1. crlmm
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_18 branch

J Wokaty authored on 24/10/2023 13:41:39
Showing 1 changed files
DESCRIPTION
History View file @ 3eab2ca
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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: 1.60.0
5 
+Version: 1.61.0
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_18 branch

J Wokaty authored on 24/10/2023 13:41:39
Showing 1 changed files
DESCRIPTION
History View file @ 1271399
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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: 1.59.0
5 
+Version: 1.60.0
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_17 branch

J Wokaty authored on 25/04/2023 13:48:29
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DESCRIPTION
History View file @ b4a59d2
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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: 1.58.0
5 
+Version: 1.59.0
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_17 branch

J Wokaty authored on 25/04/2023 13:48:29
Showing 1 changed files
DESCRIPTION
History View file @ f9044bc
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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: 1.57.0
5 
+Version: 1.58.0
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_16 branch

J Wokaty authored on 01/11/2022 15:04:22
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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
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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
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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
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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 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
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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
4 4 
         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
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-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
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-## Local Variables:
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+## Local Variables:
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 ## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
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-## End:
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+## End:
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 biocViews: Microarray, Preprocessing, SNP, CopyNumberVariation
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+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
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         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
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         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),
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         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
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+Version: 1.45.0
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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 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
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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_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
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_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
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: 1.39.1
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+Version: 1.40.0
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

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
5 
+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
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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_7 branch

vobencha authored on 30/04/2018 14:35:10
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DESCRIPTION
History View file @ cc1a98e
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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: 1.37.1
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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
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+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
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: 1.35.0
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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
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: 1.34.0
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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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@@ -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: 1.33.1
5 
+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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@@ -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: 1.33.2
5 
+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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@@ -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: 1.33.0
5 
+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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@@ -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: 1.32.0
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
30 30 
 ## 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
4 4 
         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
5 
+Version: 1.30.0
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

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
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         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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 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
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+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
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         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
4 4 
         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
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+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
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-Date: Mon 31 Mar 2014 18:08:54 EST
5 
+Version: 1.23.1
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+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
Showing 1 changed files
DESCRIPTION
History View file @ 7a75b69
... ... 
@@ -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: 1.22.0
5 
+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
Showing 1 changed files
DESCRIPTION
History View file @ 1a6fb8a
... ... 
@@ -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: 1.21.9
5 
+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
Showing 1 changed files
DESCRIPTION
History View file @ 3d8f487
... ... 
@@ -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: 1.21.8
6 
-Date: Fri Mar 28 16:26:10 EST 2014
5 
+Version: 1.21.9
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
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
Showing 1 changed files
DESCRIPTION
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
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@@ -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: