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 | |  |
| moscato1 | Windows Server 2008 R2 Standard (64-bit) / x64 | NotNeeded | OK | [ WARNINGS ] | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | WARNINGS | OK | |
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### Running command:
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### rm -rf MineICA.buildbin-libdir MineICA.Rcheck && mkdir MineICA.buildbin-libdir MineICA.Rcheck && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MineICA.buildbin-libdir MineICA_1.10.0.tar.gz >MineICA.Rcheck\00install.out 2>&1 && cp MineICA.Rcheck\00install.out MineICA-install.out && D:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MineICA.buildbin-libdir --install="check:MineICA-install.out" --force-multiarch --no-vignettes --timings MineICA_1.10.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.2-bioc/meat/MineICA.Rcheck'
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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
Package which this enhances but not available for checking: 'doMC'
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 whether package 'MineICA' can be installed ... WARNING
Found the following significant warnings:
Warning: package 'Matrix' was built under R version 3.2.5
See 'D:/biocbld/bbs-3.2-bioc/meat/MineICA.Rcheck/00install.out' for details.
* 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
* 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
** checking loading without being on the library search path ... 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 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [46s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
class-IcaSet 0.17 0.03 13.57
** running examples for arch 'x64' ... [48s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
class-IcaSet 0.2 0.02 13.68
* 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, 4 NOTEs
See
'D:/biocbld/bbs-3.2-bioc/meat/MineICA.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'MineICA' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: package 'Matrix' was built under R version 3.2.5
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
Warning: package 'Matrix' was built under R version 3.2.5
install for x64
* installing *source* package 'MineICA' ...
** testing if installed package can be loaded
Warning: package 'Matrix' was built under R version 3.2.5
* MD5 sums
packaged installation of 'MineICA' as MineICA_1.10.0.zip
* DONE (MineICA)