1. crlmm
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:04:22
Showing 1 changed files
DESCRIPTION
History View file @ 5bac5c8
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.56.0
5 
+Version: 1.57.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:04:22
Showing 1 changed files
DESCRIPTION
History View file @ 90f1862
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.55.0
5 
+Version: 1.56.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:02:46
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DESCRIPTION
History View file @ 94edd96
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.54.0
5 
+Version: 1.55.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:02:46
Showing 1 changed files
DESCRIPTION
History View file @ 1eefa13
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.53.0
5 
+Version: 1.54.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:53:43
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DESCRIPTION
History View file @ 8ed9c38
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.52.0
5 
+Version: 1.53.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:53:43
Showing 1 changed files
DESCRIPTION
History View file @ 9ecc85f
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.51.0
5 
+Version: 1.52.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:42:53
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DESCRIPTION
History View file @ 26229e6
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.50.0
5 
+Version: 1.51.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:42:53
Showing 1 changed files
DESCRIPTION
History View file @ c3560d3
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.49.1
5 
+Version: 1.50.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

remove GGdata from suggests

rscharpf authored on 01/12/2020 15:51:33
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DESCRIPTION
History View file @ b690225
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.49.0
5 
+Version: 1.49.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
... ... 
@@ -19,7 +19,7 @@ Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
19 19 
         1.23.2), illuminaio, ellipse, mvtnorm, splines, stats,
20 20 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
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         matrixStats, VGAM, parallel, graphics, limma, beanplot
22 
-Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
22 
+Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats,
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         RUnit
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 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
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         methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
... ... 
@@ -27,7 +27,8 @@ Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
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         crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R plot.R
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         snprma-functions.R utils.R zzz.R test_crlmm_package.R
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 LazyLoad: yes
30 
-## Local Variables:
30 
+## Local Variables:
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 ## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
32 
-## End:
32 
+## End:
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 biocViews: Microarray, Preprocessing, SNP, CopyNumberVariation
34 
+RoxygenNote: 7.1.1
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:35:27
Showing 1 changed files
DESCRIPTION
History View file @ 88433a9
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.48.0
5 
+Version: 1.49.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:35:27
Showing 1 changed files
DESCRIPTION
History View file @ bb8c119
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.47.0
5 
+Version: 1.48.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:19:05
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DESCRIPTION
History View file @ 4d09e85
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.46.0
5 
+Version: 1.47.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:19:05
Showing 1 changed files
DESCRIPTION
History View file @ 162ee9a
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.45.0
5 
+Version: 1.46.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Remove dependency on SNPchip

rscharpf authored on 23/11/2019 12:40:06
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DESCRIPTION
History View file @ a836381
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@@ -16,7 +16,7 @@ Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>=
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         1.17.7)
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 LinkingTo: preprocessCore (>= 1.17.7)
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 Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
19 
-        1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
19 
+        1.23.2), illuminaio, ellipse, mvtnorm, splines, stats,
20 20 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
21 21 
         matrixStats, VGAM, parallel, graphics, limma, beanplot
22 22 
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:34:55
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DESCRIPTION
History View file @ f00f0ce
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.44.0
5 
+Version: 1.45.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:08:04
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DESCRIPTION
History View file @ 6f0bbea
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.43.0
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+Version: 1.44.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:10:49
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DESCRIPTION
History View file @ 813feae
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.42.0
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+Version: 1.43.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:11
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DESCRIPTION
History View file @ 7054c21
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.41.0
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+Version: 1.42.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:28
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DESCRIPTION
History View file @ 090f347
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.40.0
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+Version: 1.41.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:45
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DESCRIPTION
History View file @ 95b6fe6
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.39.1
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+Version: 1.40.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:47:04
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DESCRIPTION
History View file @ 7b66dd2
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.39.0
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+Version: 1.39.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:37
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DESCRIPTION
History View file @ 125b018
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.38.0
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+Version: 1.39.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:10
Showing 1 changed files
DESCRIPTION
History View file @ cc1a98e
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.37.1
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+Version: 1.38.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Bug fixes to illumina genotype calling when using cdfName="nopackage" option

mritchie authored on 19/04/2018 07:17:14
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DESCRIPTION
History View file @ d49c960
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.37.0
5 
+Version: 1.37.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

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

Hervé Pagès authored on 30/10/2017 16:52:08
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DESCRIPTION
History View file @ 5bf92ab
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.36.0
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+Version: 1.37.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

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

Hervé Pagès authored on 30/10/2017 16:39:25
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DESCRIPTION
History View file @ 150e13b
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.35.0
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+Version: 1.36.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

