Anne Biton
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/MineICA |
| git_branch: master |
| git_last_commit: 7293f30 |
| git_last_commit_date: 2021-10-26 12:06:44 -0400 (Tue, 26 Oct 2021) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:08:02 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the MineICA package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MineICA.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1159/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MineICA 1.35.0 (landing page) Anne Biton
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| Package: MineICA |
| Version: 1.35.0 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MineICA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MineICA_1.35.0.tar.gz |
| StartedAt: 2022-03-17 19:35:42 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 19:39:47 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 244.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MineICA.Rcheck |
| Warnings: 3 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MineICA.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings MineICA_1.35.0.tar.gz
###
##############################################################################
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/MineICA.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* 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 '1.35.0'
* 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:
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/MineICA/man/Alist.Rd:26: missing link 'class-IcaSet'
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/MineICA/man/Slist.Rd:28: missing link 'class-IcaSet'
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/MineICA/man/class-IcaSet.Rd:321: missing link 'class-IcaSet'
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/MineICA/man/getComp.Rd:33: missing link 'class-IcaSet'
See 'D:/biocbuild/bbs-3.15-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
* 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' 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 'cm.colors'
annot2Color: no visible global function definition for 'rainbow_hcl'
annotFeatures: no visible global function definition for 'na.omit'
annotFeaturesComp: no visible global function definition for 'getEG'
annotFeaturesComp: no visible global function definition for
'getSYMBOL'
annotFeaturesComp: no visible global function definition for 'llply'
annotFeaturesComp : <anonymous> : <anonymous>: no visible global
function definition for 'median'
annotFeaturesComp : <anonymous>: no visible binding for global variable
'median'
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'
annotReciprocal: no visible global function definition for
'write.table'
buildIcaSet: no visible global function definition for 'new'
buildIcaSet: no visible global function definition for 'read.table'
buildMineICAParams: no visible global function definition for 'new'
clusVarAnalysis : <anonymous> : <anonymous>: no visible global function
definition for 'chisq.test'
clusVarAnalysis : <anonymous> : <anonymous> : <anonymous>: no visible
global function definition for 'chisq.test'
clusVarAnalysis: no visible binding for global variable 'p.adjust'
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'
clusVarAnalysis: no visible global function definition for
'write.table'
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 'cor'
clusterFastICARuns: no visible global function definition for 'hclust'
clusterFastICARuns: no visible global function definition for 'as.dist'
clusterFastICARuns: no visible global function definition for 'cutree'
clusterFastICARuns: no visible global function definition for 'agnes'
clusterFastICARuns: no visible global function definition for
'as.hclust'
clusterFastICARuns: no visible global function definition for 'pam'
clusterFastICARuns: no visible global function definition for 'kmeans'
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
'kmeans'
clusterSamplesByComp: no visible global function definition for 'pam'
clusterSamplesByComp: no visible global function definition for 'dist'
clusterSamplesByComp: no visible global function definition for
'hclust'
clusterSamplesByComp: no visible global function definition for
'cutree'
clusterSamplesByComp: no visible global function definition for 'agnes'
clusterSamplesByComp: no visible global function definition for
'as.hclust'
clusterSamplesByComp: no visible binding for global variable 'cluster'
clusterSamplesByComp: no visible global function definition for
'write.table'
clusterSamplesByComp_multiple: no visible global function definition
for '%do%'
clusterSamplesByComp_multiple: no visible global function definition
for 'foreach'
clusterSamplesByComp_multiple: no visible global function definition
for 'aggregate'
clusterSamplesByComp_multiple: no visible global function definition
for 'write.table'
compareAn: no visible global function definition for 'combn'
compareAn2graphfile : <anonymous>: no visible binding for global
variable 'cor'
compareAn2graphfile: no visible global function definition for
'write.table'
