Package: Genominator

Version: 1.40.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Genominator.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Genominator_1.40.0.tar.gz

StartedAt: 2020-04-15 02:37:40 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:40:26 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 166.6 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: Genominator.Rcheck

Warnings: 2

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:Genominator.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings Genominator_1.40.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Genominator/DESCRIPTION’ ... OK
* this is package ‘Genominator’ version ‘1.40.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'GenomeGraphs' is deprecated and will be removed from
See ‘/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck/00install.out’ for details.
* 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 ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.genominator.coverage plot.genominator.goodness.of.fit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* 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’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘qchisq’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘ppoints’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘qunif’
plot.genominator.goodness.of.fit : <anonymous>: no visible global
  function definition for ‘qqplot’
Undefined global functions or variables:
  AlignedDataFrame DisplayPars alignData chromosome gdPlot
  geneRegionBiomart makeAnnotationTrack makeBaseTrack makeGenericArray
  makeGenomeAxis mkAllStrings pData position ppoints qchisq qqplot
  qunif readAligned sread subseq tables varLabels varMetadata
Consider adding
  importFrom("stats", "ppoints", "qchisq", "qqplot", "qunif")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'ExpData,ANY,ANY'
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 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
joinExpData               11.414  0.038  11.670
addPrimingWeights          9.068  0.335   9.628
plot.genominator.coverage  6.094  0.075   6.218
* 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, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/Genominator.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL Genominator
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘Genominator’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package can be loaded from final location
Warning: Package 'GenomeGraphs' is deprecated and will be removed from
  Bioconductor version 3.11
** testing if installed package keeps a record of temporary installation path
* DONE (Genominator)

name	user	system	elapsed
ExpData	0.002	0.001	0.002
addPrimingWeights	9.068	0.335	9.628
aggregateExpData	4.769	0.024	4.888
applyMapped	2.725	0.033	2.864
collapseExpData	3.832	0.069	3.989
computeCoverage	2.142	0.032	2.222
computePrimingWeights	0.360	0.013	0.378
getRegion	0.620	0.002	0.632
importFromAlignedReads	0.000	0.000	0.001
importToExpData	1.232	0.005	1.248
joinExpData	11.414	0.038	11.670
makeGeneRepresentation	0.215	0.009	0.227
mergeWithAnnotation	1.203	0.016	1.225
plot.genominator.coverage	6.094	0.075	6.218
plot.genominator.goodness.of.fit	1.575	0.034	1.634
regionGoodnessOfFit-methods	1.455	0.029	1.542
splitByAnnotation	2.456	0.013	2.531
summarizeByAnnotation	1.311	0.009	1.339
summarizeExpData	1.365	0.009	1.437
validAnnotation	0.018	0.006	0.025
yeastAnno	0.193	0.023	0.217