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/crlmm@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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DESCRIPTION
History View file @ e1264a4
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.34.0
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+Version: 1.35.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

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/crlmm@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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DESCRIPTION
History View file @ 17c862f
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
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-Version: 1.33.1
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+Version: 1.34.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Updated DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@126742 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 14/02/2017 07:24:29
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DESCRIPTION
History View file @ 73c9e5b
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.33.2
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+Version: 1.33.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Updated DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@126740 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 14/02/2017 05:45:37
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DESCRIPTION
History View file @ 9411738
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.33.0
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+Version: 1.33.2
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

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/crlmm@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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DESCRIPTION
History View file @ 3ff30f1
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2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.32.0
5 
+Version: 1.33.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

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/crlmm@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.31.2
5 
+Version: 1.32.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Added SNP plotting functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117175 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 06/05/2016 06:53:13
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@@ -1,8 +1,8 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 
-        Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.31.1
4 
+        Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
+Version: 1.31.2
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
... ... 
@@ -10,7 +10,7 @@ Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
10 10 
         <mritchie@wehi.EDU.AU>
11 11 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
12 12 
         arrays, as well as a copy number tool specific to 5.0, 6.0, and
13 
-        Illumina platforms
13 
+        Illumina platforms.
14 14 
 License: Artistic-2.0
15 15 
 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>=
16 16 
         1.17.7)
Browse code

Also added some new plotting options and updated version number

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117088 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 03/05/2016 23:41:15
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.31.0
5 
+Version: 1.31.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Added nopackage option for krlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117087 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 03/05/2016 23:39:54
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@@ -18,13 +18,13 @@ LinkingTo: preprocessCore (>= 1.17.7)
18 18 
 Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
19 19 
         1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
20 20 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
21 
-        matrixStats, VGAM, parallel
21 
+        matrixStats, VGAM, parallel, graphics, limma, beanplot
22 22 
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
23 23 
         RUnit
24 24 
 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
25 25 
         methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
26 26 
         methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
27 
-        crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R
27 
+        crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R plot.R
28 28 
         snprma-functions.R utils.R zzz.R test_crlmm_package.R
29 29 
 LazyLoad: yes
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 ## Local Variables:
Browse code

bump version after creating 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:30:44
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.30.0
5 
+Version: 1.31.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Bump versions prior to creation of 3.3 branch

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

Dan Tenenbaum authored on 03/05/2016 21:20:18
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.29.2
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+Version: 1.30.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

replace reference to texi2dvi with pdflatex as the former has been removed from MikTex

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@112478 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 12/01/2016 20:52:19
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.29.1
5 
+Version: 1.29.2
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Fixing contact information

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@112282 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/01/2016 20:29:51
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@@ -2,11 +2,10 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.29.0
6 
-Date: Sat Oct 18 14:34:17 EST 2014
5 
+Version: 1.29.1
7 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 7 
         Ruczinski, Rafael A Irizarry
9 
-Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
8 
+Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
10 9 
         Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie
11 10 
         <mritchie@wehi.EDU.AU>
12 11 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
Browse code

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

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.28.0
5 
+Version: 1.29.0
6 6 
 Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@109589 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:36:05
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.27.0
5 
+Version: 1.28.0
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 Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Bump versions in trunk after creation of 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@102594 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 20:02:44
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.26.0
5 
+Version: 1.27.0
6 6 
 Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Bump versions prior to creating 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@102591 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 19:42:01
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.25.1
5 
+Version: 1.26.0
6 6 
 Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

bug fix to krlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@101808 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 03/04/2015 00:01:45
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.25.0
6 
-Date: Thu Sep 25 21:06:19 EST 2014
5 
+Version: 1.25.1
6 
+Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

Bumping versions after creating 3.0 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@95443 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:47:41
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.24.0
5 
+Version: 1.25.0
6 6 
 Date: Thu Sep 25 21:06:19 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Bump package versions prior to creating the 3.0 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@95439 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:38:33
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.4
5 
+Version: 1.24.0
6 6 
 Date: Thu Sep 25 21:06:19 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Added support for humanexome12v1.2a chip

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@94521 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/09/2014 11:06:52
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.3
6 
-Date: Fri Sep 19 10:10:31 EDT 2014
5 
+Version: 1.23.4
6 
+Date: Thu Sep 25 21:06:19 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

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

Commit information:

Commit id: 736588e3d47fd58358f61ce2241bb2c85b4d9a0c

update to vignette to process previously unevaluated codechunks

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-19 10:14:04 -0400
Author date: 2014-09-19 10:14:04 -0400


