BSgenome 1.38.0
H. Pages
| Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/BSgenome | | Last Changed Rev: 109589 / Revision: 109947 | | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015) |
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| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | WARNINGS | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings BSgenome_1.38.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/BSgenome.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.38.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’
‘Biostrings’ ‘rtracklayer’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... NOTE
Found the following non-portable file path:
BSgenome/inst/extdata/GentlemanLab/1000genomes/BSgenome.Hsapiens.1000g.b36female-tools/split_human_b36_female.sh
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BSgenome’ can be installed ... [12s/12s] OK
* checking installed package size ... NOTE
installed size is 7.0Mb
sub-directories of 1Mb or more:
extdata 5.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘methods’ ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘Biostrings’ ‘rtracklayer’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
‘GenomeInfoDb:::compactPrintNamedAtomicVector’
‘GenomeInfoDb:::showGenomeDescription’ ‘IRanges:::.normargSEW’
‘S4Vectors:::anyMissing’ ‘S4Vectors:::anyMissingOrOutside’
‘S4Vectors:::diffWithInitialZero’
‘S4Vectors:::makeClassinfoRowForCompactPrinting’
‘S4Vectors:::makePrettyMatrixForCompactPrinting’
‘S4Vectors:::quick_unlist’ ‘S4Vectors:::quick_unsplit’
‘S4Vectors:::recycleVector’ ‘rtracklayer:::.DNAString_to_twoBit’
‘rtracklayer:::.TwoBits_export’ ‘rtracklayer:::checkArgFormat’
‘rtracklayer:::twoBitPath’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘MaskedBSgenome’ ‘OnDiskLongTable’ ‘as.data.frame.BSgenomeViews’
‘blocksizes’ ‘breakpoints’ ‘forgeMaskedBSgenomeDataPkg’
‘getBatchesFromOnDiskLongTable’ ‘getRowsByIdFromOnDiskLongTable’
‘getRowsByIndexFromOnDiskLongTable’ ‘rowids’ ‘saveAsOnDiskLongTable’
‘saveRowidsForOnDiskLongTable’
Undocumented S4 classes:
‘MaskedBSgenome’ ‘OnDiskLongTable’
Undocumented S4 methods:
generic '[[' and siglist 'BSgenome,ANY,ANY'
generic '[[' and siglist 'FastaNamedSequences,ANY,ANY'
generic '[[' and siglist 'RdaNamedSequences,ANY,ANY'
generic '[[' and siglist 'TwobitNamedSequences,ANY,ANY'
generic 'blocksizes' and siglist 'OnDiskLongTable'
generic 'breakpoints' and siglist 'OnDiskLongTable'
generic 'colnames' and siglist 'OnDiskLongTable'
generic 'dim' and siglist 'OnDiskLongTable'
generic 'forgeMaskedBSgenomeDataPkg' and siglist
'MaskedBSgenomeDataPkgSeed'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
generic 'length' and siglist 'OnDiskNamedSequences'
generic 'names' and siglist 'FastaNamedSequences'
generic 'names' and siglist 'TwobitNamedSequences'
generic 'ncol' and siglist 'OnDiskLongTable'
generic 'ncol' and siglist 'XtraSNPlocs'
generic 'nrow' and siglist 'OnDiskLongTable'
generic 'nrow' and siglist 'XtraSNPlocs'
generic 'rowids' and siglist 'OnDiskLongTable'
generic 'seqinfo' and siglist 'FastaNamedSequences'
generic 'seqinfo' and siglist 'RdaNamedSequences'
generic 'seqinfo' and siglist 'TwobitNamedSequences'
generic 'seqnames' and siglist 'OnDiskNamedSequences'
generic 'show' and siglist 'OnDiskLongTable'
generic 'show' and siglist 'OnDiskNamedSequences'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘BSgenome.Scerevisiae.UCSC.sacCer1’
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [190s/202s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
XtraSNPlocs-class 53.993 0.720 54.922
SNPlocs-class 33.515 0.622 34.226
available.genomes 19.448 0.765 21.118
BSgenome-utils 19.711 0.155 19.893
injectSNPs 15.381 0.670 16.380
BSgenomeViews-class 11.342 0.457 21.739
BSgenome-class 6.676 0.251 7.663
getSeq-methods 6.608 0.003 6.615
bsapply 5.304 0.120 5.687
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 WARNINGs, 5 NOTEs
See
‘/home/biocbuild/bbs-3.2-bioc/meat/BSgenome.Rcheck/00check.log’
for details.