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'
compareGenes: no visible binding for global variable 'median'
cor2An: no visible global function definition for 'rcorr'
cor2An : <anonymous>: no visible global function definition for
'cor.test'
cor2An: no visible global function definition for 'cor.test'
correl2Comp: no visible global function definition for 'cor.test'
correl2Comp: no visible global function definition for 'cor'
doEnrichment: no visible global function definition for 'na.omit'
doEnrichment: no visible global function definition for 'new'
doEnrichment: no visible global function definition for 'hyperGTest'
heatmap.plus: no visible binding for global variable 'dist'
heatmap.plus: no visible binding for global variable 'agnes'
heatmap.plus : <anonymous>: no visible global function definition for
'reorder'
heatmap.plus: no visible global function definition for 'as.dendrogram'
heatmap.plus: no visible global function definition for 'as.hclust'
heatmap.plus: no visible global function definition for
'order.dendrogram'
heatmap.plus: no visible global function definition for 'par'
heatmap.plus: no visible global function definition for 'layout'
heatmap.plus: no visible global function definition for 'axis'
heatmap.plus: no visible global function definition for 'quantile'
heatmap.plus: no visible global function definition for 'heat.colors'
heatmap.plus: no visible global function definition for 'mtext'
heatmap.plus: no visible global function definition for 'frame'
heatmap.plus: no visible global function definition for 'title'
hypergeoAn: no visible global function definition for 'na.omit'
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 'capture.output'
mergeGostatsResults : <anonymous>: no visible global function
definition for '%do%'
mergeGostatsResults: no visible global function definition for 'xtable'
mergeGostatsResults: no visible global function definition for
'capture.output'
nbOccInComp: no visible global function definition for 'read.table'
nbOccInComp: no visible global function definition for 'aggregate'
nbOccInComp: no visible global function definition for 'pdf'
nbOccInComp: no visible global function definition for 'dev.off'
nbOccInComp: no visible global function definition for '%dopar%'
nbOccInComp: no visible global function definition for 'foreach'
nbOccInComp: no visible global function definition for 'xtable'
nbOccInComp: no visible global function definition for 'capture.output'
nodeAttrs: no visible global function definition for '%do%'
nodeAttrs: no visible global function definition for 'foreach'
nodeAttrs: no visible global function definition for 'write.table'
plotAllMix: no visible binding for global variable 'Mclust'
plotAllMix: no visible global function definition for 'par'
plotAllMix: no visible global function definition for 'dev.off'
plotCorGraph: no visible global function definition for 'brewer.pal'
plotCorGraph: no visible global function definition for 'llply'
plotCorGraph: no visible global function definition for 'new'
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'
plotMclust: no visible global function definition for 'points'
plotMix: no visible global function definition for 'shapiro.test'
plotMix: no visible global function definition for 'cdens'
plotMix: no visible global function definition for 'hist'
plotMix: no visible global function definition for 'points'
plotMix : <anonymous>: no visible global function definition for
'points'
plotMix: no visible global function definition for 'lm'
plotMix: no visible global function definition for 'axis'
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 binding for global variable 'lm'
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'
plotPos2classInComp: no visible global function definition for 'pdf'
plotPos2classInComp: no visible global function definition for 'par'
plotPos2classInComp: no visible global function definition for 'hist'
plotPos2classInComp: no visible global function definition for 'lm'
plotPos2classInComp: no visible global function definition for 'axis'
plotPos2classInComp: no visible global function definition for 'abline'
plotPos2classInComp: no visible global function definition for 'legend'
plotPos2classInComp: no visible global function definition for
'dev.off'
plotPosAnnotInComp : <anonymous>: no visible global function definition
for 'graphics.off'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
'pdf'
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'
plotPosOneAnnotInComp_ggplot: no visible global function definition for
'dev.off'
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: no visible global function definition for 'pdf'
plotPosSamplesInComp: no visible global function definition for 'par'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'chisq.test'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'par'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'hist'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'lm'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'axis'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'legend'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'abline'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'points'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'quantile'
