
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 12:05:25 +0100
Commit message:

 Added R/C++ functions to test indexed writing.
 
Package: beachmat
Commit: 9fc5e510cda8d0097389c081032719692d1ba269
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 11:41:51 +0100
Commit message:

 Added C++/R functions to test writing variable slices.
 
Package: beachmat
Commit: f43026d78f041f775d92c0d3e02a651a77f9998b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 11:07:24 +0100
Commit message:

 Added C++/R functions to test writing slices of rows/columns.
 
Package: beachmat
Commit: 2425462fdb19593239de8ee4e246631ccdcde0a7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-09 10:36:19 +0100
Commit message:

 Added R/C++ functions to test writing entire rows/columns.
 
Package: beachmat
Commit: c45c520cdd4eac9da15123c9df2005e055c5d5e0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 20:12:07 +0100
Commit message:

 Bugfix for multirow/col read in character HDF5 matrix.
 
Package: beachmat
Commit: 83c3bd445bd956271a84527ab4249bc0f91a22b6
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 20:10:33 +0100
Commit message:

 Added tests for character matrix input.
 
Package: beachmat
Commit: 9b2ef0213469fa0d8ff3771e63b727416e822b36
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:59:53 +0100
Commit message:

 Added logical matrix input tests.
 
Package: beachmat
Commit: 3f2db07d567e3a2996cce79d106778870e380980
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:56:19 +0100
Commit message:

 Legalized lgTMatrix inputs via the unknown_reader.
 
Package: beachmat
Commit: 5dffe7579283f9e6fb85a1b9e0480649b945d3de
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:52:01 +0100
Commit message:

 Correct type tests for numeric matrix input ('double', not 'numeric').
 
Package: beachmat
Commit: 319264d869b29f82576f38f91ebc81510de7b2a3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:50:52 +0100
Commit message:

 Legalized dgTMatrix inputs via unknown matrices.
 
Package: beachmat
Commit: 8f150a5f65e318a35071095824354999941d6df7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:48:27 +0100
Commit message:

 Added numeric matrix input tests.
 
Package: beachmat
Commit: e648aa0002c3855375bbafd5596325b068f33eb0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:31:22 +0100
Commit message:

 Check for correct matrix S4 classes in tests.
Simplified Rle creation function.
 
Package: beachmat
Commit: 8eb21480d588d0268da33aab7978722c8b0ee383
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:16:25 +0100
Commit message:

 Randomize dimensions in delayed matrix tests for some variety.
 
Package: beachmat
Commit: 48b504795fb5f6d4da514e56855741340d257dd2
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:11:50 +0100
Commit message:

 Test for correct unknown matrix reads with smaller blocks.
 
Package: beachmat
Commit: a11a9420cbe4b63e4fb7042fbb1b2d84de7b4b47
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 19:05:29 +0100
Commit message:

 Ensure unknown realization goes to the nearest block boundary.
 
Package: beachmat
Commit: 6d2254cfb5b77288ea0427f0d68b528b1d61dc7b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 18:40:06 +0100
Commit message:

 Added integer matrix input tests.
 
Package: beachmat
Commit: cd31ad40e496e8b9d501b04379014febd88133d9
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 18:39:37 +0100
Commit message:

 Export error-checking test function.
 
Package: beachmat
Commit: 1bb9e57cef214a328883aa150918fd3675a30f7a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 18:39:23 +0100
Commit message:

 Enforce vector in varslice test functions.
 
Package: beachmat
Commit: fe4cfd5d5ad48c4b65e2d1fb8905e28d9b91a67a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 18:38:22 +0100
Commit message:

 More refined control of error messages in delayed_reader.
 
Package: beachmat
Commit: 2f9a317883111c78e657f6e6282360f947ed1e7a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 17:50:55 +0100
Commit message:

 Reuse dim_checker checks in delayed_reader via static public methods.
 
Package: beachmat
Commit: f79bc1c2612a0742e7d26edcd21aaed7f9ed97dc
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 17:28:32 +0100
Commit message:

 Use 1-based indexing for Delayed multirow/col reader.
Standardized error messages.
 
Package: beachmat
Commit: 309984735b4f97d94cce40c8c5b4948ee0b7303a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 17:25:35 +0100
Commit message:

 Ensure file is open for HDF5 multirow/col reader.
Bugfix for dimensions of output DataSpace.
 
Package: beachmat
Commit: b3b70971c75baba1c3e98e4cf1491623f909114b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 17:14:20 +0100
Commit message:

 Bugfixes for block processing of unknown matrices:
- reset to 1-based indexing upon re-entry to R.
- avoid re-realization if requested block is a subset of storage.
- define separate holders for slicing and primary indices.
 
Package: beachmat
Commit: 494f951c1541d57460b6e9875a3b056debf55247
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 16:27:04 +0100
Commit message:

 Added test functions to check for correct error triggers.
 
Package: beachmat
Commit: b721b2904f4b53e8f02ff0b6657db221292baec7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 16:26:36 +0100
Commit message:

 Added test functions to check input type, type conversions.
 
Package: beachmat
Commit: e821e9424f380424c16efe3cc6af94e900417aef
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 15:42:05 +0100
Commit message:

 Fixed header guards.
 
Package: beachmat
Commit: a6be233a42e84a82e59eeb23d166c5b18c1193f4
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 15:39:55 +0100
Commit message:

 Added R/C++ code to check multi-row/col reads.
 
Package: beachmat
Commit: 66fbb83fce8f45f4dfc71eff0b9468b4d1e9fc8b
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 15:39:20 +0100
Commit message:

 Split off R code to define slice bounds for re-use.
 
Package: beachmat
Commit: cfee16508d4da5d901ee307375ea556f0a38eb91
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 15:18:23 +0100
Commit message:

 Added multi row/col getters to visible interface.
 
Package: beachmat
Commit: c02f2ff2867c7aebe6b15b9d6efe47e6d65a28a7
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 14:09:05 +0100
Commit message:

 Added C++/R code to check get_const_col_indexed getter.
 
Package: beachmat
Commit: d1f72831a6d6e23f7cfec0a1fe2085eed8d46484
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 13:56:34 +0100
Commit message:

 Added C++/R test code to check get_const_col getter.
 
Package: beachmat
Commit: 4efe002d051bf442d7704e3a6f5de3d871f51b79
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 13:50:51 +0100
Commit message:

 Broke up testing R functions for greater re-use.
 
Package: beachmat
Commit: 46aee47edf6b7591e3faa1d33c0879441c3e9ef3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 13:24:37 +0100
Commit message:

 Added C++/R test code to check variable slicing.
 
Package: beachmat
Commit: a6cf9cc02f491f2a585d5068fa691ac59d6a2379
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 13:06:45 +0100
Commit message:

 Added extern tags for read_all C++ functions.
 
Package: beachmat
Commit: 8648fb1ea7c675b6ba3e39d5a803dfdb3acb3996
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 13:06:16 +0100
Commit message:

 Renamed and exported function to check all-of-matrix read.
 
Package: beachmat
Commit: 0c6575bee8e6d97ff95042663c0322658d327cbb
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 13:04:55 +0100
Commit message:

 Added R/C++ code for checking access with constant slices.
 
Package: beachmat
Commit: 2d838a2c1733f5d3bfa19b2c5e40f9dcc47a8aba
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 13:04:29 +0100
Commit message:

 Remove registration for easier calling of test code.
 
Package: beachmat
Commit: 0a74465f9008763a66f5fded577f89d5e9c0b9e3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-07 11:00:30 +0100
Commit message:

 Spun out standard access tests into separate C++/R files.
 
Package: beachmat
Commit: 0dd05721ad13145d97980dab90743944b41db507
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 18:08:45 +0100
Commit message:

 Fixes to unknown matrix realization R functions.
 
Package: beachmat
Commit: 76e2b499a0d80bd1432e7a7329f187f0fb827432
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 17:46:26 +0100
Commit message:

 Fixes to block reloading in unknown matrices when first/last change.
 
Package: beachmat
Commit: 6f2af409716a909275db1030a003ac5b3a610af4
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 17:26:28 +0100
Commit message:

 Moved copyable_holder definition to utils.h for general use.
Added support for multi-row/column reading for delayed matrices.
Updated call to R-level set-up function for delayed matrices.
 
Package: beachmat
Commit: a69217c409ebeaa3d341f77bf0bf37c894a6e5e0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 17:25:43 +0100
Commit message:

 Separated unknown and delayed matrix R-level processing code.
 
Package: beachmat
Commit: f92cf7e76e8be3f1facae631885f9d966f22f977
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 15:30:34 +0100
Commit message:

 Support multi-row/column read for HDF5 readers.
 
Package: beachmat
Commit: 6c63fb708a5c792a7e066d1e81acbb40562766ca
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 15:10:01 +0100
Commit message:

 Support multi-row/column read for unknown matrices.
 
Package: beachmat
Commit: 95a34e927cc73e55abbb41e9b6d6ff2709c29570
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 14:39:37 +0100
Commit message:

 Added multi-row/column getter for dense matrices.
 
Package: beachmat
Commit: 6f8f652eb59b4156023c29416c631bfa6a78d830
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 14:37:57 +0100
Commit message:

 Added multi-row/column reader for C-sparse matrices.
 
Package: beachmat
Commit: c444c9367b7d805f48aafa106e668dcf1f901acf
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 14:34:55 +0100
Commit message:

 Added multi-row getter for simple matrices.
 
Package: beachmat
Commit: 599c3754be3a61310ae715bb4ad56f65bea984d8
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 14:02:33 +0100
Commit message:

 Added low-level checks for increasing row/column indices.
Reduced redundancy in other dimensionality checks.
 
Package: beachmat
Commit: c081ea424594228bbcd7b365b6b2737da343c7c3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 13:29:20 +0100
Commit message:

 Removed RLE and PSYMM from available matrix types.
 
Package: beachmat
Commit: fb97d907f4d2b13a37e79feb1912069a8167452c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 13:29:02 +0100
Commit message:

 Bugfix for unknown get_row with column subset.
 
Package: beachmat
Commit: 36b4f36fdfe740038e3346e8c000a3e5bd945de5
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 13:27:50 +0100
Commit message:

 Removed tests specific to Psym, RLE classes.
Added tests for output mode for unknown input.
 
Package: beachmat
Commit: 5bd4cd05d56f39662c599fba7c5551b1e5656ec3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 12:49:15 +0100
Commit message:

 Bugfixes for new class/file names in delayed reader code.
 
Package: beachmat
Commit: 155287cc1868e4e67e1e475b4250a126e18b1705
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 12:48:58 +0100
Commit message:

 Updated Makevars exports.
 
Package: beachmat
Commit: b4e0c02da282339594cac5eab5f57d6e6b0cde04
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 12:42:12 +0100
Commit message:

 Bugfixes related to realized character matrix/output.
 
Package: beachmat
Commit: 251e908b2632f420f5dd510d57a5f072ade3df9c
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 12:41:46 +0100
Commit message:

 Bugfixes related to code for realized LIN matrices and output.
 
Package: beachmat
Commit: 223c85eba4310d6b6bade3c37325473e763808f5
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 12:41:13 +0100
Commit message:

 Bugfixes related to LIN matrices and outputs for renamed classes.
 
Package: beachmat
Commit: 5b953e386747156f8ea12102a0d935e6e25e30b0
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 12:00:24 +0100
Commit message:

 Changed name of convenience headers for all readers/writers.
 
Package: beachmat
Commit: 668a911948afcfc60faf0655962e7bcd68989cfa
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:59:09 +0100
Commit message:

 Fixed header guards.
 
Package: beachmat
Commit: 1b4473b7a0487f93eecac2f0fd1dcac973fc9d62
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:55:39 +0100
Commit message:

 Updated realized LIN matrix/output code for new class names.
 
Package: beachmat
Commit: 791f2d09473709b9e86386e6d8350372b72fd4b3
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:52:28 +0100
Commit message:

 Updated character matrix/output code for renamed classes.
 
Package: beachmat
Commit: 5c37aa0ed9791a3498e4b7b542fb33311dd9b657
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:35:57 +0100
Commit message:

 Updated LIN output code for new class names.
 
Package: beachmat
Commit: ac5e09bec9d9f162a96202cfb35ef12dce428a39
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:32:04 +0100
Commit message:

 Updated LIN code for new class names.
 
Package: beachmat
Commit: 9b29360791a81a16c731b32edeb8a6fe856390ae
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:20:29 +0100
Commit message:

 Removed niche classes, which now fall back to 'unknown'.
 
Package: beachmat
Commit: 448c187b2822df21897bb5a11bdb6955d2f24465
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:19:48 +0100
Commit message:

 Renamed core output classes to 'writer', to distinguish from interface.
 
Package: beachmat
Commit: c4afa3c86f6dc0a8df9d3fa5aa62e9a7f30dc29a
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:16:32 +0100
Commit message:

 Consolidated all delayed code into a single file.
 
Package: beachmat
Commit: accbb86fddae013d424049ac0b2d0c3d3d872c07
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-08-06 11:13:39 +0100
Commit message:

 Renamed any_matrix to dim_checker, core matrices to 'reader'.
This avoids confusion between internal and interface classes.
 
Package: globaltest
Commit: fbab07d718e94d8ee888814165c846b56d43b4cf
Author: jellegoeman <j.j.goeman@lumc.nl>
Date: 2018-08-10 12:12:16 +0200
Commit message:

 version 5.35.1

- Patched due to change in length.Surv
- Added ylim argument to covariates()
 
Package: ensembldb
Commit: cb4dcd16a44c6968e319e30dba57fe3a32dea48e
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-08-10 09:44:38 +0200
Commit message:

 Remove reference to the BiocInstaller package
 
Package: ChIPseeker
Commit: 9e5a4bb1f39ac5fd4536fd5c9e05a789b28fba50
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2018-08-10 14:45:03 +0800
Commit message:

 flip_minor_strand parameter in getTagMatrix
 
Package: RITAN
Commit: 5c74731af36d7b392987bfb4c1aff39c8b65e292
Author: Michael Zimmermann 2017-10-18 <mtzimmermann@mcw.edu>
Date: 2018-08-10 00:09:54 -0500
Commit message:

 bugfix: syntax fixed
 

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