Package: IsoformSwitchAnalyzeR

Version: 1.0.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IsoformSwitchAnalyzeR_1.0.0.tar.gz

StartedAt: 2018-04-12 00:30:39 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 00:37:16 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 396.7 seconds

RetCode: 0

Status:  OK

CheckDir: IsoformSwitchAnalyzeR.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings IsoformSwitchAnalyzeR_1.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/IsoformSwitchAnalyzeR.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IsoformSwitchAnalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IsoformSwitchAnalyzeR’ version ‘1.0.0’
* 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 ‘IsoformSwitchAnalyzeR’ 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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
createSwitchAnalyzeRlist: no visible global function definition for
  'Rle'
expressionAnalysisPlot: no visible binding for global variable
  'Condition'
expressionAnalysisPlot: no visible binding for global variable
  'gene_expression'
expressionAnalysisPlot: no visible binding for global variable 'CI_up'
expressionAnalysisPlot: no visible binding for global variable
  'CI_down'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevelPos'
expressionAnalysisPlot: no visible binding for global variable
  'sigLevel'
expressionAnalysisPlot: no visible binding for global variable 'CI_hi'
expressionAnalysisPlot: no visible binding for global variable 'CI_low'
expressionAnalysisPlot: no visible binding for global variable 'ymax'
expressionAnalysisPlot: no visible binding for global variable
  'sigEval'
expressionAnalysisPlot: no visible binding for global variable 'idNr'
expressionAnalysisPlot: no visible binding for global variable 'IF'
extractConsequenceSummary: no visible binding for global variable
  'switchConsequence'
extractConsequenceSummary: no visible binding for global variable
  'geneFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrGenesWithConsequences'
extractConsequenceSummary: no visible binding for global variable
  'isoFraction'
extractConsequenceSummary: no visible binding for global variable
  'nrIsoWithConsequences'
extractGenomeWideAnalysis: no visible binding for global variable
  'isoform_feature'
extractGenomeWideAnalysis: no visible binding for global variable
  'value'
extractGenomeWideAnalysis: no visible binding for global variable
  'variable'
extractGenomeWideAnalysis: no visible binding for global variable
  'ymax'
extractGenomeWideAnalysis: no visible binding for global variable
  'significance'
extractGenomeWideAnalysis: no visible binding for global variable
  'idNr'
switchPlotTranscript: no visible global function definition for
  'queryHits'
switchPlotTranscript: no visible binding for global variable 'y'
switchPlotTranscript: no visible binding for global variable 'yend'
switchPlotTranscript: no visible binding for global variable 'x'
switchPlotTranscript: no visible binding for global variable 'ymin'
switchPlotTranscript: no visible binding for global variable 'xmin'
switchPlotTranscript: no visible binding for global variable 'ymax'
switchPlotTranscript: no visible binding for global variable 'xmax'
switchPlotTranscript: no visible binding for global variable 'Domain'
Undefined global functions or variables:
  CI_down CI_hi CI_low CI_up Condition Domain IF Rle geneFraction
  gene_expression idNr isoFraction isoform_feature
  nrGenesWithConsequences nrIsoWithConsequences queryHits sigEval
  sigLevel sigLevelPos significance switchConsequence value variable x
  xmax xmin y yend ymax ymin
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
isoformSwitchAnalysisCombined 17.516  0.200  17.731
IsoformSwitchTestDRIMSeq      13.260  0.084  13.830
isoformSwitchAnalysisPart1    11.056  0.120  11.184
analyzeIntronRetention         6.984  0.012   7.005
importCufflinksData            5.208  0.024   5.236
extractGenomeWideAnalysis      5.160  0.008   5.168
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘pheatmap’
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/IsoformSwitchAnalyzeR.Rcheck/00check.log’
for details.

* installing *source* package ‘IsoformSwitchAnalyzeR’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::conditions' by 'spliceR::conditions' when loading 'IsoformSwitchAnalyzeR'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'plyr::desc' by 'IRanges::desc' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'plyr::count' by 'cummeRbund::count' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'GenomicRanges::promoters' by 'cummeRbund::promoters' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::samples' by 'DRIMSeq::samples' when loading 'IsoformSwitchAnalyzeR'
Warning: replacing previous import 'cummeRbund::conditions' by 'spliceR::conditions' when loading 'IsoformSwitchAnalyzeR'
* DONE (IsoformSwitchAnalyzeR)

name	user	system	elapsed
IsoformSwitchTestDRIMSeq	13.260	0.084	13.830
analyzeCPAT	0.120	0.000	0.123
analyzeIntronRetention	6.984	0.012	7.005
analyzeORF	1.120	0.004	1.125
analyzePFAM	0.716	0.004	0.725
analyzeSignalP	0.068	0.000	0.069
analyzeSwitchConsequences	2.948	0.000	2.951
expressionAnalysisPlots	2.460	0.000	2.461
extractCallibarionStatus	0.400	0.000	0.401
extractConsequenceSummary	1.504	0.004	1.513
extractExpressionMatrix	0.288	0.004	0.294
extractGenomeWideAnalysis	5.160	0.008	5.168
extractSequence	1.428	0.004	1.434
extractSwitchSummary	0.036	0.000	0.039
extractTopSwitches	0.116	0.000	0.114
importCufflinksData	5.208	0.024	5.236
importCufflinksGalaxyData	2.040	0.000	2.043
importGTF	0.620	0.000	0.619
importRdata	3.784	0.024	3.812
isoformSwitchAnalysisCombined	17.516	0.200	17.731
isoformSwitchAnalysisPart1	11.056	0.120	11.184
isoformSwitchAnalysisPart2	4.460	0.032	4.501
isoformSwitchTest	0.064	0.000	0.064
isoformToGeneExp	2.408	0.036	2.449
preFilter	0.016	0.000	0.016
prepareCuffExample	1.968	0.028	1.997
switchAnalyzeRlist	3.724	0.016	3.744
switchPlot	2.492	0.004	2.499
switchPlotTranscript	1.520	0.004	1.524
testData	0.008	0.004	0.012