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Fixes on C code and dependencies on oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@43012 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 15/11/2009 12:54:26
Showing4 changed files

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@@ -319,4 +319,10 @@ is decoded and scanned
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  - ABset and CrlmmSetList classes are gone. Using SnpCallSetPlus and CrlmmSet
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  - Added class SegmentSet that extends CrlmmSet directly.
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+2009-11-15 B Carvalho - committed version 1.5.4
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+
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+ * removed references to old C code
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+ * added the missing files to the Collate field
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+ * fixed classes imported from oligoClasses in NAMESPACE
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+ * imported 'calls<-' from oligoClasses
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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.5.3
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+Version: 1.5.4
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 Date: 2009-11-15
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 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -12,11 +12,14 @@ Imports: affyio, preprocessCore, utils, stats, genefilter, splines, mvtnorm, oli
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 Suggests: hapmapsnp5, hapmapsnp6, genomewidesnp5Crlmm (>= 1.0.2),genomewidesnp6Crlmm (>= 1.0.2), snpMatrix, GGdata
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 Collate: AllClasses.R
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 	 AllGenerics.R
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-	 methods-ABset.R
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 	 methods-CopyNumberSet.R
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-	 methods-CrlmmSetList.R
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+         methods-CrlmmSet.R
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+         methods-CrlmmSetFF.R
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 	 methods-eSet.R
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+         methods-SnpCallSetPlus.R
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+         methods-SnpCallSetPlusFF.R
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          methods-SnpSet.R
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+         methods-SnpQSet.R
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          cnrma-functions.R
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          crlmm-functions.R
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          crlmm-illumina.R
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@@ -5,7 +5,7 @@ useDynLib("crlmm", .registration=TRUE)
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 importClassesFrom(Biobase, AnnotatedDataFrame, AssayData, eSet,
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 		  SnpSet, NChannelSet, MIAME, Versioned, VersionedBiobase, Versions)
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-importClassesFrom(oligoClasses, SnpLevelSet)
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+importClassesFrom(oligoClasses, SnpLevelSet, SnpQSet, SnpCallSet, SnpCallSetPlus, QuantificationSet)
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 importMethodsFrom(Biobase, annotation, "annotation<-", annotatedDataFrameFrom,
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                   assayData, "assayData<-", combine, dims,
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@@ -16,9 +16,7 @@ importMethodsFrom(Biobase, annotation, "annotation<-", annotatedDataFrameFrom,
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                   pubMedIds, rowMedians, sampleNames,
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                   storageMode, "storageMode<-", updateObject, varLabels)
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-
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-##importMethodsFrom(oligoClasses, chromosome, copyNumber, position)
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-importMethodsFrom(oligoClasses, chromosome, copyNumber, position, calls)
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+importMethodsFrom(oligoClasses, chromosome, copyNumber, position, calls, "calls<-")
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 ##importMethodsFrom(methods, initialize, show)
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@@ -3,20 +3,11 @@
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 #include "crlmm.h"
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 static const R_CallMethodDef CallEntries[] = {
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-    {"test", (DL_FUNC)&test, 1},
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-    {"gtypeCallerPart1nm", (DL_FUNC)&gtypeCallerPart1nm, 17},
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-    {"gtypeCallerPart2nm", (DL_FUNC)&gtypeCallerPart2nm, 19},
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-    {"gtypeCallerPart1NormalNoN", (DL_FUNC)&gtypeCallerPart1NormalNoN, 17},
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     {"gtypeCallerPart1", (DL_FUNC)&gtypeCallerPart1, 17},
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     {"gtypeCallerPart2", (DL_FUNC)&gtypeCallerPart2, 19},
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-    {"gtypeCallerPart1TNoN", (DL_FUNC)&gtypeCallerPart1TNoN, 17},
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-    {"gtypeCallerPart2TNoN", (DL_FUNC)&gtypeCallerPart2TNoN, 19},
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     {NULL, NULL, 0}
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 };
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 void R_init_crlmm(DllInfo *dll){
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     R_registerRoutines(dll, NULL, CallEntries, NULL, NULL);    
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 }
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-
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-
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-