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BioC 3.5: CHECK report for BSgenome on veracruz2

This page was generated on 2017-10-18 14:27:58 -0400 (Wed, 18 Oct 2017).

Package 154/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BSgenome 1.44.2
H. Pagès
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/BSgenome
Branch: RELEASE_3_5
Last Commit: 105b005
Last Changed Date: 2017-09-22 03:29:53 -0400 (Fri, 22 Sep 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: BSgenome
Version: 1.44.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BSgenome_1.44.2.tar.gz
StartedAt: 2017-10-18 01:10:33 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:18:12 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 458.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: BSgenome.Rcheck
Warnings: 1

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings BSgenome_1.44.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/BSgenome.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BSgenome/DESCRIPTION’ ... OK
* this is package ‘BSgenome’ version ‘1.44.2’
* 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  7.2Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
* 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
Unexported objects imported by ':::' calls:
  ‘GenomeInfoDb:::compactPrintNamedAtomicVector’
  ‘GenomeInfoDb:::showGenomeDescription’ ‘IRanges:::.normargSEW’
  ‘S4Vectors:::anyMissing’ ‘S4Vectors:::anyMissingOrOutside’
  ‘S4Vectors:::decodeRle’ ‘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’ ‘OnDiskLongTable_old’
  ‘as.data.frame.BSgenomeViews’ ‘batchsizes’ ‘blocksizes’ ‘breakpoints’
  ‘forgeMaskedBSgenomeDataPkg’
  ‘getBatchesByOverlapsFromOnDiskLongTable’
  ‘getBatchesBySeqnameFromOnDiskLongTable’
  ‘getBatchesFromOnDiskLongTable’ ‘getBatchesFromOnDiskLongTable_old’
  ‘getRowsByIdFromOnDiskLongTable’ ‘getRowsByIdFromOnDiskLongTable_old’
  ‘getRowsByIndexFromOnDiskLongTable_old’ ‘getRowsFromOnDiskLongTable’
  ‘rowids’ ‘saveAsOnDiskLongTable_old’
  ‘saveRowidsForOnDiskLongTable_old’ ‘spatialIndex’
  ‘writeOnDiskLongTable’ ‘writeOnDiskLongTableRowids’
Undocumented S4 classes:
  ‘OnDiskLongTable_old’ ‘OnDiskLongTable’ ‘MaskedBSgenome’
  ‘GRanges_OR_NULL’
Undocumented S4 methods:
  generic '[' and siglist 'XStringSet,GRangesList,ANY,ANY'
  generic '[' and siglist 'XStringSet,GenomicRanges,ANY,ANY'
  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 'batchsizes' and siglist 'OnDiskLongTable'
  generic 'blocksizes' and siglist 'OnDiskLongTable_old'
  generic 'breakpoints' and siglist 'OnDiskLongTable'
  generic 'breakpoints' and siglist 'OnDiskLongTable_old'
  generic 'dim' and siglist 'OnDiskLongTable'
  generic 'dim' and siglist 'OnDiskLongTable_old'
  generic 'dimnames' and siglist 'OnDiskLongTable'
  generic 'dimnames' and siglist 'OnDiskLongTable_old'
  generic 'dimnames' and siglist 'XtraSNPlocs'
  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 'rowids' and siglist 'OnDiskLongTable'
  generic 'rowids' and siglist 'OnDiskLongTable_old'
  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 'OnDiskLongTable_old'
  generic 'show' and siglist 'OnDiskNamedSequences'
  generic 'spatialIndex' and siglist 'OnDiskLongTable'
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 ... OK
* 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   120.127  3.455 127.439
SNPlocs-class        47.910  2.880  52.365
BSgenome-utils       24.837  0.485  26.125
BSgenomeViews-class  11.324  2.584  17.667
BSgenome-class       12.827  0.790  13.994
injectSNPs            9.147  0.899  10.312
export-methods        6.817  1.203   8.283
getSeq-methods        6.853  1.049   8.277
bsapply               7.258  0.394   7.906
BSgenomeForge         5.026  0.107   5.307
* 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: 1 WARNING, 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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-class12.827 0.79013.994
BSgenome-utils24.837 0.48526.125
BSgenomeForge5.0260.1075.307
BSgenomeViews-class11.324 2.58417.667
SNPlocs-class47.910 2.88052.365
XtraSNPlocs-class120.127 3.455127.439
available.genomes1.5110.1722.218
bsapply7.2580.3947.906
export-methods6.8171.2038.283
getSeq-methods6.8531.0498.277
injectSNPs 9.147 0.89910.312