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BioC 3.2: CHECK report for MineICA on oaxaca

This page was generated on 2016-04-23 10:26:29 -0700 (Sat, 23 Apr 2016).

Package 644/1103HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MineICA 1.10.0
Anne Biton
Snapshot Date: 2016-04-22 16:20:12 -0700 (Fri, 22 Apr 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MineICA
Last Changed Rev: 109589 / Revision: 116712
Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: MineICA
Version: 1.10.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MineICA_1.10.0.tar.gz
StartedAt: 2016-04-23 02:08:56 -0700 (Sat, 23 Apr 2016)
EndedAt: 2016-04-23 02:13:26 -0700 (Sat, 23 Apr 2016)
EllapsedTime: 269.7 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: MineICA.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MineICA_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/MineICA.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MineICA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MineICA’ version ‘1.10.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘plyr’ ‘ggplot2’ ‘scales’ ‘foreach’ ‘xtable’
  ‘biomaRt’ ‘gtools’ ‘GOstats’ ‘cluster’ ‘marray’ ‘mclust’
  ‘RColorBrewer’ ‘colorspace’ ‘igraph’ ‘Rgraphviz’ ‘graph’ ‘annotate’
  ‘Hmisc’ ‘fastICA’ ‘JADE’
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 ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MineICA’ can be installed ... [22s/23s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘biomaRt’ ‘GOstats’ ‘cluster’ ‘mclust’ ‘igraph’
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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘GOstats’ which was already attached by Depends.
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘lumiHumanAll.db’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘GOstats’ ‘Hmisc’ ‘JADE’ ‘RColorBrewer’ ‘Rgraphviz’ ‘annotate’
  ‘biomaRt’ ‘cluster’ ‘colorspace’ ‘fastICA’ ‘foreach’ ‘ggplot2’
  ‘graph’ ‘gtools’ ‘igraph’ ‘marray’ ‘mclust’ ‘methods’ ‘plyr’ ‘scales’
  ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  ‘Biobase:::annotation’ ‘Biobase:::validMsg’ ‘fpc:::pamk’
  ‘lumi:::getChipInfo’ ‘mclust:::adjustedRandIndex’
  See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘Biobase:::isValidVersion’
  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 ... NOTE
addGenesToGoReport: no visible global function definition for
  ‘geneIdsByCategory’
addGenesToGoReport: no visible global function definition for
  ‘geneIdUniverse’
addGenesToGoReport: no visible global function definition for
  ‘conditional’
addGenesToGoReport: no visible global function definition for
  ‘sigCategories’
annot2Color: no visible global function definition for ‘brewer.pal’
annot2Color: no visible global function definition for ‘heat_hcl’
annot2Color: no visible global function definition for ‘terrain_hcl’
annot2Color: no visible global function definition for ‘rainbow_hcl’
annotFeaturesComp: no visible global function definition for ‘getEG’
annotFeaturesComp: no visible global function definition for
  ‘getSYMBOL’
annotFeaturesComp: no visible global function definition for ‘llply’
annotFeaturesWithBiomaRt: no visible global function definition for
  ‘useMart’
annotFeaturesWithBiomaRt: no visible global function definition for
  ‘listFilters’
annotFeaturesWithBiomaRt: no visible global function definition for
  ‘listAttributes’
annotFeaturesWithBiomaRt: no visible global function definition for
  ‘getBM’
clusVarAnalysis: no visible global function definition for ‘%do%’
clusVarAnalysis: no visible global function definition for ‘foreach’
clusVarAnalysis: no visible global function definition for ‘ggplot’
clusVarAnalysis: no visible global function definition for ‘geom_bar’
clusVarAnalysis: no visible global function definition for ‘aes’
clusVarAnalysis: no visible binding for global variable ‘cluster’
clusVarAnalysis: no visible global function definition for ‘xlab’
clusVarAnalysis: no visible global function definition for ‘ggtitle’
clusVarAnalysis: no visible global function definition for
  ‘scale_fill_manual’
clusVarAnalysis: no visible global function definition for ‘ggsave’
clusterFastICARuns: no visible global function definition for ‘fastICA’
clusterFastICARuns: no visible global function definition for ‘%dopar%’
clusterFastICARuns: no visible global function definition for ‘foreach’
clusterFastICARuns: no visible global function definition for ‘agnes’
clusterFastICARuns: no visible global function definition for ‘pam’
clusterSamplesByComp: no visible global function definition for ‘%do%’
clusterSamplesByComp: no visible global function definition for
  ‘foreach’
clusterSamplesByComp: no visible global function definition for
  ‘Mclust’
clusterSamplesByComp: no visible global function definition for ‘pam’
clusterSamplesByComp: no visible global function definition for ‘agnes’
clusterSamplesByComp: no visible binding for global variable ‘cluster’
clusterSamplesByComp_multiple: no visible global function definition
  for ‘%do%’
clusterSamplesByComp_multiple: no visible global function definition
  for ‘foreach’
compareGenes: no visible global function definition for ‘useMart’
compareGenes: no visible global function definition for ‘%dopar%’
compareGenes: no visible global function definition for ‘foreach’
compareGenes: no visible global function definition for ‘llply’
