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BioC 2.13: CHECK report for BSgenome on moscato1

This page was generated on 2014-04-05 09:49:20 -0700 (Sat, 05 Apr 2014).

Package 100/750HostnameOS / ArchBUILDCHECKBUILD BIN
BSgenome 1.30.0
H. Pages
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/BSgenome
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  WARNINGS  OK 

Summary

Package: BSgenome
Version: 1.30.0
Command: rm -rf BSgenome.buildbin-libdir && mkdir BSgenome.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=BSgenome.buildbin-libdir BSgenome_1.30.0.tar.gz >BSgenome-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=BSgenome.buildbin-libdir --install="check:BSgenome-install.out" --force-multiarch --no-vignettes --timings BSgenome_1.30.0.tar.gz && mv BSgenome.buildbin-libdir/* BSgenome.Rcheck/ && rmdir BSgenome.buildbin-libdir
StartedAt: 2014-04-05 02:41:30 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 02:48:33 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 422.5 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BSgenome.Rcheck
Warnings: 2

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/BSgenome.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BSgenome/DESCRIPTION' ... OK
* this is package 'BSgenome' version '1.30.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 whether package 'BSgenome' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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:
  'BiocGenerics:::labeledLine' 'GenomicRanges:::showSeqlengths'
  'IRanges:::.normargSEW' 'IRanges:::anyMissing'
  'IRanges:::recycleVector'
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of the 'Writing R Extensions' manual.
* 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:
  'compatibleGenomes' 'newSNPlocs' 'referenceGenome' 'snpcount'
  'snpid2alleles' 'snpid2grange' 'snpid2loc' 'snplocs'
Undocumented S4 classes:
  'SNPlocs'
Undocumented S4 methods:
  generic '[[' and siglist 'BSgenome,ANY,ANY'
  generic '[[<-' and siglist 'BSgenome,ANY,ANY'
  generic 'compatibleGenomes' and siglist 'SNPlocs'
  generic 'organism' and siglist 'SNPlocs'
  generic 'provider' and siglist 'SNPlocs'
  generic 'providerVersion' and siglist 'SNPlocs'
  generic 'referenceGenome' and siglist 'SNPlocs'
  generic 'releaseDate' and siglist 'SNPlocs'
  generic 'releaseName' and siglist 'SNPlocs'
  generic 'seqinfo' and siglist 'SNPlocs'
  generic 'seqnames' and siglist 'GenomeDescription'
  generic 'seqnames' and siglist 'SNPlocs'
  generic 'show' and siglist 'SNPlocs'
  generic 'snpcount' and siglist 'SNPlocs'
  generic 'snpid2alleles' and siglist 'SNPlocs'
  generic 'snpid2grange' and siglist 'SNPlocs'
  generic 'snpid2loc' and siglist 'SNPlocs'
  generic 'snplocs' and siglist 'SNPlocs'
  generic 'species' and siglist 'SNPlocs'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the 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 for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'BSgenomeForge.Rnw', 'GenomeSearching.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [123s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
BSgenome-utils    41.47   0.38   44.24
getSeq-methods    22.65   1.32   24.15
injectSNPs        18.41   0.35   21.00
bsapply           13.76   0.38   14.40
available.genomes  6.13   0.34    9.25
** running examples for arch 'x64' ... [123s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
BSgenome-utils    40.95   0.39   41.70
injectSNPs        23.85   1.50   25.74
getSeq-methods    22.25   0.65   22.90
bsapply           13.02   0.35   13.37
available.genomes  5.66   0.25    8.22
* 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

WARNING: There were 2 warnings.
NOTE: There were 3 notes.
See
  'D:/biocbld/bbs-2.13-bioc/meat/BSgenome.Rcheck/00check.log'
for details.

BSgenome.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'BSgenome' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BSgenome' as BSgenome_1.30.0.zip
* DONE (BSgenome)

BSgenome.Rcheck/examples_i386/BSgenome-Ex.timings:

nameusersystemelapsed
BSgenome-class2.930.044.41
BSgenome-utils41.47 0.3844.24
BSgenomeForge0.030.000.03
GenomeData-class0.010.000.02
GenomeDataList-class0.130.010.14
GenomeDescription-class0.050.020.06
available.genomes6.130.349.25
bsapply13.76 0.3814.40
gdReduce0.060.000.06
getSeq-methods22.65 1.3224.15
injectSNPs18.41 0.3521.00

BSgenome.Rcheck/examples_x64/BSgenome-Ex.timings:

nameusersystemelapsed
BSgenome-class3.210.023.23
BSgenome-utils40.95 0.3941.70
BSgenomeForge0.030.000.03
GenomeData-class0.020.000.01
GenomeDataList-class0.020.000.02
GenomeDescription-class0.030.010.04
available.genomes5.660.258.22
bsapply13.02 0.3513.37
gdReduce0.050.000.05
getSeq-methods22.25 0.6522.90
injectSNPs23.85 1.5025.74