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@94285 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/09/2014 14:22:04
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.2
6 
-Date: Mon Aug 25 21:43:53 EDT 2014
5 
+Version: 1.23.3
6 
+Date: Fri Sep 19 10:10:31 EDT 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

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

Commit information:

Commit id: 7a7b52509b1e09bf8d3f517244f90f9045d102ca
Commit message: Set enough.men and enough.women to FALSE by default in fit.lm3 function.
Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-08-25 21:44:19 -0400
Author date: 2014-08-25 21:44:19 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@93599 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 26/08/2014 01:45:03
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.1
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-Date: Mon 10 Jun 2014 15:10:27 EST
5 
+Version: 1.23.2
6 
+Date: Mon Aug 25 21:43:53 EDT 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

Changed tolerance allowed for reading in arrays with different numbers of probes (was 10000, now 4% of total number of probes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@91227 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 10/06/2014 23:43:33
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.0
6 
-Date: Mon 31 Mar 2014 18:08:54 EST
5 
+Version: 1.23.1
6 
+Date: Mon 10 Jun 2014 15:10:27 EST
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
... ... 
@@ -19,7 +19,7 @@ LinkingTo: preprocessCore (>= 1.17.7)
19 19 
 Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
20 20 
         1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
21 21 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
22 
-        matrixStats, VGAM
22 
+        matrixStats, VGAM, parallel
23 23 
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
24 24 
         RUnit
25 25 
 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
Browse code

Second version bump after creating 2.14 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88840 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:21:21
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2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.22.0
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+Version: 1.23.0
6 6 
 Date: Mon 31 Mar 2014 18:08:54 EST
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

First version bump prior to creating 2.14 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88838 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:07:21
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.21.9
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+Version: 1.22.0
6 6 
 Date: Mon 31 Mar 2014 18:08:54 EST
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Changes to krlmm to avoid error that occurs in k-means clustering when all intensities are identical

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88225 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 01/04/2014 02:51:49
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2 2 
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3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.21.8
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-Date: Fri Mar 28 16:26:10 EST 2014
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+Version: 1.21.9
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+Date: Mon 31 Mar 2014 18:08:54 EST
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

Removed crlmm::: from .R files and set saveDate=FALSE in genotype.Illumina() man page to clean up Notes and Warnings

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88085 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 28/03/2014 12:43:01
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History View file @ 1e41609
... ... 
@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.21.7
6 
-Date: Mon Mar 10 10:06:36 EST 2014
5 
+Version: 1.21.8
6 
+Date: Fri Mar 28 16:26:10 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
... ... 
@@ -21,7 +21,7 @@ Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
21 21 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
22 22 
         matrixStats, VGAM
23 23 
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
24 
-        ellipse, RUnit, VGAM
24 
+        RUnit
25 25 
 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
26 26 
         methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
27 27 
         methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
Browse code

Added back support for human1mv1c chip (accidentally deleted)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@87249 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 10/03/2014 04:38:28
Showing 1 changed files
DESCRIPTION
History View file @ b2dc56d
... ... 
@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.21.6
6 
-Date: Mon Feb 3 09:02:42 EST 2014
5 
+Version: 1.21.7
6 
+Date: Mon Mar 10 10:06:36 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