cor2An: no visible global function definition for ‘rcorr’
doEnrichment: no visible global function definition for ‘hyperGTest’
heatmap.plus: no visible binding for global variable ‘agnes’
hypergeoAn: no visible global function definition for ‘llply’
mergeGostatsResults: no visible global function definition for
  ‘%dopar%’
mergeGostatsResults: no visible global function definition for
  ‘foreach’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘%dopar%’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘foreach’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘xtable’
mergeGostatsResults : <anonymous>: no visible global function
  definition for ‘%do%’
mergeGostatsResults: no visible global function definition for ‘xtable’
nbOccInComp: no visible global function definition for ‘%dopar%’
nbOccInComp: no visible global function definition for ‘foreach’
nbOccInComp: no visible global function definition for ‘xtable’
nodeAttrs: no visible global function definition for ‘%do%’
nodeAttrs: no visible global function definition for ‘foreach’
plotAllMix: no visible binding for global variable ‘Mclust’
plotCorGraph: no visible global function definition for ‘brewer.pal’
plotCorGraph: no visible global function definition for ‘llply’
plotCorGraph: no visible global function definition for
  ‘igraph.from.graphNEL’
plotCorGraph: no visible global function definition for ‘V’
plotCorGraph: no visible global function definition for ‘V<-’
plotCorGraph: no visible global function definition for ‘E’
plotCorGraph: no visible global function definition for ‘E<-’
plotCorGraph: no visible global function definition for
  ‘layout.fruchterman.reingold’
plotCorGraph: no visible global function definition for ‘vcount’
plotCorGraph: no visible global function definition for
  ‘tkplot.fit.to.screen’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘ggplot’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_density’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘aes’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_point’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_colour_gradientn’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘maPalette’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_x_discrete’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_hline’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘annotate’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_histogram’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_y_continuous’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_x_continuous’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_boxplot’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘theme_bw’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘geom_jitter’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘position_jitter’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘theme’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘element_text’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘unit’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_linetype_manual’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘scale_fill_manual’
plotDens2classInComp_plotOnly: no visible global function definition
  for ‘ggtitle’
plotDensAllAnnotInAllComp: no visible global function definition for
  ‘%dopar%’
plotDensAllAnnotInAllComp: no visible global function definition for
  ‘foreach’
plotDensOneAnnotInAllComp : vplayout: no visible global function
  definition for ‘viewport’
plotDensOneAnnotInAllComp: no visible global function definition for
  ‘ggsave’
plotMclust: no visible global function definition for ‘cdens’
plotMix: no visible global function definition for ‘cdens’
plotNumVarComp: no visible global function definition for ‘ggplot’
plotNumVarComp: no visible global function definition for ‘geom_point’
plotNumVarComp: no visible global function definition for ‘aes’
plotNumVarComp: no visible global function definition for ‘geom_smooth’
plotNumVarComp: no visible global function definition for
  ‘scale_colour_manual’
plotNumVarComp: no visible global function definition for
  ‘scale_shape_manual’
plotNumVarComp: no visible global function definition for ‘ggtitle’
plotNumVarComp: no visible global function definition for
  ‘scale_colour_gradientn’
plotNumVarComp: no visible global function definition for ‘maPalette’
plotPosOneAnnotInComp_ggplot : vplayout: no visible global function
  definition for ‘viewport’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘%dopar%’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘foreach’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘grid.newpage’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘pushViewport’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘viewport’
plotPosOneAnnotInComp_ggplot: no visible global function definition for
  ‘grid.layout’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘ggplot’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘geom_histogram’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘aes’
plotPosOneAnnotLevInComp_ggplot: no visible binding for global variable
