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BioC 3.3: CHECK report for BSgenome on oaxaca

This page was generated on 2016-10-13 12:56:06 -0700 (Thu, 13 Oct 2016).

Package 133/1210HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.40.1
H. Pagès
Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/BSgenome
Last Changed Rev: 118623 / Revision: 122332
Last Changed Date: 2016-06-15 11:15:45 -0700 (Wed, 15 Jun 2016)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BSgenome
Version: 1.40.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BSgenome_1.40.1.tar.gz
StartedAt: 2016-10-12 23:46:46 -0700 (Wed, 12 Oct 2016)
EndedAt: 2016-10-12 23:53:49 -0700 (Wed, 12 Oct 2016)
EllapsedTime: 422.4 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 BSgenome_1.40.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/BSgenome.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.40.1’
* package encoding: UTF-8
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.9Mb
  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:::make_zero_col_DataFrame’ ‘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:
  ‘OnDiskLongTable’ ‘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 '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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
XtraSNPlocs-class   59.231  1.914  63.758
SNPlocs-class       50.433  2.949  53.969
BSgenome-utils      29.534  0.491  30.185
available.genomes   22.769  1.064  31.577
BSgenomeViews-class 15.148  1.965  18.574
bsapply             13.780  0.845  15.611
injectSNPs          12.637  0.833  14.321
BSgenome-class      11.156  0.940  14.841
export-methods       7.683  1.265   9.321
getSeq-methods       6.951  1.406   8.377
BSgenomeForge        5.906  0.114   6.046
* 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
  ‘/Users/biocbuild/bbs-3.3-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-class11.156 0.94014.841
BSgenome-utils29.534 0.49130.185
BSgenomeForge5.9060.1146.046
BSgenomeViews-class15.148 1.96518.574
SNPlocs-class50.433 2.94953.969
XtraSNPlocs-class59.231 1.91463.758
available.genomes22.769 1.06431.577
bsapply13.780 0.84515.611
export-methods7.6831.2659.321
getSeq-methods6.9511.4068.377
injectSNPs12.637 0.83314.321