Last updated on 2025-03-19 05:53:14 CET.
| Package | WARN | NOTE | OK |
|---|---|---|---|
| ICAMS | 1 | 8 | 6 |
Current CRAN status: WARN: 1, NOTE: 8, OK: 6
Version: 2.3.12
Check: Rd cross-references
Result: NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
AnnotateDBSVCF.Rd: BSgenome
AnnotateSBSVCF.Rd: BSgenome
GeneExpressionData.Rd: data.table
ICAMS.Rd: BSgenome
MutectVCFFilesToCatalog.Rd: BSgenome
MutectVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
MutectVCFFilesToZipFile.Rd: BSgenome
NormalizeGenomeArg.Rd: BSgenome
PlotTransBiasGeneExp.Rd: data.table
PlotTransBiasGeneExpToPdf.Rd: data.table
StrelkaSBSVCFFilesToCatalog.Rd: BSgenome
StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd: BSgenome
StrelkaSBSVCFFilesToZipFile.Rd: BSgenome
VCFsToCatalogs.Rd: BSgenome
VCFsToCatalogsAndPlotToPdf.Rd: BSgenome
VCFsToDBSCatalogs.Rd: BSgenome
VCFsToSBSCatalogs.Rd: BSgenome
VCFsToZipFile.Rd: BSgenome
revc.Rd: reverseComplement
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-windows-x86_64, r-patched-linux-x86_64
Version: 2.3.12
Check: whether package can be installed
Result: WARN
Found the following significant warnings:
Rd warning: AnnotateDBSVCF.Rd:16: missing link ‘BSgenome’
Rd warning: AnnotateSBSVCF.Rd:16: missing link ‘BSgenome’
Rd warning: GeneExpressionData.Rd:10: missing link ‘data.table’
Rd warning: ICAMS.Rd:194: missing link ‘BSgenome’
Rd warning: MutectVCFFilesToCatalog.Rd:26: missing link ‘BSgenome’
Rd warning: MutectVCFFilesToCatalogAndPlotToPdf.Rd:27: missing link ‘BSgenome’
Rd warning: MutectVCFFilesToZipFile.Rd:33: missing link ‘BSgenome’
Rd warning: NormalizeGenomeArg.Rd:5: missing link ‘BSgenome’
Rd warning: NormalizeGenomeArg.Rd:20: missing link ‘BSgenome’
Rd warning: NormalizeGenomeArg.Rd:15: missing link ‘BSgenome’
Rd warning: NormalizeGenomeArg.Rd:16: missing link ‘BSgenome’
Rd warning: PlotTransBiasGeneExp.Rd:23: missing link ‘data.table’
Rd warning: PlotTransBiasGeneExpToPdf.Rd:26: missing link ‘data.table’
Rd warning: StrelkaSBSVCFFilesToCatalog.Rd:24: missing link ‘BSgenome’
Rd warning: StrelkaSBSVCFFilesToCatalogAndPlotToPdf.Rd:25: missing link ‘BSgenome’
Rd warning: StrelkaSBSVCFFilesToZipFile.Rd:31: missing link ‘BSgenome’
Rd warning: VCFsToCatalogs.Rd:41: missing link ‘BSgenome’
Rd warning: VCFsToCatalogsAndPlotToPdf.Rd:45: missing link ‘BSgenome’
Rd warning: VCFsToDBSCatalogs.Rd:29: missing link ‘BSgenome’
Rd warning: VCFsToSBSCatalogs.Rd:29: missing link ‘BSgenome’
Rd warning: VCFsToZipFile.Rd:52: missing link ‘BSgenome’
Rd warning: revc.Rd:17: missing link ‘reverseComplement’
Flavor: r-patched-linux-x86_64
Version: 2.3.12
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'BSgenome.Hsapiens.1000genomes.hs37d5',
'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2.3.12
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'BSgenome.Hsapiens.1000genomes.hs37d5',
'BSgenome.Mmusculus.UCSC.mm10'
Flavor: r-oldrel-windows-x86_64