  ‘..count..’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘scale_fill_manual’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘theme’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘element_text’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘unit’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘xlab’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘geom_point’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘scale_colour_gradientn’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘maPalette’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘geom_hline’
plotPosOneAnnotLevInComp_ggplot: no visible global function definition
  for ‘annotate’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘maPalette’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘maColorBar’
plotPosSamplesInComp : <anonymous>: no visible global function
  definition for ‘odd’
plotPosSamplesInComp_ggplot : vplayout: no visible global function
  definition for ‘viewport’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘%dopar%’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘foreach’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘ggplot’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘geom_histogram’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘aes’
plotPosSamplesInComp_ggplot: no visible binding for global variable
  ‘..count..’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘theme’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘element_text’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘unit’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘xlab’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘ggtitle’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘geom_point’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘scale_colour_gradientn’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘maPalette’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘geom_hline’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘annotate’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘grid.newpage’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘pushViewport’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘viewport’
plotPosSamplesInComp_ggplot: no visible global function definition for
  ‘grid.layout’
plot_heatmapsOnSel: no visible global function definition for
  ‘maPalette’
plot_heatmapsOnSel: no visible global function definition for ‘%do%’
plot_heatmapsOnSel: no visible global function definition for ‘foreach’
plot_heatmapsOnSel: no visible global function definition for ‘%dopar%’
plot_heatmapsOnSel: no visible global function definition for
  ‘maColorBar’
plot_heatmapsOnSel: no visible global function definition for ‘odd’
qualVarAnalysis: no visible global function definition for ‘%dopar%’
qualVarAnalysis: no visible global function definition for ‘foreach’
qualVarAnalysis : <anonymous>: no visible global function definition
  for ‘ggsave’
quantVarAnalysis: no visible global function definition for ‘%dopar%’
quantVarAnalysis: no visible global function definition for ‘foreach’
quantVarAnalysis : <anonymous>: no visible global function definition
  for ‘ggsave’
runAn: no visible global function definition for ‘useMart’
runAn: no visible global function definition for ‘%do%’
runAn: no visible global function definition for ‘foreach’
runAn: no visible global function definition for ‘maPalette’
runCompareIcaSets: no visible global function definition for ‘%do%’
runCompareIcaSets: no visible global function definition for ‘foreach’
runEnrich: no visible global function definition for ‘llply’
runEnrich: no visible global function definition for ‘listFilters’
runEnrich: no visible global function definition for ‘getBM’
runICA: no visible global function definition for ‘JADE’
runICA: no visible global function definition for ‘fastICA’
wilcoxOrKruskalOnA: no visible global function definition for ‘%dopar%’
wilcoxOrKruskalOnA: no visible global function definition for ‘foreach’
writeGenes: no visible global function definition for ‘useMart’
writeGenes: no visible global function definition for ‘listFilters’
writeGenes: no visible global function definition for ‘listAttributes’
writeGenes: no visible global function definition for ‘getBM’
writeGenes: no visible global function definition for ‘xtable’
writeGostatsHtmltable: no visible global function definition for
  ‘xtable’
writeHtmlResTestsByAnnot: no visible global function definition for
  ‘llply’
writeHtmlResTestsByAnnot: no visible global function definition for
  ‘xtable’
writeProjByComp: no visible global function definition for ‘useMart’
writeProjByComp: no visible global function definition for ‘%do%’
writeProjByComp: no visible global function definition for ‘foreach’
initialize,IcaSet : .local: no visible global function definition for
  ‘useMart’
selectContrib,IcaSet-numeric-character : .local: no visible global
  function definition for ‘%do%’
selectContrib,IcaSet-numeric-character : .local: no visible global
  function definition for ‘foreach’
selectContrib,IcaSet-numeric-character : .local: no visible binding for
  global variable ‘comp.proj’
selectContrib,IcaSet-numeric-character : .local: no visible binding for
  global variable ‘cutt’
selectContrib,list-numeric-ANY: no visible global function definition
  for ‘%do%’
selectContrib,list-numeric-ANY: no visible global function definition
  for ‘foreach’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'plotDens2classInComp_plotOnly.Rd':
  ‘ggplot2’

