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BioC 3.0: CHECK report for BSgenome on perceval

This page was generated on 2015-04-10 09:53:01 -0700 (Fri, 10 Apr 2015).

Package 113/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.34.1
H. Pages
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/BSgenome
Last Changed Rev: 97896 / Revision: 102249
Last Changed Date: 2014-12-27 21:22:34 -0800 (Sat, 27 Dec 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK  WARNINGS 
moscato1 Windows Server 2008 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 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: BSgenome
Version: 1.34.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.34.1.tar.gz
StartedAt: 2015-04-09 23:20:11 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:28:09 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 477.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BSgenome.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch BSgenome_1.34.1.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/BSgenome.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.34.1’
* 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 ... [29s/35s] OK
* checking installed package size ... NOTE
  installed size is  6.7Mb
  sub-directories of 1Mb or more:
    extdata   5.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
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
'library' or 'require' calls in package code:
  ‘Biobase’ ‘BiocInstaller’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing object imported by a ':::' call: ‘GenomicRanges:::compactPrintNamedAtomicVector’
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::labeledLine’ ‘GenomeInfoDb:::showGenomeDescription’
  ‘IRanges:::.normargSEW’ ‘rtracklayer:::.DNAString_to_twoBit’
  ‘rtracklayer:::.TwoBits_export’ ‘rtracklayer:::checkArgFormat’
  ‘rtracklayer:::twoBitPath’ ‘S4Vectors:::anyMissing’
  ‘S4Vectors:::recycleVector’
  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 ... NOTE
getDataAnnotationContribUrl: no visible global function definition for
  ‘biocinstallRepos’
forgeBSgenomeDataPkg,BSgenomeDataPkgSeed: no visible global function
  definition for ‘createPackage’
forgeMaskedBSgenomeDataPkg,MaskedBSgenomeDataPkgSeed: no visible global
  function definition for ‘createPackage’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘forgeMaskedBSgenomeDataPkg’ ‘MaskedBSgenome’
Undocumented S4 classes:
  ‘MaskedBSgenome’
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 '[[<-' and siglist 'BSgenome,ANY,ANY'
  generic 'forgeMaskedBSgenomeDataPkg' and siglist 'character'
  generic 'forgeMaskedBSgenomeDataPkg' and siglist 'list'
  generic 'forgeMaskedBSgenomeDataPkg' and siglist
    'MaskedBSgenomeDataPkgSeed'
  generic 'length' and siglist 'OnDiskNamedSequences'
  generic 'names' and siglist 'FastaNamedSequences'
  generic 'names' and siglist 'TwobitNamedSequences'
  generic 'seqinfo' and siglist 'FastaNamedSequences'
  generic 'seqinfo' and siglist 'RdaNamedSequences'
  generic 'seqinfo' and siglist 'TwobitNamedSequences'
  generic 'seqnames' and siglist 'OnDiskNamedSequences'
  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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [163s/190s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
BSgenome-utils    33.774  0.943  34.917
getSeq-methods    14.661  9.272  24.059
injectSNPs        20.426  1.878  24.500
bsapply           13.884  1.529  16.677
BSgenome-class    13.705  1.680  20.209
export-methods    11.832  1.490  18.009
available.genomes 11.491  1.529  24.088
BSgenomeForge     11.569  0.198  13.047
* 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

WARNING: There were 2 warnings.
NOTE: There were 6 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/BSgenome.Rcheck/00check.log’
for details.

BSgenome.Rcheck/00install.out:

* installing *source* package ‘BSgenome’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (BSgenome)

BSgenome.Rcheck/BSgenome-Ex.timings:

nameusersystemelapsed
BSgenome-class13.705 1.68020.209
BSgenome-utils33.774 0.94334.917
BSgenomeForge11.569 0.19813.047
GenomeData-class0.0010.0000.001
GenomeDataList-class0.0010.0000.001
SNPlocs-class0.0000.0000.001
available.genomes11.491 1.52924.088
bsapply13.884 1.52916.677
export-methods11.832 1.49018.009
gdReduce0.0010.0010.001
getSeq-methods14.661 9.27224.059
injectSNPs20.426 1.87824.500