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GIT Logs

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

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Package: CNVfilteR
Commit: f5fd8644694b64a573e7757f716ae5298bf5784b
Author: José Marcos <jpuntomarcos@gmail.com>
Date: 2023-09-27 09:55:06 +0300
Commit message:

 Version bump
Package: CNVfilteR
Commit: 8d46eff1249a9b7e26a9b607ceb4d99bd00fe8f0
Author: José Marcos <jpuntomarcos@gmail.com>
Date: 2023-09-27 09:54:58 +0300
Commit message:

 Bug fixed: CopyNumberPlots requires additional parameter
Package: scMultiome
Commit: 7ea03657b3d18d614e55073540d2a17d0cf2b005
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2023-09-26 19:21:23 -0700
Commit message:

 version bump to 1.1.1
Package: scMultiome
Commit: 8aba5d6decadc91b497a257261712d7daead1dd3
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2023-09-26 19:20:43 -0700
Commit message:

 specify experimenthub version and remove R version
Package: scMultiome
Commit: 6c1be48dc603e723acb5bab9497bacdb668662fa
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2023-09-26 19:19:58 -0700
Commit message:

 update vignette with bioc url
Package: scMultiome
Commit: e46ac09b4f774b9fd91ce3f9c12bc0d47280c4bf
Author: Xiaosai Yao <yao.xiaosai@gene.com>
Date: 2023-09-26 18:52:11 -0700
Commit message:

 remove archr2MAE and update link
Package: hoodscanR
Commit: e72b41ad68179b266ed25ae847f3fac7d8c6e9d7
Author: ningbioinfo <liu.n@wehi.edu.au>
Date: 2023-09-27 10:49:43 +1000
Commit message:

 version bump
Package: hoodscanR
Commit: fd075e0db75b5bb732b0a7bb42f86aeb9f7e7082
Author: ningbioinfo <liu.n@wehi.edu.au>
Date: 2023-09-27 10:48:32 +1000
Commit message:

 remove commented codes
Package: gemma.R
Commit: 88305b743cf313af220c87a1c4346e1b3574a739
Author: OganM <ogan.mancarci@gmail.com>
Date: 2023-09-26 01:12:56 -0700
Commit message:

 fix vignette for windows
Package: gDNAx
Commit: 4faee60dff6aabfb2ec46541efc75697f8e63a17
Author: beacalvo <beacalvo96@gmail.com>
Date: 2023-09-26 23:54:11 +0200
Commit message:

 Fixed unit test error due to update in gene annotations
Package: magpie
Commit: 86003765517156947880041c56f5268cd23307c5
Author: dxd429 <dxd429@case.edu>
Date: 2023-09-26 14:49:16 -0400
Commit message:

 1.1.3
Package: magpie
Commit: 250f873a4b9fcb091fac34fe2850fb10282b4f7a
Author: dxd429 <dxd429@case.edu>
Date: 2023-09-26 14:48:05 -0400
Commit message:

 Utest fix
Package: SurfR
Commit: a3b627bb7105458d8011b798134d97b3b3fd419d
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-09-26 18:33:18 +0200
Commit message:

 bumped the package version v0.99.10
Package: Rvisdiff
Commit: fff5ea3cda62ec8f7fdf92c4a34913b95bd3e3b5
Author: BioinfoUSAL <bioinfo@usal.es>
Date: 2023-09-26 17:41:34 +0200
Commit message:

 0.99.3
Package: AnnotationForge
Commit: 6e8f15bb2da2c05c9b6a15ec91c7e7824a3a5725
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2023-09-26 11:38:03 -0400
Commit message:

 Update viableIDs.rda for release 3.18
Package: LipidSigR
Commit: 080925904d4c272aeae75cf7e662866654b11758
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 23:23:42 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: c6b27a5df1513c5b882b0a890a9798f08632b1ec
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 23:19:07 +0800
Commit message:

 Add files via upload
Package: rpx
Commit: a84c0de091c911b86baf440b4e038f99898f318e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2023-09-26 16:37:23 +0200
Commit message:

 Merge branch 'master' into devel
Package: rpx
Commit: 4a2372e0541e0eff26550daae04f0b6fa8e89d9b
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2023-09-26 16:36:16 +0200
Commit message:

 cite issue in news entry
Package: rpx
Commit: 6485755788c71be046b0b47fc3e3583cca6c5444
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2023-09-26 16:35:35 +0200
Commit message:

 fix stupid generated - close #25
Package: rpx
Commit: a1ba3b9edc5df0bb5efe8c6bff4091f27a25845c
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2023-03-13 17:12:00 +0100
Commit message:

 new gh devel version
Package: LipidSigR
Commit: 0cb52cda299252b229850b7805f9ac4ff5042673
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 22:26:41 +0800
Commit message:

 Add files via upload
Package: wateRmelon
Commit: 0e65f734001214da3cab29f06bc5a3766ddf2f92
Author: lschal <lschal@essex.ac.uk>
Date: 2023-09-26 15:07:38 +0100
Commit message:

 versbump
Package: wateRmelon
Commit: f257f4688db1d46466dece36187da98d3456a293
Author: lschal <lschal@essex.ac.uk>
Date: 2023-09-26 15:05:40 +0100
Commit message:

 .createAnnotation.R updated for epicV2.  fixes adjustedDasen
Package: wateRmelon
Commit: 560a185ceaf7346eb6e714b2ffa0f810bbe2506a
Author: lschal <lschal@essex.ac.uk>
Date: 2023-09-26 09:38:34 +0100
Commit message:

 epicv2clean rox manual
Package: LipidSigR
Commit: 84bf401e1bd166df166c0dd83c8c79397bf57a9a
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:48:36 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: 271c5d971c99fa8b7423f99c973f102df39d7324
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:48:13 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: 8cc4cfc51fcbce42547338b460de77f44a3c3bd2
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:47:54 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: ea8514298ad50f22256cb5152c46cadbb3b9ced1
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:47:27 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: ec45a0046915667409b9d80783adb6f1b82a7501
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:46:55 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: 5b8e6f3fc0caa724c9209d10dcc1be71fa183e3f
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:46:29 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: 540a81bdc714b8bbe8cbad1a827735aaa52b977f
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:46:02 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: 1def0af1e8e0555eeedee431721765fd71d8c207
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:45:29 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: 261430fdb06d5694ebb95ed54128928e06f164aa
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:44:21 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: e00b77c0a7a697778ede633a16b6741c9c106ff8
Author: hcliu <chenglabomics@gmail.com>
Date: 2023-09-26 21:20:31 +0800
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: LipidSigR
Commit: bbf0e76a966474cb62a12959e1350f5c00123eb4
Author: BioinfOMICS <87956787+BioinfOMICS@users.noreply.github.com>
Date: 2023-08-07 10:50:38 +0800
Commit message:

 Update DESCRIPTION
Package: LipidSigR
Commit: edc78b8c9a3d66f4047c2e2828bffc4e31be9c26
Author: BioinfOMICS <87956787+BioinfOMICS@users.noreply.github.com>
Date: 2023-07-27 14:49:00 +0800
Commit message:

 Update Hclustering.R
Package: LipidSigR
Commit: ddd94a6fc919410f7be0f71258caa2b9379e0d11
Author: BioinfOMICS <87956787+BioinfOMICS@users.noreply.github.com>
Date: 2023-07-27 14:48:14 +0800
Commit message:

 Update corr_heatmap.R
Package: LipidSigR
Commit: 5eff17dabcb45303f4ed3cd0cbf931e91e16eee9
Author: BioinfOMICS <87956787+BioinfOMICS@users.noreply.github.com>
Date: 2023-07-17 10:16:07 +0800
Commit message:

 Update README.md
Package: LipidSigR
Commit: 021ea6199cc4013431f0672b9d40f70dd9dc17b2
Author: BioinfOMICS <87956787+BioinfOMICS@users.noreply.github.com>
Date: 2023-07-17 10:11:00 +0800
Commit message:

 Update DESCRIPTION
Package: LipidSigR
Commit: 94315da412846289d5cbf27c8c2c63a01d950066
Author: BioinfOMICS <87956787+BioinfOMICS@users.noreply.github.com>
Date: 2023-07-17 10:08:21 +0800
Commit message:

 Update README.md
Package: LipidSigR
Commit: 86d45b7f498dbcb9bcc0ea9ce421dbdb8843498f
Author: TMSWCChenglab <87956787+TMSWCChenglab@users.noreply.github.com>
Date: 2023-04-09 12:50:24 +0800
Commit message:

 Update DESCRIPTION
Package: LipidSigR
Commit: 6b424eaa1abb68c6a4ffd07168ed904fbc458bf7
Author: TMSWCChenglab <87956787+TMSWCChenglab@users.noreply.github.com>
Date: 2023-04-09 12:37:58 +0800
Commit message:

 Add files via upload
Package: LipidSigR
Commit: fe6ccf57eaa55ea0c6441da3d29eff122f799ea6
Author: TMSWCChenglab <87956787+TMSWCChenglab@users.noreply.github.com>
Date: 2023-04-09 12:37:07 +0800
Commit message:

 Delete man directory
Package: SurfR
Commit: 61062ea3b60c305984a0126d8410acab7c8ee65f
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-09-26 13:43:14 +0200
Commit message:

 bumped the package version v0.99.9
Package: hoodscanR
Commit: 4665e5b75872a2e98b1369fe5e358212ea24d321
Author: ningbioinfo <liu.n@wehi.edu.au>
Date: 2023-09-26 21:28:29 +1000
Commit message:

 version bump
Package: hoodscanR
Commit: c3ac8354905311a068aabc0783ea9875082f5d5e
Author: ningbioinfo <liu.n@wehi.edu.au>
Date: 2023-09-26 21:28:02 +1000
Commit message:

 small bug fix
Package: hoodscanR
Commit: 6237c20d76bef1a10f03a878940c13756b45a303
Author: ningbioinfo <liu.n@wehi.edu.au>
Date: 2023-09-26 21:09:55 +1000
Commit message:

 updates: - documentation update about output values
- output variable/names parameter added to many functions
- validity checks for spatialCoords are added to related functions
- for loops are gone.
Package: shiny.gosling
Commit: 2820f94bf981148860692527a7a9d36c0382c760
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-26 16:54:35 +0530
Commit message:

 fix: remove eval=FALSE & bump version
Package: SurfR
Commit: ef891acb2ed5fa65ddc32a4a89e789d95989a3a6
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-09-26 13:21:15 +0200
Commit message:

 bumped the package version v0.99.8
Package: shiny.gosling
Commit: b099e50e7272f52bf6d8e4827b174f598896526e
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-26 16:34:37 +0530
Commit message:

 bump version to trigger build
Package: scviR
Commit: 2e6e9c74076037416464b71870012b3fee80d92f
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2023-09-26 06:47:40 -0400
Commit message:

 update the version of scvi-tools in use, along with  pandas, matplotlib,
scanpy and numpy (but keep pandas < 2.0.0)
Package: simona
Commit: afa9de75767a36500bb4b8c0ff33f900ecb1bb87
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-09-26 11:52:13 +0200
Commit message:

 remove .o files
Package: simona
Commit: b60cca2cd327911478f989155526356c59b3193b
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-09-26 11:50:49 +0200
Commit message:

 revised according to the review comments
Package: easylift
Commit: f79a393faa40862c8f75d0d741568ce2f17c6bad
Author: nahid18 <nahidpatwary50@gmail.com>
Date: 2023-09-26 15:37:18 +0600
Commit message:

 feat: additional tests
Package: SurfR
Commit: 3bd8748b9444dbb46f63de90ac3edd1073e11148
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-09-26 09:03:56 +0200
Commit message:

 bumped the package version v0.99.7
Package: ClassifyR
Commit: 56eb65f01d90acf12f0fd3c46dc69f774e563b55
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2023-09-26 17:00:03 +1000
Commit message:

 - In extremeGradientBoostingPredictInterface, expand the test data set to one-hot encoding format before subsetting it by selected features from training.
Package: edgeR
Commit: eca0fbb45ec2e5800b46d1546035867802f8aedf
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2023-09-26 15:02:40 +1000
Commit message:

 edgeR 3.99
- Lizhong Chen's updates to glmQLFit() including changes to C code.
Package: easylift
Commit: e4091e245542d8d50523a3f3d07deeba3123c54f
Author: nahid18 <nahidpatwary50@gmail.com>
Date: 2023-09-26 09:14:17 +0600
Commit message:

 feat: further improvements
Package: easylift
Commit: 5aaae8d8ca28a36fddd394f0177b33488a9de2bc
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2023-09-25 20:32:50 -0400
Commit message:

 add bfc argument, use temp location for testing
Package: TSAR
Commit: 724531673f7e83eabec84e44d9d5c9c4011acabd
Author: CGAO123 <candygao2015@outlook.com>
Date: 2023-09-25 19:25:00 -0400
Commit message:

 update gitignore file
Package: TSAR
Commit: 9b61aec629aa2ec023b33a48d69f286e656ef943
Author: CGAO123 <candygao2015@outlook.com>
Date: 2023-09-25 18:53:16 -0400
Commit message:

 com
Package: TSAR
Commit: 476ebd1a25e0b1d854df2f82aabf8a0e8dbf0d7b
Author: CGAO123 <candygao2015@outlook.com>
Date: 2023-09-25 21:11:50 -0400
Commit message:

 increase version number
Package: TSAR
Commit: 42fddccd55472eb4010a37733321e3adcdff953f
Author: CGAO123 <candygao2015@outlook.com>
Date: 2023-09-25 18:15:54 -0400
Commit message:

 re-conf
Package: TSAR
Commit: 2edea04a97dd83e5421be3454fd0429a5b54203a
Author: CGAO123 <candygao2015@outlook.com>
Date: 2023-09-25 18:13:49 -0400
Commit message:

 resolve conflict
Package: TSAR
Commit: ffa6c3073a89d7b28e310f6fbe2480b92e9a5fa3
Author: CGAO123 <candygao2015@outlook.com>
Date: 2023-09-25 18:32:23 -0400
Commit message:

 pull upstream to sync
Package: DeProViR
Commit: 5fbd3382148dad89b534272904f94aa1acda348d
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 16:20:40 -0600
Commit message:

 version bumo
Package: DeProViR
Commit: 99134be98ab270d02a6e62d35102056901b16e0e
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 16:07:06 -0600
Commit message:

 version bump
Package: DeProViR
Commit: d7c59285f11825dde5ed83495567111c704338bd
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 16:05:48 -0600
Commit message:

 add more example
Package: DeProViR
Commit: f3b114d233e68be63d4256a44e105da3e7923470
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 15:50:18 -0600
Commit message:

 version bump
Package: easylift
Commit: 7b558a0b0b9321df0a71e3b89a7753f9c36612d3
Author: nahid18 <nahidpatwary50@gmail.com>
Date: 2023-09-26 03:38:52 +0600
Commit message:

 feat: readme update
Package: DeProViR
Commit: b8917db524832d950e2dfe07fd88d51d8677c474
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 15:37:37 -0600
Commit message:

 edited vignette
Package: DeProViR
Commit: f6c6cbd3fe603c4d6f9bd10618017d9c73d97784
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 15:37:03 -0600
Commit message:

 edit some examples
Package: easylift
Commit: aa2acc51d6525ff7048dc98b0aee26f4ab3dc894
Author: nahid18 <nahidpatwary50@gmail.com>
Date: 2023-09-26 03:22:37 +0600
Commit message:

 feat: fixes
Package: DeProViR
Commit: 0dad6483bcd2adb4a2a0e6e7ac306c01c0f0e9ef
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 15:09:12 -0600
Commit message:

 version bump
Package: DeProViR
Commit: 9915c00c8a93476a532884d4dad45d97a4d7a54f
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 14:39:02 -0600
Commit message:

 changes path
Package: DeProViR
Commit: 9bffca021a64db9f2aa8845ae91c1748a5177d24
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 14:36:56 -0600
Commit message:

 man files
Package: DeProViR
Commit: 1d3092aeebafe39ea66f584c8b6d2e85ba69c93e
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 14:34:47 -0600
Commit message:

 edit like
Package: DeProViR
Commit: 12a6787f23d63fef0929036fa698b103d203f1a7
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 14:29:13 -0600
Commit message:

 edited path
Package: curatedPCaData
Commit: ae20f852e4a8612eb76830039924181ce10fd2c1
Author: Syksy <teemu.daniel.laajala@gmail.com>
Date: 2023-09-25 22:21:03 +0300
Commit message:

 Versio bump to trigger build
Package: DeProViR
Commit: 993d9fd9a02bad23c7d5ebec35474874174454d2
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 13:55:37 -0600
Commit message:

 edit test input
Package: DeProViR
Commit: ff77b3f13dc008436934db9b68946199980a24e3
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2023-09-25 13:54:47 -0600
Commit message:

 edit the test set
Package: ENmix
Commit: a03864be0ba4aecfd6f799f87895cd5fc29ca3bd
Author: Zongli Xu <xuz@lxd-02010942.niehs.nih.gov>
Date: 2023-09-25 15:20:22 -0400
Commit message:

 bugfix

Signed-off-by: Zongli Xu <xuz@lxd-02010942.niehs.nih.gov>
Package: easylift
Commit: 8d1a9d449db2f59507085dc27eabbb6056f57951
Author: nahid18 <nahidpatwary50@gmail.com>
Date: 2023-09-26 01:00:01 +0600
Commit message:

 feat: minor update
Package: GSVA
Commit: 25165ca220e98a871b110274e9308f6c3b513350
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2023-09-25 20:45:49 +0200
Commit message:

 Merge pull request #111 from rcastelo/new_api

New API for GSVA based on method-specific parameter objects
Package: GSVA
Commit: 424dc393a19fcb3c7c92aaad16f4a35e18abc28b
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2023-09-25 19:55:21 +0200
Commit message:

 Improving consistency in the documentation of help pages and vignette in the new API
Package: GSVA
Commit: c7f48ade5da63010793a5ffa430027dd7a7e104d
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-25 17:16:16 +0200
Commit message:

 Merge pull request #110 from axelklenk/new_api

migrate vignette to new API; work around eSet/annotation() problem
Package: GSVA
Commit: 30a33bdd9ae4ffc1796495ea4f63850664ddfee3
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-25 16:43:55 +0200
Commit message:

 migrate vignette to new API; work around eSet/annotation() problem
Package: GSVA
Commit: 8994ac4bcb94394a573962fffc156a100a27aef5
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-25 13:29:06 +0200
Commit message:

 Merge pull request #109 from axelklenk/new_api

add slots and constructor arguments for 'annotation', 'minSize', and …
Package: GSVA
Commit: 82c26966d4da861f6f6d02f399a13bb10a8bfe3f
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-25 13:21:06 +0200
Commit message:

 add slots and constructor arguments for 'annotation', 'minSize', and 'maxSize' to parameter objects; remove the latter two from gsva()
Package: GSVA
Commit: ba3a6f8cd5b8490e061b1e785a6a74c3baf01cd8
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-24 22:16:22 +0200
Commit message:

 Merge pull request #108 from axelklenk/new_api

Add argument 'assay' to parameter objects to make example(gsva) work.
Package: GSVA
Commit: a18b04b8b8dca8140288b8571b9ae6d6d6cb9819
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-24 22:01:04 +0200
Commit message:

 Add argument 'assay' to parameter objects to make example(gsva) work.
Package: GSVA
Commit: b0d132aa03941078f04e8605badc498ced959acc
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2023-09-21 17:47:45 +0200
Commit message:

 Fixed documentation and other stuff
Package: GSVA
Commit: 36f7ebe09ac3b3dd2da6d5e255b9e61137d179d0
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-21 14:01:29 +0200
Commit message:

 Merge pull request #107 from axelklenk/new_api

add code and docs for deprecation of old interface; add docs for new …
Package: GSVA
Commit: aa61b1ec769618d7830ee26a1665d93a3f8baa1b
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-21 13:57:22 +0200
Commit message:

 add code and docs for deprecation of old interface; add docs for new interface; eliminate argument parallel.sz; fix .gitignore
Package: GSVA
Commit: 7ca884b3672fe675c47f7b541b9a07c741580a54
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-15 23:49:26 +0200
Commit message:

 Merge pull request #106 from axelklenk/new_api

New API -- now including man/*.Rd files
Package: GSVA
Commit: 7e948443f62a3c911fb29079c7f67d0d52316582
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-15 23:28:03 +0200
Commit message:

 no idea what git is doing to me here...
Package: GSVA
Commit: 0bb99f0d4cff9e537f769d1e62f1fc4fe85d5160
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-15 23:13:55 +0200
Commit message:

 fix .gitignore to have man/*.Rd files properly tracked.
Package: GSVA
Commit: d123bc4e4d287aa700bc72af91d24813b998a78e
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-15 23:13:55 +0200
Commit message:

 fix .gitignore to have man/*.Rd files properly tracked.
Package: GSVA
Commit: 31d7e7f8f8a8ab4ba78caaf31f716b4bed78b2e4
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-15 19:57:40 +0200
Commit message:

 Merge pull request #105 from axelklenk/new_api

New API implementation as discussed
Package: GSVA
Commit: efd45fc259000bc9f1ef3dfdda1f3c54c11337d5
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-15 19:49:29 +0200
Commit message:

 Merge branch 'dev_new_api' into new_api
Package: GSVA
Commit: 6f943119e1b31f5266a7f723914e17383e711a08
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-15 19:41:39 +0200
Commit message:

 New API first version, more documentation and unit tests to be added; existing code using the 'old' API should continue work.
Package: GSVA
Commit: 87d62586a13f2022c0b4d0dffb713ab1b167761a
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-13 16:40:50 +0200
Commit message:

 Merge pull request #104 from axelklenk/new_api

Restore original generic and signature for gsva(); add show methods for parameter objects
Package: GSVA
Commit: 3db152209d30827d3e2abac82fba52e83394afe5
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-13 15:40:19 +0200
Commit message:

 Merge branch 'dev_new_api' into new_api
Package: GSVA
Commit: fb7295903bb7195d9962db63db9f2f7adababbdf
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-13 15:38:31 +0200
Commit message:

 add show methods for parameter classes.
Package: GSVA
Commit: e47881442a2c92a31a7790d11355d080a29d8cb2
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-13 13:20:46 +0200
Commit message:

 restore previous gsva generic and method signatures
Package: GSVA
Commit: 0bdf1c021e51c26c75147e90d384a47ad277b68a
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-12 17:09:01 +0200
Commit message:

 Merge pull request #103 from axelklenk/new_api

New api
Package: GSVA
Commit: 25e70eac30767704f6951b5a17b25e28d619a387
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-12 16:52:15 +0200
Commit message:

 Merge branch 'dev_new_api' into new_api
Package: GSVA
Commit: 0a2f8df1d2fdc63b74fb742d1e4bd8df69baec27
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-12 14:53:02 +0200
Commit message:

 Initial implementation of New API for all methods and gene set containers and almost all data containers. (TODO: continue refactoring, document and test.)
Package: GSVA
Commit: da4e6b125affa48b42d94a8e802794d246031902
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-06 11:29:27 +0200
Commit message:

 add class unions for new_api next step
Package: GSVA
Commit: f92d4c6bccc16c5b485d0f1117862306b688b25c
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-05 10:02:42 +0200
Commit message:

 Merge branch 'dev_new_api' into new_api
Package: GSVA
Commit: 8b3c590e1d1d29aa9fa585236d5e7851f639c577
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-04 14:19:51 +0200
Commit message:

 add regression test based on the vignette and an output file for comparison generated by the released version
Package: GSVA
Commit: dfeab61cd588f77cf52e9e49dc69371151ec6a74
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-04 09:16:03 +0200
Commit message:

 add an experimental regression test based on the vignette -- work in progress!
Package: GSVA
Commit: cd9abfba0a0370acfc849c421a823989163e5b26
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-01 17:47:32 +0200
Commit message:

 add rnorm() and rpois() to NAMESPACE imports and save 'stats::' when using them to generate test data
Package: GSVA
Commit: cce4456d10a978239b1a9400106f464e510457cc
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-09-01 17:08:17 +0200
Commit message:

 Merge pull request #102 from axelklenk/new_api

New api update
Package: GSVA
Commit: 27f4b1750ea5c3ca3ef26ff4e2ccf7b5c3653276
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-09-01 15:58:26 +0200
Commit message:

 add unit tests for dispatch on unnamed arguments.
Package: GSVA
Commit: 743a96f1457faedb82ca0ca9d6f1b53348e5f7a3
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-31 18:08:34 +0200
Commit message:

 two minor modifications to make the remaining WARNING and NOTE disappear.
Package: GSVA
Commit: 21ac45d37fde701fa095b34d46ecd70af574ce6b
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-30 18:01:28 +0200
Commit message:

 document new gsva methods to get rid of check warnings.
Package: GSVA
Commit: 480d69f9ab83416e5bce991f6fcd5bccff091732
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-28 17:21:12 +0200
Commit message:

 add unit tests for dispatch by param objects; rename param objects to comply to upper camel case convention.
Package: GSVA
Commit: 0c5e0b4d7bbba354e9d2f92e51d00c2d9a3ab3a3
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-25 18:17:19 +0200
Commit message:

 add matrix/list methods for zscore, ssgsea, gsva; modify to use param for internal dispatch and parameters. Testgit add R/gsvaNewAPI.R
Package: GSVA
Commit: 21fd00e614095b959df6e156bda13b26a9bf4309
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-25 16:39:15 +0200
Commit message:

 add 'param' argument (as missing) to all 'gsva' S4 methods to silence warnings during check.  add roxygen2 documentation for newAPI methods.
Package: GSVA
Commit: 969f0f8d4e57615d4ced2a26ba05aab26351409f
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-23 17:53:37 +0200
Commit message:

 add S4 method for dispatching on PLAGE parameter object
Package: GSVA
Commit: e444aab35cc9d3667e6156b672791db0213c3954
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-18 19:00:54 +0200
Commit message:

 add automated generation of test input data
Package: GSVA
Commit: a08f0492c35ffb597e0b4584d601611e9bd0c91a
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-14 16:49:59 +0200
Commit message:

 add simple unit tests for method-specific parameter objects and their constructors
Package: GSVA
Commit: c460cb17e89ddb7afc43c327b7b961daefa78afa
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-01 19:26:58 +0200
Commit message:

 fix --as-cran NOTE on using title case in the package title :-)
Package: GSVA
Commit: d5b2d25ee4ae12ca241fca1462099f1f57d88a5f
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-08-01 17:03:08 +0200
Commit message:

 merge in a couple of unrelated fixes from devel
Package: GSVA
Commit: 2f717566d0c250a329df4c70f999181a921d2602
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-07-26 14:28:07 +0000
Commit message:

 fix bug in gsvaParam contructor (add match.arg for kcdf, duh); sync slots and parameters documentation for gsvaParam class and constructor
Package: GSVA
Commit: 981dc7b086acdd7e0ae6e3909c38b35b2a0c1fa5
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-07-24 15:32:17 +0200
Commit message:

 Merge pull request #98 from rcastelo/96-gsva-method-parameter-class-and-constructor

fix oversight in gsvaParam definition causing a Check error
Package: GSVA
Commit: a4b627a81b447cfc5889588127e029f131224048
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-07-24 13:29:47 +0000
Commit message:

 fix oversight in gsvaParam definition causing a Check error
Package: GSVA
Commit: 093c2188bf1ddb294118d1f623cb39fade4ca72f
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-07-24 14:46:12 +0200
Commit message:

 Merge pull request #97 from rcastelo/96-gsva-method-parameter-class-and-constructor

96 gsva method parameter class and constructor
Package: GSVA
Commit: e90ee3527ca22a7010d87377eec369935e76a173
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-07-24 14:09:26 +0200
Commit message:

 Merge branch '96-gsva-method-parameter-class-and-constructor' of github.com:rcastelo/GSVA into 96-gsva-method-parameter-class-and-constructor
Package: GSVA
Commit: 65e233fb75159de8c833e5e66e59cc04bebddfb0
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-07-24 11:49:13 +0000
Commit message:

 add gsvaParam class and constructor with argument names and documentation as before; switch from camel case to underscore names for getters (ssgseaParam and gsvaParam); and don't forget to update NAMESPACE
Package: GSVA
Commit: 194b3a8053942e746ffe55b76da169201262e5cb
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-07-24 11:49:13 +0000
Commit message:

 add gsvaParam class and constructor with argument names and documentation as before; switch from camel case to underscore names for getters (ssgseaParam and gsvaParam)
Package: GSVA
Commit: e2226985ed8e4a4132d28eb6705fef4d46c3a35f
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-07-14 17:16:32 +0200
Commit message:

 Merge pull request #95 from rcastelo/85-ssgsea-method-parameter-class-and-constructor

85 ssgsea method parameter class and constructor
Package: GSVA
Commit: 59a1ea81a1c507675e42d3c3c0b246e1c7a5fd3f
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-07-14 15:00:24 +0000
Commit message:

 ... and don't forget various updates to .gitignore
Package: GSVA
Commit: dc54f198ce6748f61f2de4e8c27ddcc8b33161dd
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-07-14 14:59:31 +0000
Commit message:

 finalize ssGSEA; remove allGenerics.R and, on second thoughts, make ssgseaParam getters *functions* instead of methods
Package: GSVA
Commit: f1008e1193d518e88e100f00bb675a8285c64e5b
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-07-10 13:17:17 +0200
Commit message:

 Merge pull request #94 from rcastelo/devel

new_api sync to devel, 2nd attempt
Package: GSVA
Commit: 3874d4cc7114d11139f8d62197c64fc7f85422a7
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-04-25 14:22:28 +0000
Commit message:

 move constructors from allClasses.R to method-specific R files; add class definition, constructor and two get methods for ssGSEA to fix #85; add generics for get methods to new file allGenerics.R
Package: GSVA
Commit: c121192758f821eaaf4f435e429bc0dccf836d79
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-04-18 14:47:47 +0200
Commit message:

 Merge pull request #84 from rcastelo/78-plage-method-parameter-class-and-constructor

add PLAGE method parameter class and constructor; modify CITATION to …
Package: GSVA
Commit: d1796a100256639fc582080b741f5636e0162e4d
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-04-18 12:27:13 +0000
Commit message:

 add PLAGE method parameter class and constructor; modify CITATION to work with both latin1 and UTF-8 encodings
Package: GSVA
Commit: 6aafa42451bd5593e23c767ce9712fec5249a1f3
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-04-17 16:06:06 +0200
Commit message:

 Merge pull request #83 from rcastelo/73-zscore-method-parameter-class-and-constructor

73 zscore method parameter class and constructor
Package: GSVA
Commit: bb2f161dd36396d342138c115698c9d7e7e0ba1f
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-04-17 16:02:39 +0200
Commit message:

 Delete register_cmethods.o

Had been added by accident.
Package: GSVA
Commit: ce5c72d2dccd379af4119778a887ee8ad9c409f1
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-04-17 16:02:26 +0200
Commit message:

 Delete ks_test.o

Had been added by accident.
Package: GSVA
Commit: 4d8e009d60e11159e058d43725e93730a26e1b65
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-04-17 16:02:15 +0200
Commit message:

 Delete kernel_estimation.o

Had been added by accident.
Package: GSVA
Commit: 9fa3bb0fc1668c123ba86515ed34cd3b779af095
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-04-17 16:01:47 +0200
Commit message:

 Delete GSVA.so

Had beed added by accident.
Package: GSVA
Commit: 3a6b337ab9b160af7ac64c5caa6166962172e0d5
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2023-04-17 15:56:58 +0200
Commit message:

 Merge pull request #82 from rcastelo/devel

merge in changes to devel
Package: GSVA
Commit: 8cbada77d3423d54fc3569990012e2d559ba9d20
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2023-04-03 17:30:44 +0200
Commit message:

 fix issue #73: add zscore method parameter class and constructor (and a virtual superclass)
Package: SurfR
Commit: 22e777a337b9244e880f0f44d8cc46e76e786a01
Author: maurizio.aurora@hsr.it <maurizio.aurora@hsr.it>
Date: 2023-09-25 20:18:30 +0200
Commit message:

 bumped the package version 0.99.6
Package: magpie
Commit: aaa4cd230fbec2e64ad887d159ee5b37f834efa6
Author: dxd429 <dxd429@case.edu>
Date: 2023-09-25 14:12:51 -0400
Commit message:

 1.1.2
Package: magpie
Commit: 68b94f9302dbe5ab586263ce436bd92d69d51bff
Author: dxd429 <dxd429@case.edu>
Date: 2023-09-25 14:10:48 -0400
Commit message:

 datasets Rd
Package: KEGGREST
Commit: 2b192943e7e8b4866bc27fd5ef85a1657a9bde5b
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 14:06:21 -0400
Commit message:

 version bump 1.41.4
Package: KEGGREST
Commit: 27e262efee641f196fecc64d61fd632c94d63b3a
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 14:06:14 -0400
Commit message:

 add unit tests for keggCompounds
Package: KEGGREST
Commit: c251881f330971044c0af26d756a397b1970dbdc
Author: Kristina Riemer <kristina.riemer@weecology.org>
Date: 2021-11-30 13:15:51 -0700
Commit message:

 Add man page for keggCompounds function
Package: KEGGREST
Commit: 9ccdfaf3802de0080ee5a60944941fdb6e1ef73b
Author: Kristina Riemer <kristina.riemer@weecology.org>
Date: 2021-11-30 13:00:17 -0700
Commit message:

 Rename function for getting list of compounds from pathway
Package: KEGGREST
Commit: 9886c91efdd8ae5bb32b287dd8cf51422508c4fb
Author: Kristina Riemer <kristina.riemer@weecology.org>
Date: 2021-11-30 12:52:33 -0700
Commit message:

 Fix indentation error
Package: KEGGREST
Commit: e0e117c521d989bfb148277cd765dd18ebde28be
Author: Kristina Riemer <kristina.riemer@weecology.org>
Date: 2021-07-08 13:48:50 -0700
Commit message:

 Add function for getting compound list from pathway
Package: magpie
Commit: a75d50065c87b6ff89da795ba9f371a4f3961f2a
Author: dxd429 <dxd429@case.edu>
Date: 2023-09-25 13:42:40 -0400
Commit message:

 1.1.1

Merge remote-tracking branch 'upstream/devel' into devel

# Conflicts:
#	DESCRIPTION
Package: magpie
Commit: 4aeb5dabc774fc5c79bd6038a00d3865d1f890de
Author: dxd429 <dxd429@case.edu>
Date: 2023-09-25 13:18:08 -0400
Commit message:

 0.99.11
Package: KEGGREST
Commit: af36ddfbf72d0af3d1139349851ee74709b941d5
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 13:29:41 -0400
Commit message:

 version bump 1.41.3
Package: KEGGREST
Commit: 1f4ccad2f3b7b9d1ce6adf120e914e0c5221d2f2
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 13:29:36 -0400
Commit message:

 remove escaped #s in Rd file
Package: KEGGREST
Commit: 57dce7b1667c1d1fb8cd135b5623ae8dec174413
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 13:29:14 -0400
Commit message:

 remove test_KEGGREST_package.R file
Package: KEGGREST
Commit: d078fd4814e9a30410109ee930b0c9014320d914
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 13:05:00 -0400
Commit message:

 version bump 1.41.2
Package: KEGGREST
Commit: 696d03e4e4f17825ee082523380e8ab8e563bcde
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 13:04:56 -0400
Commit message:

 add stop_for_status in .get.kegg.url
Package: KEGGREST
Commit: 2e1538546746c2a303f2de12e21f6ea5b5713848
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 12:57:18 -0400
Commit message:

 version bump 1.41.1
Package: KEGGREST
Commit: e59771c55047e481c056f7ff0466fb5317400443
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 12:58:44 -0400
Commit message:

 update NEWS
Package: KEGGREST
Commit: d0844c9c541ed72c3f96b0b975ac9d0a31a63e74
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2023-09-25 12:56:23 -0400
Commit message:

 using httr always with default

- rename function to .get.kegg.url
Package: KEGGREST
Commit: f900a2f67912004c2953ce21029591a4fa6162a5
Author: Marcel Ramos <LiNk-NY@users.noreply.github.com>
Date: 2023-09-25 12:49:31 -0400
Commit message:

 Merge pull request #22 from CogDisResLab/devel

fix: correct the url parsing
Package: KEGGREST
Commit: b1dcf1d55ffe1ba9e02ed7a3fa249fcb98d83b97
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2023-09-21 20:09:40 -0400
Commit message:

 fix: correct the url parsing
Package: easylift
Commit: 395f5ee6458c6d571275a913e4be4b12da4ec380
Author: nahid18 <nahidpatwary50@gmail.com>
Date: 2023-09-25 21:36:16 +0600
Commit message:

 feat: updated test
Package: easylift
Commit: a6de3cb6a192099c8efeec285c997d5ee82e6904
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2023-09-25 10:17:49 -0400
Commit message:

 tweak help
Package: metabolomicsWorkbenchR
Commit: 9a9032febf88a4747c01c7d15fe7cea0300f72b1
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2023-09-25 15:56:55 +0100
Commit message:

 version bump and update news
Package: metabolomicsWorkbenchR
Commit: 7fa231b25094399fb70b83ed0d634b387fb34610
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2023-09-25 15:38:32 +0100
Commit message:

 update vignettes

- exclude large data downloads from cache
- add example data to internals for testing / vignette
- better 0 results handling
Package: shiny.gosling
Commit: 90a421ae1dfeab664b34c8499cd365ef8729092f
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-25 19:35:45 +0530
Commit message:

 bump version
Package: DESeq2
Commit: a24ecc00a7531f3ee5aeca25771c9b2ebc4b6e0b
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2023-09-25 09:54:34 -0400
Commit message:

 results man page fix, resolves #85
Package: shiny.gosling
Commit: 5da55d10175b776a688f25c46528218bf40460ad
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-25 19:01:02 +0530
Commit message:

 Merge pull request #113 from Appsilon/dev

Main <- Dev
Package: shiny.gosling
Commit: 2b1a1913ee1c620d18911d468470d29072fab7cc
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-25 17:27:30 +0530
Commit message:

 Merge pull request #125 from Appsilon/anirban.bump-version

Anirban.bump version
Package: shiny.gosling
Commit: 20e7fca5e849c460a1112f029ae57a885e1e130f
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-25 10:58:21 +0530
Commit message:

 Merge pull request #121 from Appsilon/anirban.better-vignettes

Anirban.better vignettes
Package: shiny.gosling
Commit: 9a0334fd764232f0af5e31352cbf057ccbdeb8b5
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-14 12:53:36 +0530
Commit message:

 bump version
Package: shiny.gosling
Commit: 73b96dd62270769af74441eb7826a4d14c2b371c
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-13 13:56:39 +0530
Commit message:

 Merge pull request #116 from Appsilon/e2e-tests

E2e tests
Package: shiny.gosling
Commit: 023decc68c354317b0fc41796f89274833f251a9
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-11 13:30:25 +0530
Commit message:

 fix: spellings
Package: shiny.gosling
Commit: 55ab0d02a58e11c2762e45013669e70175b4edfb
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-09-11 13:17:49 +0530
Commit message:

 fix: broken links and library calls
Package: shiny.gosling
Commit: 4106f44eb4d2e9f5af37f30a51e6efd545ff5f65
Author: federiva <federivadeneira@gmail.com>
Date: 2023-08-24 10:26:45 -0300
Commit message:

 Merge branch 'dev' of github.com:Appsilon/shiny.gosling into e2e-tests
Package: shiny.gosling
Commit: 9f3d24db037a19c0670455e18a0f3922e528d381
Author: Federico Rivadeneira <federivadeneira@gmail.com>
Date: 2023-08-23 16:37:31 -0300
Commit message:

 feat: Simplifying script for running tests (#120)

* feat: Simplifying script for running tests

* chore: Adding optparse

* Update tests/run_cypress_tests.sh

Co-authored-by: Vedha Viyash <49812166+vedhav@users.noreply.github.com>

* fix: Adding folders

* style: lintr

* fix: Adding run_example_app helper script

* fix: Moving e2e folder

---------

Co-authored-by: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Package: shiny.gosling
Commit: 989c20370e8796611070d5b9370e88ea052b0b2c
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-18 18:22:59 +0530
Commit message:

 fix: add ggbio to wordlist
Package: shiny.gosling
Commit: d79d2f2e7e7c99e483db35b90dfd5c1d926e66c0
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-18 18:09:41 +0530
Commit message:

 fix: revert example changes
Package: shiny.gosling
Commit: 0d1b0ae055b87234d0602ed729d18133603a1a1e
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-18 18:07:51 +0530
Commit message:

 fix: add new words to wordlist and arrange them alphabetically
Package: shiny.gosling
Commit: 5c52ed998ceef538c03630cd683611419a8d18db
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-18 18:05:30 +0530
Commit message:

 docs: improve and add vignette
Package: shiny.gosling
Commit: 6771b38b37dafe05a3ad4c62589d570ac8b07cfa
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-18 17:16:10 +0530
Commit message:

 docs: add and improve vignettes
Package: shiny.gosling
Commit: 82edc25678aa87ac6ce158d4101d812097090f7c
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-18 13:23:06 +0530
Commit message:

 docs: add vignette with explanation of multivec data
Package: shiny.gosling
Commit: 41d1d4488d5d9b0fd11abc1d71b2590ce57575cf
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 18:51:24 +0530
Commit message:

