BioC 3.2: CHECK report for Genominator on oaxaca

Package: Genominator

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Genominator_1.24.0.tar.gz

StartedAt: 2015-10-27 04:03:47 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:06:09 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 141.6 seconds

RetCode: 0

Status:  OK

CheckDir: Genominator.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings Genominator_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/Genominator.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Genominator/DESCRIPTION’ ... OK
* this is package ‘Genominator’ version ‘1.24.0’
* 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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Genominator’ can be installed ... [11s/15s] 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
* 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 to packages already attached by Depends:
  ‘GenomeGraphs’ ‘IRanges’
  Please remove these calls from your code.
'library' or 'require' call to ‘ShortRead’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GenomeGraphs’ ‘RSQLite’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addPrimingWeights: no visible global function definition for
  ‘varLabels’
addPrimingWeights: no visible global function definition for
  ‘alignData’
addPrimingWeights: no visible global function definition for ‘subseq’
addPrimingWeights: no visible global function definition for ‘sread’
addPrimingWeights: no visible global function definition for
  ‘AlignedDataFrame’
addPrimingWeights: no visible global function definition for ‘pData’
addPrimingWeights: no visible global function definition for
  ‘varMetadata’
computePrimingWeights: no visible global function definition for
  ‘mkAllStrings’
computePrimingWeights : p.compute: no visible global function
  definition for ‘tables’
computePrimingWeights : p.compute: no visible global function
  definition for ‘subseq’
computePrimingWeights : p.compute: no visible global function
  definition for ‘sread’
importFromAlignedReads : weights.AlignedRead: no visible global
  function definition for ‘varLabels’
importFromAlignedReads : weights.AlignedRead: no visible global
  function definition for ‘alignData’
importFromAlignedReads : importObject: no visible global function
  definition for ‘position’
importFromAlignedReads : importObject: no visible global function
  definition for ‘chromosome’
importFromAlignedReads : importObject: no visible global function
  definition for ‘varLabels’
importFromAlignedReads : importObject: no visible global function
  definition for ‘alignData’
importFromAlignedReads: no visible global function definition for
  ‘readAligned’
makeAnnoFactory: no visible global function definition for
  ‘DisplayPars’
makeAnnoFactory : regionAnno.Biomart: no visible global function
  definition for ‘geneRegionBiomart’
makeAnnoFactory : regionAnno.AnnoData: no visible global function
  definition for ‘makeAnnotationTrack’
makeRegionPlotter : <anonymous>: no visible global function definition
  for ‘DisplayPars’
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
  function definition for ‘makeBaseTrack’
makeRegionPlotter : <anonymous> : <anonymous>: no visible global
  function definition for ‘makeGenericArray’
makeRegionPlotter : <anonymous>: no visible global function definition
  for ‘makeGenomeAxis’
makeRegionPlotter : <anonymous>: no visible global function definition
  for ‘gdPlot’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
addPrimingWeights 5.212   0.12   5.374
joinExpData       5.035   0.03   5.073
* 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 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/Genominator.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
ExpData	0.002	0.001	0.002
addPrimingWeights	5.212	0.120	5.374
aggregateExpData	1.810	0.010	1.821
applyMapped	1.268	0.027	1.297
collapseExpData	1.825	0.035	1.865
computeCoverage	1.031	0.023	1.056
computePrimingWeights	0.507	0.017	0.525
getRegion	0.292	0.001	0.294
importFromAlignedReads	0.001	0.000	0.001
importToExpData	0.570	0.006	0.577
joinExpData	5.035	0.030	5.073
makeGeneRepresentation	0.221	0.004	0.225
mergeWithAnnotation	0.541	0.005	0.546
plot.genominator.coverage	3.025	0.046	3.078
plot.genominator.goodness.of.fit	0.716	0.016	0.734
regionGoodnessOfFit-methods	0.704	0.016	0.720
splitByAnnotation	1.000	0.005	1.005
summarizeByAnnotation	0.526	0.005	0.532
summarizeExpData	0.595	0.006	0.602
validAnnotation	0.019	0.002	0.021
yeastAnno	0.170	0.012	0.182