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 : <anonymous>: no visible global function
definition for 'mtext'
plotPosSamplesInComp : <anonymous>: no visible global function
definition for 'title'
plotPosSamplesInComp: no visible global function definition for
'dev.off'
plotPosSamplesInComp_ggplot: no visible global function definition for
'pdf'
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'
plotPosSamplesInComp_ggplot: no visible global function definition for
'dev.off'
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 'pdf'
plot_heatmapsOnSel: no visible global function definition for
'plot.new'
plot_heatmapsOnSel: no visible global function definition for 'legend'
plot_heatmapsOnSel: no visible global function definition for 'dev.off'
plot_heatmapsOnSel: no visible global function definition for '%dopar%'
plot_heatmapsOnSel: no visible global function definition for 'par'
plot_heatmapsOnSel: no visible global function definition for
'maColorBar'
plot_heatmapsOnSel: no visible global function definition for 'odd'
qualVarAnalysis : <anonymous> : <anonymous>: no visible global function
definition for 'wilcox.test'
qualVarAnalysis : <anonymous> : <anonymous>: no visible global function
definition for 'kruskal.test'
qualVarAnalysis: no visible binding for global variable 'p.adjust'
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 : <anonymous> : <anonymous>: no visible global
function definition for 'cor.test'
quantVarAnalysis: no visible binding for global variable 'p.adjust'
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'
readA: no visible global function definition for 'read.table'
readS: no visible global function definition for 'read.table'
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 : <anonymous>: no visible global function definition for
'na.omit'
runEnrich: no visible global function definition for 'na.omit'
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'
subIcaSet: no visible global function definition for 'validObject'
wilcoxOrKruskalOnA: no visible global function definition for '%dopar%'
wilcoxOrKruskalOnA: no visible global function definition for 'foreach'
wilcoxOrKruskalOnA: no visible global function definition for
'wilcox.test'
wilcoxOrKruskalOnA: no visible global function definition for
'kruskal.test'
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'
writeGenes: no visible global function definition for 'capture.output'
writeGostatsHtmltable: no visible global function definition for
'xtable'
writeGostatsHtmltable: no visible global function definition for
'capture.output'
writeHtmlResTestsByAnnot: no visible global function definition for
'llply'
writeHtmlResTestsByAnnot: no visible global function definition for
'xtable'
writeHtmlResTestsByAnnot: no visible global function definition for
'capture.output'
writeProjByComp: no visible global function definition for 'useMart'
writeProjByComp: no visible global function definition for '%do%'
writeProjByComp: no visible global function definition for 'foreach'
writeRnkFiles : <anonymous>: no visible global function definition for
'write.table'
A<-,IcaSet: no visible global function definition for 'validObject'
Afile<-,MineICAParams: no visible global function definition for
'validObject'
S<-,IcaSet: no visible global function definition for 'validObject'
SByGene<-,IcaSet: no visible global function definition for
'validObject'
Sfile<-,MineICAParams: no visible global function definition for
'validObject'
[<-,IcaSet-ANY-ANY-ANY: no visible global function definition for
'validObject'
[<-,MineICAParams-ANY-ANY-ANY: no visible global function definition
for 'validObject'
annot2col<-,MineICAParams: no visible global function definition for
'validObject'
annotfile<-,MineICAParams: no visible global function definition for
'validObject'
chipManu<-,IcaSet: no visible global function definition for
'validObject'
chipVersion<-,IcaSet: no visible global function definition for
'validObject'
compNames<-,IcaSet: no visible global function definition for
'validObject'
dat<-,IcaSet: no visible global function definition for 'validObject'
datByGene<-,IcaSet: no visible global function definition for
'validObject'
datfile<-,MineICAParams: no visible global function definition for
'validObject'
genesPath<-,ANY: no visible global function definition for
'validObject'
indComp<-,IcaSet: no visible global function definition for
'validObject'
initialize,IcaSet: no visible global function definition for 'new'
initialize,IcaSet: no visible global function definition for 'useMart'
initialize,IcaSet: no visible global function definition for
'callNextMethod'
mart<-,IcaSet: no visible global function definition for 'validObject'
organism<-,IcaSet: no visible global function definition for
'validObject'
package<-,IcaSet: no visible global function definition for
'validObject'
pvalCutoff<-,MineICAParams: no visible global function definition for
'validObject'
refSamples<-,IcaSet: no visible global function definition for
'validObject'
resPath<-,ANY: no visible global function definition for 'validObject'
sampleNames<-,IcaSet: no visible global function definition for
'callNextMethod'
selCutoff<-,MineICAParams: no visible global function definition for
'validObject'
selectContrib,IcaSet-numeric-character: no visible global function
definition for '%do%'
selectContrib,IcaSet-numeric-character: no visible global function
definition for 'foreach'
selectContrib,IcaSet-numeric-character: no visible binding for global
variable 'comp.proj'
selectContrib,IcaSet-numeric-character: 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'
setA<-,IcaSet: no visible global function definition for 'validObject'
setAfile<-,MineICAParams: no visible global function definition for
'validObject'
setAnnot2col<-,MineICAParams: no visible global function definition for
'validObject'
setAnnotation<-,IcaSet: no visible global function definition for
'validObject'
setAnnotfile<-,MineICAParams: no visible global function definition for
'validObject'
setChipManu<-,IcaSet: no visible global function definition for
'validObject'
setChipVersion<-,IcaSet: no visible global function definition for
'validObject'
setDatfile<-,MineICAParams: no visible global function definition for
'validObject'
setGenesPath<-,ANY: no visible global function definition for
'validObject'
setIndComp<-,IcaSet: no visible global function definition for
'validObject'
setLabelsComp<-,IcaSet: no visible global function definition for
'validObject'
setMart<-,IcaSet: no visible global function definition for
'validObject'
setPackage<-,IcaSet: no visible global function definition for
'validObject'
setPvalCutoff<-,MineICAParams: no visible global function definition
for 'validObject'
setRefSamples<-,IcaSet: no visible global function definition for
'validObject'
setResPath<-,ANY: no visible global function definition for
'validObject'
setSByGene<-,IcaSet: no visible global function definition for
'validObject'
setSelCutoff<-,MineICAParams: no visible global function definition for
'validObject'
setSfile<-,MineICAParams: no visible global function definition for
'validObject'
setTypeID<-,IcaSet: no visible global function definition for
'validObject'
setWitGenes<-,IcaSet: no visible global function definition for
'validObject'
show,IcaSet: no visible global function definition for 'callNextMethod'
typeID<-,IcaSet: no visible global function definition for
'validObject'
witGenes<-,IcaSet: no visible global function definition for
'validObject'
Undefined global functions or variables:
%do% %dopar% ..count.. E E<- JADE Mclust V V<- abline aes aggregate
agnes annotate as.dendrogram as.dist as.hclust axis brewer.pal
callNextMethod capture.output cdens chisq.test cluster cm.colors
combn comp.proj conditional cor cor.test cutree cutt dev.off dist
element_text fastICA foreach frame geneIdUniverse geneIdsByCategory
geom_bar geom_boxplot geom_density geom_histogram geom_hline
geom_jitter geom_point geom_smooth getBM getEG getSYMBOL ggplot
ggsave ggtitle graphics.off grid.layout grid.newpage hclust
heat.colors heat_hcl hist hyperGTest igraph.from.graphNEL kmeans
kruskal.test layout layout.fruchterman.reingold legend listAttributes
listFilters llply lm maColorBar maPalette median mtext na.omit new
odd order.dendrogram p.adjust pam par pdf plot.new points
position_jitter pushViewport quantile rainbow_hcl rcorr read.table
reorder scale_colour_gradientn scale_colour_manual scale_fill_manual
scale_linetype_manual scale_shape_manual scale_x_continuous
scale_x_discrete scale_y_continuous shapiro.test sigCategories
terrain_hcl theme theme_bw title tkplot.fit.to.screen unit useMart
validObject vcount viewport wilcox.test write.table xlab xtable
Consider adding
importFrom("grDevices", "cm.colors", "dev.off", "graphics.off",
"heat.colors", "pdf")
importFrom("graphics", "abline", "axis", "frame", "hist", "layout",
"legend", "mtext", "par", "plot.new", "points", "title")
importFrom("methods", "callNextMethod", "new", "validObject")
importFrom("stats", "aggregate", "as.dendrogram", "as.dist",
"as.hclust", "chisq.test", "cor", "cor.test", "cutree",
"dist", "hclust", "kmeans", "kruskal.test", "lm", "median",
"na.omit", "order.dendrogram", "p.adjust", "quantile",
"reorder", "shapiro.test", "wilcox.test")
importFrom("utils", "capture.output", "combn", "read.table",
"write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'Alist.Rd':
'class-IcaSet'
Missing link or links in documentation object 'Slist.Rd':
'class-IcaSet'
Missing link or links in documentation object 'class-IcaSet.Rd':
'class-IcaSet'
Missing link or links in documentation object 'getComp.Rd':
'class-IcaSet'
Missing link or links in documentation object 'runAn.Rd':
'[Category:class-GOHyperGParams]{GOHyperGParams}'
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
'MineICAParams'
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 files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
clusterFastICARuns 0.86 0.15 29.32
* 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: 3 WARNINGs, 4 NOTEs
See
'D:/biocbuild/bbs-3.15-bioc/meat/MineICA.Rcheck/00check.log'
for details.