modify to new biocViews to DESCRIPTION file

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

Sonali Arora authored on 04/03/2014 22:12:21
Showing 1 changed files
DESCRIPTION
History View file @ d94b2bc
... ... 
@@ -1,58 +1,34 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 
-Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.21.5
5 
-Date: Mon Feb  3 09:02:42 EST 2014
6 
-Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 
-Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 
-Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
3 
+Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 
+        Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
+Version: 1.21.6
6 
+Date: Mon Feb 3 09:02:42 EST 2014
7 
+Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 
+        Ruczinski, Rafael A Irizarry
9 
+Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
10 
+        Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie
11 
+        <mritchie@wehi.EDU.AU>
12 
+Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
13 
+        arrays, as well as a copy number tool specific to 5.0, 6.0, and
14 
+        Illumina platforms
9 15 
 License: Artistic-2.0
10 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7)
16 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>=
17 
+        1.17.7)
11 18 
 LinkingTo: preprocessCore (>= 1.17.7)
12 
-Imports: methods,
13 
-         Biobase (>= 2.15.4),
14 
-         BiocGenerics,
15 
-         affyio (>= 1.23.2),
16 
-         illuminaio,
17 
-         ellipse,
18 
-         mvtnorm,
19 
-         splines,
20 
-         stats,
21 
-         SNPchip,
22 
-         utils,
23 
-	 lattice,
24 
-	 ff,
25 
-	 foreach,
26 
-         RcppEigen (>= 0.3.1.2.1),
27 
-	 matrixStats,
28 
-	 VGAM
29 
-Suggests: hapmapsnp6,
30 
-          genomewidesnp6Crlmm (>= 1.0.7),
31 
-          GGdata,
32 
-          snpStats,
33 
-	  ellipse,
34 
-	  RUnit,
35 
-	  VGAM
36 
-Collate: AllGenerics.R
37 
-	 AllClasses.R
38 
-	 methods-AssayData.R
39 
-	 methods-CNSet.R
40 
-	 methods-CNSetLM.R
41 
-	 methods-eSet.R
42 
-         methods-SnpSuperSet.R
43 
-	 methods-PredictionRegion.R
44 
-         cnrma-functions.R
45 
-	 cnset-accessors.R
46 
-         crlmm-functions.R
47 
-	 crlmmGT2.R
48 
-         crlmm-illumina.R
49 
-         krlmm.R
50 
-	 snprma-functions.R
51 
-         utils.R
52 
-         zzz.R
53 
-	 test_crlmm_package.R
19 
+Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
20 
+        1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
21 
+        utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
22 
+        matrixStats, VGAM
23 
+Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
24 
+        ellipse, RUnit, VGAM
25 
+Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
26 
+        methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
27 
+        methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
28 
+        crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R
29 
+        snprma-functions.R utils.R zzz.R test_crlmm_package.R
54 30 
 LazyLoad: yes
55 
-biocViews: Microarray, Preprocessing, SNP, Bioinformatics,CopyNumberVariants
56 31 
 ## Local Variables:
57 32 
 ## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
58 33 
 ## End:
34 
+biocViews: Microarray, Preprocessing, SNP, CopyNumberVariation
Browse code

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

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

Dan Tenenbaum authored on 04/02/2014 18:07:39
Showing 1 changed files
DESCRIPTION
History View file @ 8bfebd1
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.21.4
4 
+Version: 1.21.5
5 5 
 Date: Mon Feb  3 09:02:42 EST 2014
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

merged matt's changes on the collab branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@86002 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/02/2014 14:03:16
Showing 1 changed files
DESCRIPTION
History View file @ c27ba9c
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.21.1
5 
-Date: Wed Oct 30 21:42:52 EDT 2013
4 
+Version: 1.21.4
5 
+Date: Mon Feb  3 09:02:42 EST 2014
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@82281 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/10/2013 01:45:39
Showing 1 changed files
DESCRIPTION
History View file @ eaa7924
... ... 
@@ -1,13 +1,8 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-<<<<<<< HEAD
5 
-Version: 1.21.0
6 
-Date: Wed Oct 30 21:27:01 EDT 2013
7 
-=======
8 
-Version: 1.19.9
9 
-Date: Fri Oct 25 14:00:41 EDT 2013
10 
->>>>>>> 9a92fa5d0719c007647a5b14c24201d277db3f1b
4 
+Version: 1.21.1
5 
+Date: Wed Oct 30 21:42:52 EDT 2013
11 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
12 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
13 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

fix bug in construction of NChannelSet

- thanks to Alex Baras for finding and supplying patch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@82280 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/10/2013 01:45:34
Showing 1 changed files
DESCRIPTION
History View file @ 4d398a2
... ... 
@@ -1,8 +1,13 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
+<<<<<<< HEAD
4 5 
 Version: 1.21.0
5 6 
 Date: Wed Oct 30 21:27:01 EDT 2013
7 
+=======
8 
+Version: 1.19.9
9 
+Date: Fri Oct 25 14:00:41 EDT 2013
10 
+>>>>>>> 9a92fa5d0719c007647a5b14c24201d277db3f1b
6 11 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 12 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 13 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

merge with upstream change made at bioc

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@82279 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/10/2013 01:45:27
Showing 1 changed files
DESCRIPTION
History View file @ 34a5a07
... ... 
@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 4 
 Version: 1.21.0
5 
-Date: Tue Oct 01 14:48:41 EDT 2013
5 
+Date: Wed Oct 30 21:27:01 EDT 2013
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -53,3 +53,6 @@ Collate: AllGenerics.R
53 53 
 	 test_crlmm_package.R
54 54 
 LazyLoad: yes
55 55 
 biocViews: Microarray, Preprocessing, SNP, Bioinformatics,CopyNumberVariants
56 
+## Local Variables:
57 
+## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
58 
+## End:
Browse code