 Merge pull request #118 from Appsilon/anirban.vcf-vignette

Anirban.vcf vignette and examples
Package: shiny.gosling
Commit: 58fd6793c1ff72129bcb8813fea003762b857c28
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 18:09:23 +0530
Commit message:

 fix: reverse change of library to require
Package: shiny.gosling
Commit: 5fa4338275e195ecb98f6e2551bcf0256af44fcb
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 15:33:25 +0530
Commit message:

 fix: remove BiocManager from description
Package: shiny.gosling
Commit: 92ba875a82625ffb5823067a543cf983c0173e4a
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 14:19:17 +0530
Commit message:

 fix: spellings
Package: shiny.gosling
Commit: 1888e4ed2f68d3380232dceb4129614f9b27f8d4
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 14:02:14 +0530
Commit message:

 fix: spelling errors
Package: shiny.gosling
Commit: 9fda9f90f4698a7cd2af6bc4a7229b135c86c855
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 13:53:04 +0530
Commit message:

 fix: update wordlist
Package: shiny.gosling
Commit: 324de9b1aa22f09abf901f4c33e6fe479cb1e9ed
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 13:46:39 +0530
Commit message:

 fix: circos vcf example
Package: shiny.gosling
Commit: 74a0b4eeec9c4273be1d816a5280500004fdc372
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 13:43:49 +0530
Commit message:

 fix: add more description to VCF.Rmd
Package: shiny.gosling
Commit: 047a5d660f80cfdc79272df2af77f1327f1485ad
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 13:10:49 +0530
Commit message:

 fix: add more descriptions
Package: shiny.gosling
Commit: d060803610d9a25bb164cd583faf92e40cfa5699
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 13:08:13 +0530
Commit message:

 Update inst/examples/circosVcfData/app.R

Co-authored-by: Federico Rivadeneira <federivadeneira@gmail.com>
Package: shiny.gosling
Commit: b5d35587682e9c6e567a97ab893d0d77aff60d6a
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 13:07:54 +0530
Commit message:

 fix: add and update descriptions
Package: shiny.gosling
Commit: 95b8d113b28ea067f14d41f1b8391e862ef075f0
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-03 12:18:27 +0530
Commit message:

 fix: change library to require
Package: shiny.gosling
Commit: 52ae644ce84a3d215c772635ec9cf0d5d3abb944
Author: federiva <federivadeneira@gmail.com>
Date: 2023-08-01 14:39:47 -0300
Commit message:

 fix: Incrementing timeout for screesnhots
Package: shiny.gosling
Commit: f9af8d2ecf1bbdd48a9326682cb3bbba346b41e7
Author: federiva <federivadeneira@gmail.com>
Date: 2023-08-01 13:18:44 -0300
Commit message:

 fix: Removing unused job
Package: shiny.gosling
Commit: 0172442e2297fcb0bf7cf682502511624bd504e2
Author: federiva <federivadeneira@gmail.com>
Date: 2023-08-01 12:38:26 -0300
Commit message:

 fix: Removing unused script
Package: shiny.gosling
Commit: 036512ead0f78622dbc74c6dd76ad5712490aeaf
Author: federiva <federivadeneira@gmail.com>
Date: 2023-08-01 12:24:56 -0300
Commit message:

 fix: Passing port as options
Package: shiny.gosling
Commit: f10a5e67fd3ace28e2eed890cf1c442481c08c63
Author: federiva <federivadeneira@gmail.com>
Date: 2023-08-01 12:14:38 -0300
Commit message:

 fix: specifying IP
Package: shiny.gosling
Commit: 88c2012a70d6470cafc6de359f1a72a6b3f98373
Author: federiva <federivadeneira@gmail.com>
Date: 2023-08-01 12:13:34 -0300
Commit message:

 fix: typo
Package: shiny.gosling
Commit: d77c76748ddbcce0b7b49059c636c7f36c8864d5
Author: federiva <federivadeneira@gmail.com>
Date: 2023-08-01 12:13:30 -0300
Commit message:

 fix: conf
Package: shiny.gosling
Commit: ed456f43f609609fa944eb2e0f1c60fa87cd85fb
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-01 16:30:43 +0530
Commit message:

 fix: set ci timeout to 60m
Package: shiny.gosling
Commit: f708529214dfffa4c3212a1029d5e5e1f6f93e30
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-08-01 13:36:35 +0530
Commit message:

 try: pak version stable
Package: shiny.gosling
Commit: 397422cc02e7f7a326b9686e746651ca370cccbd
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 23:18:37 +0530
Commit message:

 fix: rename example
Package: shiny.gosling
Commit: d35d9b846f059cd7e233728512645e1a10cd931c
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 23:17:51 +0530
Commit message:

 fix: rename example
Package: shiny.gosling
Commit: 702cea7e29076d175d8a857e8a7a84dd5e120216
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 23:17:35 +0530
Commit message:

 fix: rename example
Package: shiny.gosling
Commit: ce450a0952c203f099e2bf49f80a1d03ab9ea604
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 23:10:40 +0530
Commit message:

 fix: examples
Package: shiny.gosling
Commit: 3c0b718d34f20f56142179d6d4120249b078cfe2
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 23:01:19 +0530
Commit message:

 fix: replace Visualising with Visualizing
Package: shiny.gosling
Commit: 412fc5edf8c1e54482f5ca4f2ee06823404587c5
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 22:53:50 +0530
Commit message:

 fix: typo
Package: shiny.gosling
Commit: d5406bde017d288ed6d7361bbba4d8ede63a8655
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 22:52:40 +0530
Commit message:

 fix: set eval=FALSE for all vignettes
Package: shiny.gosling
Commit: cb6bec36d8cdb97748b239c8452fd0bd42b509a5
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 22:33:13 +0530
Commit message:

 fix: update decription
Package: shiny.gosling
Commit: f52693d13796932b3001da8d631d86c97d72c869
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 22:14:32 +0530
Commit message:

 fix: description
Package: shiny.gosling
Commit: 5499b5eae703fae5aae9961c3e6f6b728fd3f7c6
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 22:10:36 +0530
Commit message:

 fix: add genomic packages
Package: shiny.gosling
Commit: 4827ce24afcf8a242c60a62ef0bf26bdbbc4c9dd
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 21:43:53 +0530
Commit message:

 fix: circos spelling
Package: shiny.gosling
Commit: d8d902c5ac32b2156934da166d8128c551d866af
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 21:38:35 +0530
Commit message:

 fix: lints
Package: shiny.gosling
Commit: 646c2fc611bf819f79ef7a1596a06f7a47928176
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 21:10:37 +0530
Commit message:

 fix: set run-app to eval=FALSE and add images of apps
Package: shiny.gosling
Commit: 603289a85f7933a939a33e9231ffe5fc093b08e1
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-31 20:22:03 +0530
Commit message:

 feat: add circos plots and sessionInfo
Package: shiny.gosling
Commit: ac19f34706a9fd1d32b07e489c3a3da837899fa3
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-31 01:34:09 -0300
Commit message:

 fix: ci syntax
Package: shiny.gosling
Commit: 54f0556c72ae95618daf25a51f3ca27702442db1
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-31 01:33:08 -0300
Commit message:

 fix: ci
Package: shiny.gosling
Commit: 98877ceabe816569e4ab0ba7c18d64fbe30f982c
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-31 01:25:31 -0300
Commit message:

 fix
Package: shiny.gosling
Commit: 23761e7274c6b98ff286f76c4df538b8326b53d6
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-31 01:02:29 -0300
Commit message:

 feat: Ensuring that the script returns when a test fails
Package: shiny.gosling
Commit: 686e56525c22c628f421eca1d6cc04e0e565e567
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-31 00:52:36 -0300
Commit message:

 fix: Adding .lock file
Package: shiny.gosling
Commit: e38545858b140267052fc8f1c15cf6f5970427ab
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-31 00:49:44 -0300
Commit message:

 feat: adding CI
Package: shiny.gosling
Commit: d214b3c66b0b97293b47643e2dbe3bc9536e08db
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-30 23:53:07 -0300
Commit message:

 fix: Updating README
Package: shiny.gosling
Commit: 0db8808ffd3b0528f5a70b8a008b945873042020
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-30 23:33:40 -0300
Commit message:

 fix: Removing hardcoded port
Package: shiny.gosling
Commit: 757d705612ac7fbbf5d15844c5cb70af735037c0
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-30 23:33:25 -0300
Commit message:

 feat: Adding readme
Package: shiny.gosling
Commit: 555c99177e6e2268ae2b12251e183b8a21039b2d
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-30 23:33:17 -0300
Commit message:

 feat: Adding port
Package: shiny.gosling
Commit: e51cffce8c362aff2f5abf21c7deccc853458df7
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-30 23:33:09 -0300
Commit message:

 chore: sorting
Package: shiny.gosling
Commit: 92ded6b45024487e44f84cef951cf23a6b2f7c3c
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-30 23:32:54 -0300
Commit message:

 chore: reordering
Package: shiny.gosling
Commit: 7adf0ca5c0484493ef9996e87fdb8eb5fda58ba4
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-29 16:43:22 -0300
Commit message:

 fix: Removing
Package: shiny.gosling
Commit: f783a4a2e4ee16700fc700fd4063e531b14dd11a
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-29 16:43:01 -0300
Commit message:

 feat: Adding threshold at 5 percent
Package: shiny.gosling
Commit: 307ae8b6543fca9e5c3efa69d0dbdaaf283e9268
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-28 15:46:49 -0300
Commit message:

 fix: Avoid appending
Package: shiny.gosling
Commit: bdbd08d1e17585266a2406c44591558f505d79a8
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-28 19:19:57 +0530
Commit message:

 Merge pull request #117 from Appsilon/anirban.fix-delection-spelling

fix: deletion spelling is wrong: delection
Package: shiny.gosling
Commit: 3f13961a5b4a321f5ed84145f4c7829464ae79aa
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-28 18:58:36 +0530
Commit message:

 Merge branch 'dev' into anirban.fix-delection-spelling
Package: shiny.gosling
Commit: a30b2c4c6ec43af0f4050ad2d7596e8310a1cee4
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-28 18:39:09 +0530
Commit message:

 fix: deletion spelling is wrong: delection
Package: shiny.gosling
Commit: e58804a63193f2ef7f520722a4e05029f8dbfd88
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 21:23:26 -0300
Commit message:

 fix: adding paths
Package: shiny.gosling
Commit: 6fe70f668cba308f9679f636bc9b75e9d447be70
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:50:15 -0300
Commit message:

 feat: adding script to run all of the tests
Package: shiny.gosling
Commit: 04d2f9b645ee0a638e1573dac8f5521919acb593
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:43:05 -0300
Commit message:

 tests: Adding tests
Package: shiny.gosling
Commit: 8b84fc353cde120bcd74105fe382a990bc742fcc
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:35:12 -0300
Commit message:

 tests: Adding sarsCov
Package: shiny.gosling
Commit: ea31763f8c95faf7cd93a8da08c70f1685f47efb
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:27:35 -0300
Commit message:

 feat: Adding template for code generating scripts
Package: shiny.gosling
Commit: 88ff42f22bb9f473d8584716178a591e4217c36f
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:27:09 -0300
Commit message:

 tests: Adding tests for ruleMarks
Package: shiny.gosling
Commit: 66d6a41d6feebd4e848da5b3d0539ece3efae35b
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:26:51 -0300
Commit message:

 tests: Adding tests for lineChart
Package: shiny.gosling
Commit: 9320bf0275acba837ef9026998963acc0ac4b24d
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:25:22 -0300
Commit message:

 feat: adding multitrack
Package: shiny.gosling
Commit: a9298271841e6faec5b38a2435b84112dd48c449
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:24:18 -0300
Commit message:

 feat: Adding pointplot
Package: shiny.gosling
Commit: da75055ed4ef6f16cb0b8ba8b9a8124556f81119
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:23:27 -0300
Commit message:

 feat: adding ideogram
Package: shiny.gosling
Commit: d7b3878024e8395004d132b0cb5e02af7ffe41a4
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 20:22:14 -0300
Commit message:

 feat: Adding script to create testfiles
Package: shiny.gosling
Commit: 21295b94a3a0cf25e99a565911da6d409ba236f3
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 19:27:59 -0300
Commit message:

 feat: Adding circularVisualEncoding test
Package: shiny.gosling
Commit: fbf3cafbc95f0724d4d8d2893194c70a73e8144a
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 19:21:22 -0300
Commit message:

 chore: empty line
Package: shiny.gosling
Commit: 9e8e195e0cfd87182b7e3783630f4252c2d87965
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 09:24:35 -0300
Commit message:

 feat: Adding snapshot tests for areachart
Package: shiny.gosling
Commit: 3cc0f08d4a045f650096b1e7e6a57a827400826e
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 09:20:34 -0300
Commit message:

 feat: Adding tests and scripts for barchart
Package: shiny.gosling
Commit: 45aa1d209c8df8535b092106e1b24cca7d47b11d
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 09:20:11 -0300
Commit message:

 feat: Adding R script for barchart example
Package: shiny.gosling
Commit: 21d9d2feb7d2f9bb1664fd59daef70da75c8a32a
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 09:19:44 -0300
Commit message:

 fix: Specifying port
Package: shiny.gosling
Commit: 7d072cb82ada32f9c73b9cc398a2c96bb43e5b2f
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:20:58 -0300
Commit message:

 fix: Updating screenshots https://github.com/cypress-io/cypress/issues/3324#issuecomment-542414532
Package: shiny.gosling
Commit: faddc6b70153a4c571ab131d66a6f24bad677ad6
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:20:45 -0300
Commit message:

 chore: Adding cypress/videos
Package: shiny.gosling
Commit: fe0bd4595d3b7eb0cd55985fd2c8bb42fcee4cca
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:20:36 -0300
Commit message:

 fix: Updating script running tests
Package: shiny.gosling
Commit: 0300845c3a7c9cda4add99d4ef80f05666d51149
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:12:55 -0300
Commit message:

 fix: removing commented code
Package: shiny.gosling
Commit: a4c6d8e42882bb02970db823a0e6b96221ed83b2
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:08:34 -0300
Commit message:

 fix: Revert accidentally pushed to dev
Package: shiny.gosling
Commit: ac48deff6b3e94bccb78bcf74e8587966bf04dde
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:02:33 -0300
Commit message:

 feat: Adding R scripts
Package: shiny.gosling
Commit: 1ed34e55716d03ce08e3a967ed3fb74e0084c505
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:02:12 -0300
Commit message:

 feat: registering plugin
Package: shiny.gosling
Commit: 01e9192baaf638b8f90295936b5c71571ec4d911
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:02:00 -0300
Commit message:

 feat: Adding e2e test for circularLinearWithBrush example
Package: shiny.gosling
Commit: adde28755e5432bbd3ff59331385d4b4313baacd
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:01:00 -0300
Commit message:

 feat: Adding scripts
Package: shiny.gosling
Commit: cecd76e2c35e44fe6d05055eb055be8b2012d985
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:00:48 -0300
Commit message:

 feat: adding plugins
Package: shiny.gosling
Commit: 7f87b926410e87f5acd9a8260413b29ab02a659b
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:00:11 -0300
Commit message:

 chore: adding cypress paths
Package: shiny.gosling
Commit: 16af90534ff7f4d3e121c78c368f3400b4b0fb91
Author: federiva <federivadeneira@gmail.com>
Date: 2023-07-24 08:00:01 -0300
Commit message:

 chore: Adding cypress paths
Package: shiny.gosling
Commit: 0aeba46f249e67870858e6c1c32d712c60889b21
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 18:50:20 +0530
Commit message:

 Merge pull request #108 from Appsilon/vedha.milestone-1-changes

Improving the usage of csv data and adding a way to use a GRanges object as source
Package: shiny.gosling
Commit: 435f3636a0de550a3a44d1ed82583fdc2d4b6769
Author: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Date: 2023-07-20 18:31:41 +0530
Commit message:

 Merge pull request #110 from Appsilon/anirban.examples

fix: add bar chart, line chart, point plot and ideogram example
Package: shiny.gosling
Commit: 0759bb749c4216232f0737e91ebf6371ae2163eb
Author: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Date: 2023-07-20 18:28:24 +0530
Commit message:

 Merge pull request #112 from Appsilon/anirban.fix-lints

fix: lints
Package: shiny.gosling
Commit: 646bbb17b1c2587a9706ea6e457caf6827dbbc30
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 18:08:08 +0530
Commit message:

 fix: remove renv and proj files
Package: shiny.gosling
Commit: b11bd8c56acebef55e9a0553843afbf4ff0625b9
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 18:02:36 +0530
Commit message:

 fix: update doc
Package: shiny.gosling
Commit: c7827b026951984720f87462ea0405ebf7fa0594
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 17:48:59 +0530
Commit message:

 fix: lints and spellings;
Package: shiny.gosling
Commit: 352d866ce3798d38ab8b22f8385138c676b92df1
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 17:24:34 +0530
Commit message:

 fix: update documentation
Package: shiny.gosling
Commit: 73e73e187d62341052461419636b5fb8375c0450
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 17:21:53 +0530
Commit message:

 fix: add documentation to genomicFieldsToConvert; remove deprecated code;
Package: shiny.gosling
Commit: d81189e9432b2da5e57bf440739612cf2e9a485b
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 20:20:49 +0530
Commit message:

 fix: rename app files to app.R
Package: shiny.gosling
Commit: fcec2b71882eb360b1d681595a76a0dd169ceccf
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 19:46:40 +0530
Commit message:

 fix: lints
Package: shiny.gosling
Commit: 1ff02580717e73488f8bb513a6f0c3692f5ec943
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 19:34:18 +0530
Commit message:

 fix: add documentation for genomicFieldsToConvert
Package: shiny.gosling
Commit: e48cd77f01e6663d1c1b16b26096eb0f7c7c7fca
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 19:23:30 +0530
Commit message:

 feat: add rule mark chart
Package: shiny.gosling
Commit: 963ce4953696a4848e2a75bf7d2b30ffb9930876
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 17:34:17 +0530
Commit message:

 feat: add area and text chart example
Package: shiny.gosling
Commit: f1a2c6050dd978331609069e693fe9ff22e25c81
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-06 17:49:35 +0530
Commit message:

 fix: add bar chart, line chart, point plot and ideogram example
Package: shiny.gosling
Commit: 9e58de1421414562ad030033c534e8ebb99437ac
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 17:34:22 +0530
Commit message:

 fix: more lints
Package: shiny.gosling
Commit: 64dec5ababb2e3fc96a9106ab628b02522b1e538
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 17:32:49 +0530
Commit message:

 fix: lints
Package: shiny.gosling
Commit: f0db2e2ab9ca7225b9941c73678f217e845f2fa7
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 17:31:01 +0530
Commit message:

 fix: lints
Package: shiny.gosling
Commit: 4eb76dec9449f0c55dda1b8522713a9c9ff84026
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-20 17:15:51 +0530
Commit message:

 fix: indent
Package: shiny.gosling
Commit: c7ead73478e87c0e3fce6d9eeed4bc96d5ef9c40
Author: Vedha Viyash <vedha@LEVI.local>
Date: 2023-07-20 12:03:59 +0530
Commit message:

 revert: use the older RoxygenNote
Package: shiny.gosling
Commit: 8302144f4ab36927a8f622bba8cb02c1cefcb7ae
Author: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Date: 2023-07-20 12:01:24 +0530
Commit message:

 Merge pull request #109 from Appsilon/anirban.plot-csv

fix: csv files copy to .gosling
Package: shiny.gosling
Commit: 20b676ec216b8fb18273c5762b00771a71c7f5ee
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 19:38:16 +0530
Commit message:

 fix: add mode = "wb" for win
Package: shiny.gosling
Commit: 49841954e89f018c28b8f58c96f2ce17a80a663c
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 17:42:02 +0530
Commit message:

 add: method = "auto"
Package: shiny.gosling
Commit: 5f1098b8eaf57ef61d3e64fef4c6ee93083aa396
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 17:20:37 +0530
Commit message:

 fix: set core.longpaths
Package: shiny.gosling
Commit: 2cb54bbe4979607915a421a7a6407b4af308ad5a
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 17:00:51 +0530
Commit message:

 fix: remove fread
Package: shiny.gosling
Commit: d16f03f74af6215cd09552be56c4ab3982957519
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 16:53:52 +0530
Commit message:

 fix: install R.utils
Package: shiny.gosling
Commit: 902a74398964e14919e0136aede7465f628b231f
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 16:40:14 +0530
Commit message:

 fix: add repo
Package: shiny.gosling
Commit: 6744ef37d5577053bbc72e6cd6567e6ec73cce70
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 16:34:23 +0530
Commit message:

 fix: install data.table
Package: shiny.gosling
Commit: 2858bb0972e790117083db123da47386a86f8db0
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 16:27:44 +0530
Commit message:

 try: fread
Package: shiny.gosling
Commit: 41f5023d113cf6e4a82572ef1a8d58e4716cf25d
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 15:55:35 +0530
Commit message:

 fix: add gzfile
Package: shiny.gosling
Commit: 6a40c0e1c97881e12c03478fac3c824793e54589
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 15:37:15 +0530
Commit message:

 fix: print path
Package: shiny.gosling
Commit: c7fbc04cc83bcb8030569e431306d737a64ef787
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 15:20:40 +0530
Commit message:

 fix: try normalizePath
Package: shiny.gosling
Commit: 04246a32ad62d658f3ecd384d2075bd1bbd2e5ed
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-13 14:54:34 +0530
Commit message:

 fix: shorten file name for windows
Package: shiny.gosling
Commit: fa5ee4385961b5f6109c96a0280c7cbc6882b396
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-06 20:10:40 +0530
Commit message:

 fix: remove # nolint
Package: shiny.gosling
Commit: ee2fd55084e58178fe702c936575b319c64cae65
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-06 20:07:54 +0530
Commit message:

 fix: use link shortner
Package: shiny.gosling
Commit: 145ad034e4d18af466d79c566d1c0f620b29b017
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-06 19:39:19 +0530
Commit message:

 fix: update documentation
Package: shiny.gosling
Commit: 38918e8c19edd4f727218f3743797d9f6b7a8308
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-06 19:03:24 +0530
Commit message:

 fix: add utils:: to read.csv
Package: shiny.gosling
Commit: 79bc99f0925cda2e286308bed15527449249b704
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-06 19:01:53 +0530
Commit message:

 fix: add documentation for missing parameters in track_data_gr
Package: shiny.gosling
Commit: cf2d2d1777984701581b613df9aa7a028d68085a
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-06 18:52:56 +0530
Commit message:

 fix: add documentation for new functions
Package: shiny.gosling
Commit: 35a731d9f1852452034d33c43928ad3b01239e3f
Author: Anirban Shaw <anirbanshaw24@gmail.com>
Date: 2023-07-06 17:41:50 +0530
Commit message:

 fix: csv files copy to .gosling
Package: shiny.gosling
Commit: 362a5faebe1676d49d1d3deb3b49e045fdcea95f
Author: vedhav <vedhaviyash4@gmail.com>
Date: 2023-06-27 12:29:15 +0530
Commit message:

 chore: have a default example as NA so just calling run_example() would display examples
Package: shiny.gosling
Commit: 9e49afd26713fd9fbbe4bb272d76a5a09bb17d8c
Author: vedhav <vedhaviyash4@gmail.com>
Date: 2023-06-16 19:07:49 +0530
Commit message:

 chore: remove unused package dependency and move GenomicRanges to suggests
Package: shiny.gosling
Commit: 4d0cea5427c172ea5a06862e0d7cd5f5299cd61d
Author: vedhav <vedhaviyash4@gmail.com>
Date: 2023-06-16 18:47:27 +0530
Commit message:

 feat: adding a vignette for using a GRanges object in gosling
Package: shiny.gosling
Commit: 94f350247162628e380d2805a0bb7737f2e2ccc4
Author: vedhav <vedhaviyash4@gmail.com>
Date: 2023-06-16 18:05:25 +0530
Commit message:

 chore: making the print.gosling invisible and making the print method consistent
Package: shiny.gosling
Commit: 073287e70c74cd7efcacdcf6c4fd84c517c5bc0b
Author: vedhav <vedhaviyash4@gmail.com>
Date: 2023-06-16 17:43:32 +0530
Commit message:

 chore: building document and fixing R CMD checks
Package: shiny.gosling
Commit: d4532c0c9a0f07b0881d077f56bb62dc7b1e6546
Author: vedhav <vedhaviyash4@gmail.com>
Date: 2023-06-16 17:20:32 +0530
Commit message:

 feat: adding a data wrapper for csv and GenomicRanges object

Changes:
* The use_gosling now adds a static resource directory .gosling to save local data and serve them
* The gosling component has a shiny and gosling class with a print.gosling function
* fix some lint errors
Package: shiny.gosling
Commit: 1459956eeef6122d0b6ef687c90077d8d7b9331f
Author: vedhav <vedhaviyash4@gmail.com>
Date: 2023-06-15 04:25:30 +0530
Commit message:

 Merge branch 'main' into dev
Package: shiny.gosling
Commit: 5e869f09e236c2a00e2f1134ecabb02bee28d58f
Author: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Date: 2023-06-02 15:03:22 +0530
Commit message:

 Merge pull request #107 from Appsilon/add-code-coverage-check

ci: Add code coverage check to the CI.
Package: shiny.gosling
Commit: e2d2dd2097e31d785f6efe60e2f39439b7130595
Author: Jakub Nowicki <kuba@appsilon.com>
Date: 2023-06-02 09:23:25 +0200
Commit message:

 ci: Add code coverage check to the CI.
Package: shiny.gosling
Commit: 9f080940b504584c0e6f0c6c58eeb64771cd2f78
Author: Jakub Nowicki <kuba@appsilon.com>
Date: 2023-04-20 08:47:57 +0200
Commit message:

 Merge pull request #106 from Appsilon/update-appsilon-readme-section

Update appsilon readme section
Package: shiny.gosling
Commit: 9faba6548585b0cd45e28b0db9dc8ad1b1c2bdc0
Author: Jakub Nowicki <kuba@appsilon.com>
Date: 2023-04-18 16:28:09 +0200
Commit message:

 chore: Update WORDLIST.
Package: shiny.gosling
Commit: db4813f726f1d6c6ee41f7dd5d2ca9bb0b0c8759
Author: Jakub Nowicki <kuba@appsilon.com>
Date: 2023-04-18 16:27:16 +0200
Commit message:

 chore: Update Appsilon section in the README.
Package: shiny.gosling
Commit: dc8d3e3c4d7fc29a53ab9ba26d481ea3c505ba39
Author: Vedha Viyash <49812166+vedhav@users.noreply.github.com>
Date: 2023-04-18 13:06:35 +0530
Commit message:

 Merge pull request #92 from Appsilon/fix.renderGosling

fix: Using renderReact
Package: shiny.gosling
Commit: 564c4335705971625fd27a8ba32d9f6284130fb1
Author: federiva <federivadeneira@gmail.com>
Date: 2023-04-17 15:13:03 -0300
Commit message:

 style: lintr, spellcheck
Package: shiny.gosling
Commit: 9ddad8dcd7d3d4f3c472c7f4fee9c66aabe66e36
Author: federiva <federivadeneira@gmail.com>
Date: 2023-04-17 15:03:51 -0300
Commit message:

 docs: Updating
Package: shiny.gosling
Commit: 83606243cae83567945a57ee59558046e14f9673
Author: federiva <federivadeneira@gmail.com>
Date: 2023-04-12 09:03:57 -0300
Commit message:

 docs: Updating docs
Package: shiny.gosling
Commit: c74b31a8ce2b1e64733e389d8b4517665fe33e86
Author: federiva <federivadeneira@gmail.com>
Date: 2023-04-12 09:02:14 -0300
Commit message:

 Merge branch 'fix.renderGosling' of github.com:Appsilon/shiny.gosling into fix.renderGosling
Package: shiny.gosling
Commit: 48bb2618279dd0430c5234a7ae2537a049099a6a
Author: federiva <federivadeneira@gmail.com>
Date: 2023-04-12 09:02:08 -0300
Commit message:

 fix: Removing unneeded folder
Package: shiny.gosling
Commit: dfb577a24603c00d1ed2c56ed9fffc8cee540b4e
Author: vedhav <vedhaviyash4@gmail.com>
Date: 2023-04-12 13:35:40 +0530
Commit message:

 Merge branch 'dev' into fix.renderGosling
Package: shiny.gosling
Commit: 2e0fe85dc2d6dd5a67f53022c3f20873ac26ae4f
Author: federiva <federivadeneira@gmail.com>
Date: 2023-04-11 16:33:31 -0300
Commit message:

 fix: Using renderReact
Package: shiny.gosling
Commit: 8781243c17ea3837760ef020e2e143a7f3a44f8e
Author: Jakub Nowicki <kuba@appsilon.com>
Date: 2023-03-17 16:07:04 +0100
Commit message:

 Merge pull request #85 from Appsilon/add-cross-domain-ga-tag

chore: Add second GA tag.
Package: shiny.gosling
Commit: a86171fa307f736b6d8f44d685821568f09d07ac
Author: Jakub Nowicki <kuba@appsilon.com>
Date: 2023-03-17 14:50:35 +0100
Commit message:

 fix: Fix quotation marks.
Package: shiny.gosling
Commit: 3f66e09bb34d99f9d1bbf11adc3792f0cfe145d2
Author: Jakub Nowicki <kuba@appsilon.com>
Date: 2023-03-17 12:51:22 +0100
Commit message:

 chore: Add second GA tag.
Package: signeR
Commit: 328f76417a4743e868579355e509cf4c46e329c0
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2023-09-25 10:21:36 -0300
Commit message:

 Moved the source repository to TojalLab
Fixed issue when running with fixed signatures matrix
Reduced the maxeval time in rare cases when there is no convergence
Package: YAPSA
Commit: c81f0dd0e0745f4c83cae175f85dc28d05a5de22
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-09-25 15:19:54 +0200
Commit message:

 removed build/ folder
Package: YAPSA
Commit: 89c36690c9a3bf1902492d5b1e9adec575f32e27
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-09-25 15:19:07 +0200
Commit message:

 removed build/ folder
Package: Spectra
Commit: 6d16816bad6d3e0d545cbb7d9b037649a914923b
Author: jorainer <johannes.rainer@gmail.com>
Date: 2023-09-25 14:21:23 +0200
Commit message:

 fix: fix issue #302

- Allow optional parameters (...) to avoid errors if
`filterFourierTransformArtefacts` is combined with another peaks function.
Package: pcaMethods
Commit: ecab0452cd129e95e7a01d731074fdee55204146
Author: Henning Redestig <henning.redestig@iff.com>
Date: 2023-09-25 13:40:46 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: pcaMethods
Commit: bd4eb8c1e77219b76806c1b4e8e768368c110de8
Author: Kevin Wright <kw.stat@gmail.com>
Date: 2020-06-18 16:54:12 -0500
Commit message:

 Add doi for source paper.
Package: pcaMethods
Commit: d785ef5bbdfce19d140b7bfe1214aab540bfe67e
Author: Henning Redestig <henning.red@gmail.com>
Date: 2020-05-05 10:30:21 +0200
Commit message:

 doc: add orcid for henning too
Package: pcaMethods
Commit: 832d7c0c1adf3ed721226676cec438b21dd3d3a5
Author: Kevin Wright <kw.stat@gmail.com>
Date: 2020-05-01 07:33:27 -0500
Commit message:

 doc: add orcid for k wright
Package: pcaMethods
Commit: 22e492448e994f71c136e52b498811a0dfd25c4c
Author: Henning Redestig <henning.red@gmail.com>
Date: 2019-11-03 19:55:39 +0100
Commit message:

 fix: q2 only returned result of last iteration when using nruncv>1
Package: pcaMethods
Commit: 923ff26a6e400ecfac041d04543c8e5a4f4c0f83
Author: Henning Redestig <henning.red@gmail.com>
Date: 2019-11-03 18:28:32 +0100
Commit message:

 fix: robustSvd use default l1 coef when all input data missing

Can happen when data is small and norms become small. If so return
zero.
Package: pcaMethods
Commit: cf5826ad96e8d7069bb75699ea3ea059cd8a8f51
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:34:44 -0400
Commit message:

 bump x.y.z version to odd y after creation of RELEASE_3_10 branch
Package: pcaMethods
Commit: 3d8eb4d8d1c30da5339e84dc607a9da637ca8d76
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-10-29 13:07:44 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
Package: pcaMethods
Commit: 878b556245df62bf809d3f1c13630cb64be9f38f
Author: Henning Redestig <henning.red@gmail.com>
Date: 2019-10-13 15:23:07 +0200
Commit message:

 fix: R2VX was based on unscaled residuals

Gave wrong results if matrix scaled within PCA function.
Package: pcaMethods
Commit: 2e30fbb8ae744a99a92af5ca6bdc5f39aeeef569
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-05-02 12:10:43 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_9    branch
Package: pcaMethods
Commit: c2fd553aa477e6c916ed157d4b50e57139e9c502
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2019-05-02 11:53:06 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of            RELEASE_3_9 branch
Package: pcaMethods
Commit: 3822e8dd07f4e7c8bd9b2bbb7d0818873dd123f0
Author: Henning Redestig <henning.red@gmail.com>
Date: 2018-11-25 15:48:46 +0100
Commit message:

 bumpversion: patch release with doc
Package: pcaMethods
Commit: 2d63f0ecdb2774ca384bb583db5f682854b5d3f3
Author: Henning Redestig <henning.red@gmail.com>
Date: 2018-11-25 15:43:48 +0100
Commit message:

 doc: add ggplot example
Package: pcaMethods
Commit: 3c61cf99d6854dec15ae7199271989f1b12df0db
Author: Henning Redestig <henning.red@gmail.com>
Date: 2018-11-25 15:43:35 +0100
Commit message:

 chore: remove lint
Package: pcaMethods
Commit: 60f6bb1f843212c9f607194845bb16d08a87664d
Author: Henning Redestig <henning.red@gmail.com>
Date: 2018-11-25 15:43:15 +0100
Commit message:

 chore: use rbuildignore
Package: pcaMethods
Commit: e74fcb1b2906132771124d29a63a130bcb34879b
Author: Henning Redestig <henning.red@gmail.com>
Date: 2018-11-25 15:42:59 +0100
Commit message:

 refactor: remove lint in package repo
Package: pcaMethods
Commit: b466027eed5f6e3c22d5e12b5934d5f998d9423b
Author: Henning Redestig <henning.red@gmail.com>
Date: 2018-11-24 22:12:16 +0100
Commit message:

 chore: update output for new roxygen version
Package: pcaMethods
Commit: bc1a709fc6693b8708e8db21ad2529448baa49a5
Author: Henning Redestig <henning.red@gmail.com>
Date: 2018-11-24 20:34:46 +0100
Commit message:

 chore: ignore binaries
Package: pcaMethods
Commit: 7e3da3eed77eb98b3f5c840cb729b44e05ed7b72
Author: vobencha <vobencha@gmail.com>
Date: 2018-10-30 11:54:27 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
Package: pcaMethods
Commit: a63e50ea325b245cd93d71dae2f02a8db9101b2c
Author: vobencha <vobencha@gmail.com>
Date: 2018-10-30 11:41:43 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
Package: pcaMethods
Commit: 9d8ddf062f9d17a3d357535445da6eb9c16d6dc2
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-08-30 13:53:59 -0400
Commit message:

 replace BiocInstaller biocLite mentions with BiocManager
Package: pcaMethods
Commit: 713a270b43a09401726d4e3def2a9e49984e1430
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2018-04-30 10:41:37 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_7 branch
Package: pcaMethods
Commit: a78a6357fd4457477d3d2eb5229a3358a95e1e5e
Author: vobencha <valerie.obenchain@roswellpark.org>
Date: 2018-04-30 10:35:05 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch
Package: pcaMethods
Commit: 0209b9afad0354c9a3081e6f8df5b15b3a8aa9b2
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-10-30 12:52:06 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_6 branch
Package: pcaMethods
Commit: 700f713e41e8c2ebe10879538406fd2e7d44ab93
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2017-10-30 12:39:18 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch
Package: pcaMethods
Commit: 321974b22c2185a123b78fad00458086fd8533b9
Author: Herve Pages <hpages@fhcrc.org>
Date: 2017-04-24 19:50:57 +0000
Commit message:

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 8f00d97843792fdb7f9399675e6f0fb024452a63
Author: Herve Pages <hpages@fhcrc.org>
Date: 2017-04-24 19:25:24 +0000
Commit message:

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 488cede62f232838a811dfa2af1b2248e87ae5a3
Author: Herve Pages <hpages@fhcrc.org>
Date: 2016-10-17 19:10:43 +0000
Commit message:

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@122712 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 963f3dcb37fb490b8a4fbe419bb3002ed3e4567c
Author: Herve Pages <hpages@fhcrc.org>
Date: 2016-10-17 18:45:06 +0000
Commit message:

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@122710 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: e5cd0cb7d7b36fcaf27c1c0ef897ebebedc7050b
Author: Dan Tenenbaum <dtenenba@fhcrc.org>
Date: 2016-05-03 21:30:44 +0000
Commit message:

 bump version after creating 3.3 branch


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@117081 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 23ce62afe6f93c2ebde2ff84cab492b3e2c07116
Author: Dan Tenenbaum <dtenenba@fhcrc.org>
Date: 2016-05-03 21:20:18 +0000
Commit message:

 Bump versions prior to creation of 3.3 branch


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@117079 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: d16ac113f675040d921ea44ccd17f43eaed892d0
Author: Henning Redestig <henning.red@googlemail.com>
Date: 2016-01-30 20:30:22 +0000
Commit message:

 add example for ggplot

From: Henning Redestig <henning.red@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@113107 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 18e687675bc507abccc7a7d187aa78bceb51857e
Author: Henning Redestig <henning.red@googlemail.com>
Date: 2016-01-17 17:20:20 +0000
Commit message:

 not kept up-to-date anymore

From: Henning Redestig <henning.red@gmail.com>

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@112639 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 6d471a021d963e413fbc55c191625da3829f193e
Author: Henning Redestig <henning.red@gmail.com>
Date: 2016-01-16 21:08:20 +0100
Commit message:

 to try a git-svn commit
Package: pcaMethods
Commit: 101ba26eaee6b4632b359ac3aa0be5801b86e113
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2016-01-16 19:57:25 +0000
Commit message:

 tons of changes from git




git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@112623 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 342fa27cc5ab1d18af810dcee91df924c794959c
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-10-13 19:59:53 +0000
Commit message:

 Bumped version number of all packages after creation of 3.2 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@109592 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: ff94012cc9578d959c68a8d74ea578338d0b48db
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-10-13 19:36:05 +0000
Commit message:

 Bumped versions of all packages prior to creating 3.2 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@109589 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 0cf5a716903e9763a6974bf4bd6633873b8077d0
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-04-16 20:02:44 +0000
Commit message:

 Bump versions in trunk after creation of 3.1 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@102594 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 66bf7bae278f818fad8dac81e3f54be61c916052
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-04-16 19:42:01 +0000
Commit message:

 Bump versions prior to creating 3.1 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@102591 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 8b9c8b17dab267c5a9b530cac1a43ea1c36bd2b1
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2015-02-07 11:32:32 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 1 commit.

Commit information:

Commit id: fcea96afcecf5f1c3613d343c2ada180d4a42659

    add variable specific cross-validation

Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2015-02-07 12:32:03 +0100
Author date: 2015-02-07 12:32:03 +0100


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@99185 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 9fb283fb7084b992cd88071f96ebf2bb8e6b4ce1
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-11-19 23:10:22 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 4 commits.

Commit information:

Commit id: 08b7fc9456072ec456fa2dd1c02cc52443d4423c

    continued cleanup

Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2014-11-20 00:06:27 +0100
Author date: 2014-11-20 00:06:27 +0100

Commit id: b59e61f4c08517259050bfb6c55125d3940bdbc4

    Merge branch 'master' of https://github.com/hredestig/pcaMethods

    Conflicts:
    	DESCRIPTION
    
Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2014-11-17 22:11:59 +0100
Author date: 2014-11-17 22:11:59 +0100

Commit id: fdd14fbf6f8047ebc2dc295bb2614e56a8569d91

    squash! cleanup action

Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2014-11-17 22:09:25 +0100
Author date: 2014-11-17 22:09:25 +0100

Commit id: d29a57cde2c8d1bf6efcd1c5404033f0c597a155

    cleanup action

    - stop using Makevars scripts as new Rcpp does not need them
    - get rid of R cmd check warnings
    
Committed by: Henning Redestig
Author Name: Henning Redestig
Commit date: 2014-11-17 21:47:24 +0100
Author date: 2014-11-17 21:46:13 +0100


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@96928 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 51f85639049adfd4f95962fafaec748c99b2cc0e
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-13 21:47:41 +0000
Commit message:

 Bumping versions after creating 3.0 release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@95443 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: dfed52d232366e2ad97ec8f06cc3ce28e5d4b4a4
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-10-13 21:38:33 +0000
Commit message:

 Bump package versions prior to creating the 3.0 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@95439 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: c77bafa848c894deb37c3a03ed9e0ac275936995
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-04-11 21:21:21 +0000
Commit message:

 Second version bump after creating 2.14 release branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@88840 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: f66d050e820d5cc09db24ccd7576ccfc45eb6a58
Author: d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-04-11 21:07:21 +0000
Commit message:

 First version bump prior to creating 2.14 branch.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@88838 bc3139a8-67e5-0310-9ffc-ced21a209358
Package: pcaMethods
Commit: 10f5e59201362a26d1279e11c4fd76462016f554
Author: h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358>
Date: 2014-03-24 21:12:26 +0000
Commit message:

 Commit made by the Bioconductor Git-SVN bridge.
Consists of 3 commit(s).

Commit information:

    Commit id: a6284fd51282c74c8156434ceee8688cf8f9d084
    Commit message:
    add llsImpute and llsImputeAll to the all methods to make it work with kEstimate
    Committed by Henning Redestig 
    Commit date: 2014-03-12T22:33:22+01:00

    Commit id: cd00c5e11215bb49b0b35808476b8faa117360a2
    Commit message:
    use na.rm=TRUE for weightedMedian for proper handling of missing values in robustPca
    Committed by Henning Redestig 
    Commit date: 2014-03-12T22:34:33+01:00

    Commit id: 3c515ce2ce739b2f931d314bc378eaff6174bee4
    Commit message:
    bump versin
    Committed by Henning Redestig 
    Commit date: 2014-03-24T22:11:48+01:00

From: Bioconductor Git-SVN Bridge <bioc-sync@bioconductor.org>

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@87810 bc3139a8-67e5-0310-9ffc-ced21a209358
 </pre>
    </div>
  
    

      Package: pcaMethods

      Commit: 91b14f7010ad8d21c5eb715c432de361ae8b8091

      Author:  s.arora <s.arora@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2014-03-04 22:12:21 +0000

      Commit message:


	  
		
 modify to new biocViews to DESCRIPTION file



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@87035 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 9fb822772ef756fe3ff34f2e73549eded5feb8db

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2014-02-04 18:07:39 +0000

      Commit message:


	  
		
 bumped version as all packages that depend on Rcpp must be rebuilt

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@86058 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 5339af4dd516227c2d29fd9ac41f3a4fceeba841

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2013-12-01 12:26:56 +0000

      Commit message:


	  
		
 switch to ISNAN for c++ compatbility

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@83778 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 1e12da7d21c6b72f8e31815dbd46b4851ef78935

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2013-10-14 21:47:19 +0000

      Commit message:


	  
		
 bump version after release branch has been created

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@81644 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 6227b7c294fadbf3ae4ec100836dde4590d0b4bc

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2013-10-14 21:29:21 +0000

      Commit message:


	  
		
 bump versions prior to creating BioC 2.13 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@81642 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: a356662523247289d14dd59ce9fef3db3654c8ce

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2013-04-03 22:06:11 +0000

      Commit message:


	  
		
 Bump y in version x.y.z to odd number in devel

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@75270 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 01fe07daa6fa9c7bfdcb52e568cf56631435b046

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2013-04-03 21:32:27 +0000

      Commit message:


	  
		
 bump y of x.y.z version number for BioC 2.12 release

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@75263 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 0943dd6dbafba79cb3b2455a1b83d6a87ff56d71

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2013-03-12 21:43:34 +0000

      Commit message:


	  
		
 remove wrong warning about missing values in robustPca

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@74244 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: fd0500893ac0aa9c994d66ce02f869313f8b76df

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-10-01 22:43:56 +0000

      Commit message:


	  
		
 bump package versions after creating 2.11 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@70052 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 85a3e447d79a2ec403ef0379d2410b44b008aa18

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-10-01 22:16:24 +0000

      Commit message:


	  
		
 Bump all packages before creating 2.11 branch.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@70050 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 7d4a347098004e884526adb1edf3c3f2e0787863

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-09-12 18:57:14 +0000

      Commit message:


	  
		
 weightedMedian is moving out of aroma.light so switch dependency

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@69380 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 104edc34c9e3f63ac0cc431f7391b1a26be0107e

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-07-18 17:37:10 +0000

      Commit message:


	  
		
 bug in docu

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67793 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 2c8f1eca9b2c21f850195f05df471059586e2e58

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-07-16 21:04:56 +0000

      Commit message:


	  
		
 bug in progressbar for xval

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67696 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 4e991a5788968db030cfbf7d5a3ed6a9c5d842a6

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-07-10 05:32:59 +0000

      Commit message:


	  
		
 summary function repaired

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67495 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: d6ac9a117f83aad56eec34b96c78499905bb097e

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-07-09 21:46:08 +0000

      Commit message:


	  
		
 version info update


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67485 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 23b8806bd0add6b3b920bcda4b25cc9e7b9f7d70

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-07-09 21:40:36 +0000

      Commit message:


	  
		
 now warns if user sets svd for data with missing values

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67484 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 6c4a5ea198e50c903b313f604c642c43070b4787

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-07-09 06:11:59 +0000

      Commit message:


	  
		
 bad args for txtp


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67457 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 145fa2d036aa52af47a223bab3d687ba96389b23

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-07-08 21:37:48 +0000

      Commit message:


	  
		
 handle data frames, convert ot data frames'



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@67437 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 92c1f22d36fac5f45ac843d5f82a2c04fae72fee

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-06-18 21:54:56 +0000

      Commit message:


	  
		
 bump version again

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66810 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: cfdf8f55d14fdcfbdf832aab566bdfd34b32a0bc

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-06-18 21:54:12 +0000

      Commit message:


	  
		
 export scores.pcaRes to avoid breaking packages that also load the pls package and thereby mask the S4 method from pcaMethods

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66809 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 4c19a97f6dac5a2c05b8629d4ed5164ab569bcc1

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-06-16 09:59:06 +0000

      Commit message:


	  
		
 and re-bump version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66772 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: fbab93099ca4a5991f5f465de2ed0453afa2ad21

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-06-16 09:58:20 +0000

      Commit message:


	  
		
 forgot to commit new file

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66771 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 48b81705fdda9bbd84e0e8b42d9579d3733ec77b

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-06-14 20:54:43 +0000

      Commit message:


	  
		
 cleanup, and hopefully better organization of S3/S4 methods

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@66741 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: ee5193b393c2bcfed58e0406639cb6d1ecaab346

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-03-30 22:15:56 +0000

      Commit message:


	  
		
 bumped version numbers after creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@64680 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 88836da15aded643266a3efb00583588f280b308

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-03-30 22:05:02 +0000

      Commit message:


	  
		
 first version bump prior to creating 2.10 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@64678 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: f920db61aab026143faa24c48d014bab07283083

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-03-09 22:58:23 +0000

      Commit message:


	  
		
 import residuals from BiocGenerics

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@63704 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 1be2ecc40ac4593940c1fe14d6d997ecadffaa7d

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2012-03-05 19:53:55 +0000

      Commit message:


	  
		
 added setGeneric(residuals)

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@63492 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: e80d2b2b8d0fa78d75b7588a51999be2da1218ce

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2011-10-31 23:12:28 +0000

      Commit message:


	  
		
 version bump for start of 2.10 development cycle

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@59924 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 9f8e182c665c151c4814611dfbc17939a31e43b2

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2011-10-31 22:59:03 +0000

      Commit message:


	  
		
 bumped package version numbers prior to creating 2.9 branch

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@59920 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 61fb07debed8877271ee9fc1d2845da4a85a4361

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2011-05-31 21:32:08 +0000

      Commit message:


	  
		
 cope with new roxygen version

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@55927 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: a1fbb1de55450e6978b578fa139a20181468f7e2

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2011-05-31 20:10:54 +0000

      Commit message:


	  
		
 error fix in dmodx function

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@55924 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: bf1519740ccbbfbd47d1f13293ff1e6bcde00967

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2011-04-13 22:36:43 +0000

      Commit message:


	  
		
 Bumped version numbers again for new BioC 2.9 devel cycle.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@54802 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: da17ae02ca8053323a1a85d801a54fbdb8f5a69a

      Author:  d.tenenbaum <d.tenenbaum@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2011-04-13 22:27:35 +0000

      Commit message:


	  
		
 Bumped version numbers for BioC 2.8 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@54800 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: e377f8952733a3cbf2abcf686d9351e6f5a4b5a0

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2011-01-17 14:41:39 +0000

      Commit message:


	  
		
 appears i forgot to bump version number


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@51949 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 58dd7d6b5738583029fc043b12d9686a499b7598

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-11-28 10:31:31 +0000

      Commit message:


	  
		
 use NumericMatrix everywhere for consistency

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@51082 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 73ce94d31672b25fad800e5458be096db3476a0c

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-11-28 10:16:38 +0000

      Commit message:


	  
		
 changes in Rcpp

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@51081 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: d7b81d8d8ed6aa94c9b439d3cb85d97b79dfc591

      Author:  hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-10-18 05:57:44 +0000

      Commit message:


	  
		
 Bumped version numbers again for new BioC 2.8 devel cycle.
ERRATA: Previous bump was for BioC 2.7 release (of course), not 2.6!


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@50295 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 24494e1bf6c01b70c20e023fa142f04e57af47a1

      Author:  hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-10-18 05:34:23 +0000

      Commit message:


	  
		
 Bumped version numbers for BioC 2.6 release


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@50293 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: cd83287f496a023c74b97b7192c99243360f5e84

      Author:  hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-09-12 07:02:07 +0000

      Commit message:


	  
		
 Rterm.exe changed location in R-2.12, better to use R.exe

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@49356 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 63682a6d0034a3e52c9dab21b70e9cef4992907e

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-04-22 18:45:15 +0000

      Commit message:


	  
		
 Bumped version numbers for BioC 2.7 trunk

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@46405 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 93337ad711d95d2bebf7c09bf50e9c1f488901cb

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-04-22 18:21:23 +0000

      Commit message:


	  
		
 Bumped version numbers for BioC 2.6 release

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@46401 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 09c0f85901c2dcd0de33bb16cecf5e35c0f15e4c

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-03-31 00:21:32 +0000

      Commit message:


	  
		
 version bump


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@45604 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 01696ad4a190203c9331633d88bf17e591cd8d30

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-03-31 00:17:05 +0000

      Commit message:


	  
		
 bug fix in pareto scaling which caused it to revert to uv scaling


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@45603 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 10225e7d039de4bf496599e2b5f0518f06467d08

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-02-28 13:10:23 +0000

      Commit message:


	  
		
 added subset slot again for capius sake

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44926 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 75b55c4f43032692e10a09d5a4d834526d867968

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-02-28 12:13:10 +0000

      Commit message:


	  
		
 fix subsetting problem

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44925 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 6498ae29f29e38d96e8b81472e82ca716e45d043

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-02-05 08:29:25 +0000

      Commit message:


	  
		
 tjo

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44517 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 096f7d3368124935b2b20f49c1a25f404df337ae

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-02-04 04:04:30 +0000

      Commit message:


	  
		
 added missing argument descriptions 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44483 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: c97c05a843965286b7f3f48dd4e6fde2f1a3c4ce

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-23 05:29:07 +0000

      Commit message:


	  
		
 more documentation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44188 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 303d40ab4fe10a6a53fbc8d9bc080c7a00dcb60c

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-23 05:25:39 +0000

      Commit message:


	  
		
 migration to roxygen and improved pre-processing

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@44187 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 1c46bfdac9e48275b176b59f18eab96c0b156939

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-08 01:42:37 +0000

      Commit message:


	  
		
 just a reformat of the news file. Nicer for emacs users shouldn't matter for vim users.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43898 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 07ad4e6d5b69feb3c6e08b85d7485f6de7e1348f

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-05 08:40:36 +0000

      Commit message:


	  
		
 bugfix in xval

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43850 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 50d0cb91f111a09246eb7aba6ffbad5302a39066

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-05 07:28:28 +0000

      Commit message:


	  
		
 previous fix

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43849 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: ebeecf379652ee9a21918521b1e57600b779de78

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-05 07:15:37 +0000

      Commit message:


	  
		
 bug in Krzanowski CV

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43848 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: edec6cf851cd49213ba6c96f95c7f06a43f236ab

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-05 06:07:19 +0000

      Commit message:


	  
		
 new makevars scripts, previous didnt work because Rscript is not in path

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43847 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 435f1aac4fd8e99ec9a973df019ac56d19331eeb

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-05 05:31:13 +0000

      Commit message:


	  
		
 Rscript not reachable on bioconductors test servers so trying env R instead

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43845 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 7ec0101936315185684586990566c1582eb9daae

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-04 01:42:36 +0000

      Commit message:


	  
		
 cpp version of nipals delivers same results as R version now on iris and metaboliteData

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43819 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 19974019d478cc582bfe1348ef2e41cdb7635482

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2010-01-02 15:22:23 +0000

      Commit message:


	  
		
 C++ version of nipalsPca still gives wrong R2

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43813 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 1b6e3a6166b59408d167e3bd2f8e2b59c2851860

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-12-30 04:47:45 +0000

      Commit message:


	  
		
 improved cv including cv for svd type pca

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@43787 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 31d439d517d84ec61b61760c357d5d84d6a2706a

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-11-02 01:41:34 +0000

      Commit message:


	  
		
 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42777 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 49c78f5f3c0631b6248d879ba11c1ec2827ac79b

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-11-02 01:41:09 +0000

      Commit message:


	  
		
 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42776 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 947fea686e9d829e76752c781e1ef52c9462d74d

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-11-02 01:39:42 +0000

      Commit message:


	  
		
 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42775 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: bba2c39cd171f887f625df5598bf20ff3e06df54

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-11-02 01:38:45 +0000

      Commit message:


	  
		
 must be in inst

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42774 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 6c0defe77a0af5c0e5067d03c06c61ef3392d7cd

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-11-02 01:20:56 +0000

      Commit message:


	  
		
 added citation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42773 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: faac0a3552f6e6441b13c053348233703ba166ed

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-10-27 23:45:24 +0000

      Commit message:


	  
		
 Package version bump for BioC 2.6 devel.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42686 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: be40d9c1339995fdea9e3e0de30cd7ead6629bc9

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-10-27 23:33:29 +0000

      Commit message:


	  
		
 Package version bump for BioC 2.5 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42684 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 39731fea6ff210e6e8814f730b29542b66ef5a68

      Author:  c.wong <c.wong@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-09-29 23:44:36 +0000

      Commit message:


	  
		
 Fixed Rd files with duplicatd name 'pcaRes' by changing the name tag of
class.nlpcaNet.Rd to 'pcaNet', instead of 'pcaRes'.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@42054 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 05aa5255374a14acdf411526e87f7637121d08f8

      Author:  n.gopalakrishnan <n.gopalakrishnan@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-09-24 20:03:23 +0000

      Commit message:


	  
		
 Fixed man page warnings

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@41936 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: f7cc5099800bdba964b9dd8976e41cbf49291786

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-09-06 03:06:55 +0000

      Commit message:


	  
		
 Reformatted the Licence information in DESCRIPTION files to bring them into compliance.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@41539 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 23a9cbc71fbc1549bc1a048f4180b83cca3e7238

      Author:  w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-07-09 02:37:27 +0000

      Commit message:


	  
		
 added missing slots to class documentation

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@40572 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: c49acbb9a8de7ea77cf33d06447564b3b7d1bc85

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-04-20 23:44:07 +0000

      Commit message:


	  
		
 Bumped pkg versions for BioC 2.5 devel line.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@39015 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: e2e010442fb47250ed7889a1931ea845df103490

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-04-20 23:24:12 +0000

      Commit message:


	  
		
 Bumped pkg versions for BioC 2.4 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@39013 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 8b1f79ded2381e0c82ab54453adfde6592bfa929

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-03-19 22:07:09 +0000

      Commit message:


	  
		
 Changed biocViews entry of Statistics to Bioinformatics.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@38070 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 61ea818026766c9a64732a326ce262d01a1f0551

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-03-11 11:09:32 +0000

      Commit message:


	  
		
 added kevin's biplot function and some getter functions

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@37906 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 037d27fd7cfc095ceb81346c1e614dbc2611abcc

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-02-23 10:37:28 +0000

      Commit message:


	  
		
 bugfix

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@37565 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 795fa028d29271a2780c6efe859d9c70ede2058d

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-02-23 05:12:30 +0000

      Commit message:


	  
		
 added predict and residuals methods

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@37564 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: d3576d34aa4e428cdcad48209f8bddf972b2407c

      Author:  c.wong <c.wong@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2009-02-06 18:54:46 +0000

      Commit message:


	  
		
 fixed Rdversion 2 parser warnings  


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@37210 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 2455aa683924f6c3ae3a030867703839c900f801

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2008-10-29 07:56:51 +0000

      Commit message:


	  
		
 Fixed warnings and notes

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34968 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 376fd7f82e593d4728329632a2556a4d6838e15e

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2008-10-27 05:55:03 +0000

      Commit message:


	  
		
 mistake..