Missing link or links in documentation object 'plotPosOneAnnotLevInComp_ggplot.Rd':
  ‘ggplot2’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 ... [22s/35s] OK
Examples with CPU or elapsed time > 5s
              user system elapsed
class-IcaSet 0.952  0.017  13.974
* 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, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/MineICA.Rcheck/00check.log’
for details.

MineICA.Rcheck/00install.out:

* installing *source* package ‘MineICA’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for ‘sampleNames<-’ in package ‘MineICA’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MineICA)

MineICA.Rcheck/MineICA-Ex.timings:

nameusersystemelapsed
annotFeatures0.3910.0110.402
annotFeaturesComp2.2200.0202.243
annotFeaturesWithBiomaRt0.0020.0000.001
annotInGene1.0560.0111.069
annotReciprocal0.0090.0000.009
buildIcaSet0.4780.0220.522
buildMineICAParams0.0210.0170.039
class-IcaSet 0.952 0.01713.974
class-MineICAParams0.0040.0000.005
clusVarAnalysis0.1400.0180.158
clusterFastICARuns0.1390.0080.148
clusterSamplesByComp1.0250.0181.077
clusterSamplesByComp_multiple0.2970.0160.312
compareAn0.7010.0210.750
compareAn2graphfile0.6720.0160.690
compareGenes0.0010.0010.001
cor2An0.0280.0060.034
getProj0.0340.0080.042
getSdExpr0.0030.0000.003
hypergeoAn0.0020.0010.002
nbOccByGeneInComp0.0190.0020.021
nbOccInComp0.1760.0150.192
nbOccInComp_simple0.0630.0150.079
nodeAttrs0.0070.0010.008
plotAllMix0.6190.0050.640
plotCorGraph1.0940.0201.157
plotDensAllAnnotInAllComp0.0010.0010.001
plotDensOneAnnotInAllComp0.0010.0000.001
plotMclust0.0860.0000.086
plotMix0.0860.0000.087
plotPosAnnotInComp0.0010.0000.001
plotPosSamplesInComp0.0010.0010.001
plot_heatmapsOnSel0.0020.0000.001
qualVarAnalysis0.4590.0190.479
quantVarAnalysis0.1770.0260.204
relativePath0.0010.0000.001
runAn0.0000.0000.001
runCompareIcaSets0.8220.0270.851
runEnrich0.0010.0010.001
runICA0.0620.0010.064
selectContrib0.0010.0000.001
selectFeatures_IQR0.0950.0130.108
selectWitnessGenes0.2130.0160.230
writeGenes0.0030.0000.003
writeGostatsHtmltable0.0110.0010.012
writeProjByComp0.0010.0000.001