bump version after release branch has been created

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

Dan Tenenbaum authored on 14/10/2013 21:47:19
Showing 1 changed files
DESCRIPTION
History View file @ dfcb149
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.20.0
4 
+Version: 1.21.0
5 5 
 Date: Tue Oct 01 14:48:41 EDT 2013
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

bump versions prior to creating BioC 2.13 branch

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

Dan Tenenbaum authored on 14/10/2013 21:29:21
Showing 1 changed files
DESCRIPTION
History View file @ 291177d
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.8
4 
+Version: 1.20.0
5 5 
 Date: Tue Oct 01 14:48:41 EDT 2013
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

merge with collab

* collab:
Update DESCRIPTION
bug fixed for krlmm option, documentation changes

es

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@81002 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2013 12:03:56
Showing 1 changed files
DESCRIPTION
History View file @ 1d875d3
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.7
5 
-Date: Mon Sep 30 10:06:41 EDT 2013
4 
+Version: 1.19.8
5 
+Date: Tue Oct 01 14:48:41 EDT 2013
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -53,6 +53,3 @@ Collate: AllGenerics.R
53 53 
 	 test_crlmm_package.R
54 54 
 LazyLoad: yes
55 55 
 biocViews: Microarray, Preprocessing, SNP, Bioinformatics,CopyNumberVariants
56 
-## Local Variables:
57 
-## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
58 
-## End:
Browse code

fix conflict in description

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@80947 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/09/2013 14:07:17
Showing 1 changed files
DESCRIPTION
History View file @ ba1a7d7
... ... 
@@ -2,6 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 4 
 Version: 1.19.7
5 
+Date: Mon Sep 30 10:06:41 EDT 2013
5 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -23,13 +24,15 @@ Imports: methods,
23 24 
 	 ff,
24 25 
 	 foreach,
25 26 
          RcppEigen (>= 0.3.1.2.1),
26 
-	 matrixStats
27 
+	 matrixStats,
28 
+	 VGAM
27 29 
 Suggests: hapmapsnp6,
28 30 
           genomewidesnp6Crlmm (>= 1.0.7),
29 31 
           GGdata,
30 32 
           snpStats,
31 33 
 	  ellipse,
32 
-	  RUnit
34 
+	  RUnit,
35 
+	  VGAM
33 36 
 Collate: AllGenerics.R
34 37 
 	 AllClasses.R
35 38 
 	 methods-AssayData.R
... ... 
@@ -49,4 +52,7 @@ Collate: AllGenerics.R
49 52 
          zzz.R
50 53 
 	 test_crlmm_package.R
51 54 
 LazyLoad: yes
52 
-biocViews: Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants
55 
+biocViews: Microarray, Preprocessing, SNP, Bioinformatics,CopyNumberVariants
56 
+## Local Variables:
57 
+## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
58 
+## End:
Browse code

fix syntax error

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@79516 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/08/2013 22:34:26
Showing 1 changed files
DESCRIPTION
History View file @ 71f28ae
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.6
4 
+Version: 1.19.7
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

merging from collab

* collab:
add warning in vignette about NAs with BafLrrSetList function
Added Human Omni Express Exome 8 v1.1b as a supported chip
updated version number of pacakge and man pages to reflect these changes
skeleton for krlmm capability added. genotype.Illumina() can now take and XY object as input
update copynumber.Rnw to use BafLrrSetList
updates to vignettes
update namespace

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@79138 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/07/2013 01:37:34
Showing 1 changed files
DESCRIPTION
History View file @ 808cfec
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.2
4 
+Version: 1.19.6
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -22,7 +22,7 @@ Imports: methods,
22 22 
 	 lattice,
23 23 
 	 ff,
24 24 
 	 foreach,
25 
-         RcppEigen,
25 
+         RcppEigen (>= 0.3.1.2.1),
26 26 
 	 matrixStats
27 27 
 Suggests: hapmapsnp6,
28 28 
           genomewidesnp6Crlmm (>= 1.0.7),
... ... 
@@ -43,6 +43,7 @@ Collate: AllGenerics.R
43 43 
          crlmm-functions.R
44 44 
 	 crlmmGT2.R
45 45 
          crlmm-illumina.R
46 
+         krlmm.R
46 47 
 	 snprma-functions.R
47 48 
          utils.R
48 49 
          zzz.R
Browse code

bumped version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@77033 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/05/2013 17:42:28
Showing 1 changed files
DESCRIPTION