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34912 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 428e9357e3e0c16971c9ae5bd764fa920eedf135

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2008-10-27 05:50:42 +0000

      Commit message:


	  
		
 Fixed slplot so that it accepts differnt arguments for the scores and loading plots and complains if sl and ll are of wrong size. Added a show method as that often is the default function and not print. Small bugfix in nipals pca. Nipals pca is however poorly tested and might change again soon.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34911 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 4958f209271f2359e1671524ea2bc506f63e9c2f

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2008-10-21 22:46:31 +0000

      Commit message:


	  
		
 Bumping version numbers for BioC 2.4 devel.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34814 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: c6c217cdfafcb0cff00282904a617f64d224943e

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2008-10-21 22:32:58 +0000

      Commit message:


	  
		
 Bumping version numbers for BioC 2.3 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@34811 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: fd7c053d928e8c4dbb35b6644f4c62bbfd11e7fc

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2008-04-30 00:25:58 +0000

      Commit message:


	  
		
 Updating the version number for the trunk post-BioC 2.2 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@31432 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: e0e6a4f5929b6ea86796266e478ccb8296d155df

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2008-04-29 23:50:18 +0000

      Commit message:


	  
		
 Updating the version number for the BioC 2.2 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@31430 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 84b7c0b8d1ca5e9b12bc1bf559dcdd87099e20a7

      Author:  p.aboyoun <p.aboyoun@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2008-02-27 23:36:54 +0000

      Commit message:


	  
		
 Replaced usage of soon to be defunct class exprSet with ExpressionSet.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@30244 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 303168d85180d0535a4c58a753dcfd9f0adc8e99

      Author:  w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-10-08 10:33:45 +0000

      Commit message:


	  
		
 Fixed tiny bug in the slplot function preventing the ellipse to be drawn

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@27836 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: de59d20530a66052dcf60d6f9effdc05999c7062

      Author:  hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-10-03 01:16:39 +0000

      Commit message:


	  
		
 2nd version bump: bumped y to y+1 in version number x.y.z for all packages in bioc_2.1.manifest (so now y is odd again in trunk).

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@27716 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 76e5b19a0f3658d81bd93761e38edca7599dc394

      Author:  hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-10-03 00:41:09 +0000

      Commit message:


	  
		
 1st version bump: bumped version number x.y.z of all packages in bioc_2.1.manifest (if y was odd: y<-y+1, if y was even: y<-y+2, in all cases z <- 0).

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@27709 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 1571c1be378eb4990d226722b6962dc105c8e7a0

      Author:  mtmorgan@fhcrc.org <mtmorgan@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-09-25 18:26:10 +0000

      Commit message:


	  
		
 Remove dependence on R without version specification

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@27507 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: b9b8af5a8cbcf85fb9901f8582a25318376c9c16

      Author:  h.redestig <h.redestig@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-06-15 06:46:22 +0000

      Commit message:


	  
		
 Applied Kevin Wrights diff for faster nipals. Nipals PCA really should be re-written in C for further speed improvement

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@25394 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: a02542e0d0239e78145f2988686192fd99c477fa

      Author:  sethf <sethf@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-05-12 04:56:41 +0000

      Commit message:


	  
		
 SaveImage is deprecated, using LazyLoad instead


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24616 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: e26bf31b453a7a3fcc9166d2327f1897d8d33699

      Author:  hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-24 18:31:42 +0000

      Commit message:


	  
		
 Bumped again version number x.y.z for all packages in bioc_2.0.manifest (y<-y+1).

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24217 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: ae676d3080dca7019e76f88322318b1e29662869

      Author:  hpages@fhcrc.org <hpages@fhcrc.org@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-24 18:21:48 +0000

      Commit message:


	  
		
 BioC 2.0 release version bump: bumped version number x.y.z for all packages in bioc_2.0.manifest (if y was odd: y<-y+1, if y was even: y<-y+2, in all cases z <- 0).

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24214 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 26bb63c8af153b1d3f28dde3d592018f28a95354

      Author:  w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-20 08:09:12 +0000

      Commit message:


	  
		
 svnImpute returned too many scores/loadings, this was fixed. And now we also assign correct row/column names to scores/loading matrices

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24065 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: f1d2ec5d8c429b0d135966f6d2e85bf3229e9901

      Author:  w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-19 02:19:08 +0000

      Commit message:


	  
		
 nipals(center=T) was also accidentially sclaing the data, as we used scale(data, center=T). This has been fixed.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@24012 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: c2ee00ec4a9fedd0b0ca810ab78291c1e8e58348

      Author:  w.stacklies <w.stacklies@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-13 07:18:48 +0000

      Commit message:


	  
		
 added .onLoad method, SaveImage in DESCRIPTION was set to true. Lets hope this will fix the check error on bioconductor

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23835 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 51a3e59aef6c59ba609cb603da9863b25086b503

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-10 07:16:02 +0000

      Commit message:


	  
		
 little bug in vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23724 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 66c31a7c547e4d247090c28976f0f51488877d26

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-10 07:11:53 +0000

      Commit message:


	  
		
 added vingette discussing handling of data with outliers

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23723 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 8d0085346e700ca5cbf50b4602890846f7f8d768

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-10 02:40:52 +0000

      Commit message:


	  
		
 

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23717 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: c367d43e21231faaeca866dc4a035aba8bcd2f8b

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-04-10 02:40:23 +0000

      Commit message:


	  
		
 added a svd method that is robust to outliers. Also a pca method based on this robust svd.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@23716 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 8cf2bb8a582a9417403287377704e4b5c3289afc

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-27 17:03:46 +0000

      Commit message:


	  
		
 '}' missing


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22857 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: cf432a2feda2b8ddfd291f1a49063a56f6851cdb

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-27 13:24:13 +0000

      Commit message:


	  
		
 added docu for the asExprSet function

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22855 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 62aaa8303db3d2d78291be2d4e9fd2bcc9747803

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-25 17:35:41 +0000

      Commit message:


	  
		
 changed number of components for kEstimate to 5 to speed vignette creation up a bit.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22820 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: a241126fcfee847548238e996f6a63897e20bd5a

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-25 16:44:45 +0000

      Commit message:


	  
		
 New method to convert pcaRes to exprSet, pca() does no longer retrun an exprSet object if exprSet was given as input, use asExprSet instead. Fixed a bug in the missing value vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22819 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: fd0e499254ea0334632a85013149dec03f6158de

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-23 14:32:39 +0000

      Commit message:


	  
		
 added vignette on missing value estimation for those who only wants that

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22792 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 613ca4b0d018934a7f1073fd0fde40c838b6bb18

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-21 11:01:09 +0000

      Commit message:


	  
		
 Removed ellipse dependance by adding a simple (unexported) function for computing Hotelling ellipses. Added a todo file with some random thoughts that occured to me whilst using pcaMethods.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22722 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: b494a22178b406163d914a949447acc9d1ae60b8

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-15 07:38:45 +0000

      Commit message:


	  
		
 Documentation updates, fixed a latex bug that prevented the package from beeing build correctly

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22633 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 102e25bb13db53f85b4e0ba85958af5d10d05a9e

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-14 06:36:55 +0000

      Commit message:


	  
		
 kEstimate was not implemented in the fastest way :) This has been fixed now. Also it is now possible to get the estimation error for each individual incomplete variable. This allows to easily see for wich variables missing value imputation makes senes, and from wich we should better keep our fingers off.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22623 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 47627b4ed275e3a3d77ed6e6f2b1fd4fd9280cf1

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-09 10:44:50 +0000

      Commit message:


	  
		
 Forgot to do a cvs add :))

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22500 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 04f0809d627f8fed03d78c11db39af082c040494

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-09 10:43:44 +0000

      Commit message:


	  
		
 Added a new method called kEstimateFast. This also estimates the best number
of components / similar genes for missing value estimation. In contrast to
kEstimate no cross validation is performed. The method just used 
original - estimate for all complete observations. This is a more rough
estimate than provided by kEstimate.

Fixed a bug in kEstimate and nlpca.

Documentation updates.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22499 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 66528bb732c2da2da8ff3d1617d3f5df54f24617

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-07 12:33:18 +0000

      Commit message:


	  
		
 Bugfix in docu regarding kEstimate change


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22462 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: a8581983add70ab3b1a42b7ed801adf21f87de13

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-05 17:06:11 +0000

      Commit message:


	  
		
 Upgraded (hopefully) plotPcs so it works with Sweave and gives prettier output by basing it on pairs() instead of the not so beatiful slplot()

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22431 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: b072dc100905d70504d17a946bab6e8804a8c12f

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-05 16:08:29 +0000

      Commit message:


	  
		
 K-Estimate now supports NRMSEP and Q2 as error measure.
Some documentation updates.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22429 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: df100043fb5311332315bf65a1d3adce0c3d4a2b

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-05 07:24:06 +0000

      Commit message:


	  
		
 Tiny bugfixes and I bumped to 1.7.0 as this should be considered a
devel version and not release. Lets stay on 1.7.Z until everything
works as meant.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22423 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 58f7f6011e4135da09c0c38b7d5fd77b971f1bdd

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2007-02-02 14:52:59 +0000

      Commit message:


	  
		
 Added support for Non-linear PCA and made corresponding additions to
the documentations. Also added simulated example data for use with
nlpca.

Changed Q2 cross-validation to guarantee that no full column or row is
ever deleted. This is done by deleting diagonals from the matrix
instead of values with random indices. The drawback here is that no
less than a full diagonal can be deleted so the possible folds are
limited, but this should be of no practical importance.

The screeplot function was removed and replaced with plotR2 as
screeplot is a generic function from stats with a rigid definiton
which can not be safely modified (npcs in argument vs nPcs e.g.). 

Removed exclamation marks from warnings, messaged. I find them
obnoxious. Also, i changed the use of the word 'gene' as a row in an
expression matrix is not a 'gene' but a _variable_ measuring the
expression estimates of a gene.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@22378 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 3a37959fe69aedefae5ecadc256dcbfe6ab24ca3

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2006-12-13 02:58:21 +0000

      Commit message:


	  
		
 This is a major update of pcaMethods.

A missing value estimation method called llsImpute was included 
to allow better rating and comparison of the obtained results.
The method is based on the paper by Kim et al, Bioinformatics 2005,
for details see the documentation.
Together with this method the nniRes (nearest neighbour imputation)
was introduced, serving as return object for missing value estimation
based on nearest neighbour imputation.

Further updates:
ppca : The threshold was changed to 1e-5, this leads to much more stable
  results
kEstimate : The interface changed slightly, maxPcs was replaced by evalPcs.
  Now the user may enter arbitrary arrays of integer numbers, e.g. c(2,5,6)
  or 1:5 or 4:10.
pca : now includes method nni, a wrapper for llsImpute, similar to pca.
  A new print method for class nniRes was also included.

Some documentation updates. 



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@21474 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: ee6231e13513ec3c0138f187d6b008bbc10a77c1

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2006-10-23 19:23:36 +0000

      Commit message:


	  
		
 - changed threshold in ppca to 1e-5. This will lead to more stable results.
- Added parameter skipInac to decide weather inaccurate vectors of the orthonormal
  base should be skipped or not. FALSE is the default value, this is the opposite
  behaviour than in the 1.9 version. However receiving results of lower dimension
  than expected often leads to errors.
- Updated vignette, the syntax was not uniform, e.g. we were talking about
- eigenvectors, loadings, PCs, etc. Now we refere to loadings throughout the
  whole document.
- Added a picture explaining why pca does not define a density model.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@20786 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 5f0bf7d3d468d8d1446ba725a81e95b45002bbbd

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2006-10-18 16:11:52 +0000

      Commit message:


	  
		
 Removed \cr from vingnette that caused errors during build

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@20649 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
    

      Package: pcaMethods

      Commit: 57d4c8093dfe3b95e5a10cf8ce7eea1b436ac064

      Author:  stacklies@mpimp-golm.mpg.de <stacklies@mpimp-golm.mpg.de@bc3139a8-67e5-0310-9ffc-ced21a209358> 

      Date: 2006-10-18 15:20:52 +0000

      Commit message:


	  
		
 kEstimate now prints a warning when the method is used on complete matrices without the allGenes = TRUE option.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods@20645 bc3139a8-67e5-0310-9ffc-ced21a209358
 

    

  
  


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