MineICA.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL MineICA
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'MineICA' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'sampleNames<-' in package 'MineICA'
** help
*** installing help indices
converting help for package 'MineICA'
finding HTML links ... done
A html
Alist html
finding level-2 HTML links ... done
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/MineICA/man/Alist.Rd:26: missing link 'class-IcaSet'
Slist html
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/MineICA/man/Slist.Rd:28: missing link 'class-IcaSet'
addGenesToGoReport html
annot2Color html
annotCarbayo html
annotFeatures html
annotFeaturesComp html
annotFeaturesWithBiomaRt html
annotInGene html
annotReciprocal html
buildIcaSet html
buildMineICAParams html
build_sortHeatmap html
class-IcaSet html
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/MineICA/man/class-IcaSet.Rd:321: missing link 'class-IcaSet'
class-MineICAParams html
clusVarAnalysis html
clusterFastICARuns html
clusterSamplesByComp html
clusterSamplesByComp_multiple html
compareAn html
compareAn2graphfile html
compareGenes html
cor2An html
correl2Comp html
dat html
dataCarbayo html
doEnrichment html
getComp html
Rd warning: D:/biocbuild/bbs-3.15-bioc/meat/MineICA/man/getComp.Rd:33: missing link 'class-IcaSet'
getProj html
getSdExpr html
hgOver html
hypergeoAn html
icaSetCarbayo html
icaSetKim html
icaSetRiester html
icaSetStransky html
indComp html
mergeGostatsResults html
nbOccByGeneInComp html
nbOccInComp html
nbOccInComp_simple html
nodeAttrs html
plotAllMix html
plotCorGraph html
plotDens2classInComp_plotOnly html
plotDensAllAnnotInAllComp html
plotDensOneAnnotInAllComp html
plotMclust html
plotMix html
plotPosAnnotInComp html
plotPosOneAnnotInComp_ggplot html
plotPosOneAnnotLevInComp_ggplot html
plotPosSamplesInComp html
plot_heatmapsOnSel html
qualVarAnalysis html
quantVarAnalysis html
readA html
readS html
relativePath html
runAn html
runCompareIcaSets html
runEnrich html
runICA html
selectContrib html
selectFeatures_IQR html
selectWitnessGenes html
wilcoxOrKruskalOnA html
writeGenes html
writeGostatsHtmltable html
writeHtmlResTestsByAnnot html
writeProjByComp html
writeRnkFiles html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (MineICA)
Making 'packages.html' ... done
MineICA.Rcheck/MineICA-Ex.timings
| name | user | system | elapsed | |
| annotFeatures | 0.25 | 0.05 | 0.30 | |
| annotFeaturesComp | 2.22 | 0.00 | 2.28 | |
| annotFeaturesWithBiomaRt | 0 | 0 | 0 | |
| annotInGene | 1.18 | 0.01 | 1.19 | |
| annotReciprocal | 0.01 | 0.00 | 0.01 | |
| buildIcaSet | 0.35 | 0.02 | 0.63 | |
| buildMineICAParams | 0.01 | 0.00 | 0.54 | |
| class-IcaSet | 0.24 | 0.01 | 1.27 | |
| class-MineICAParams | 0.00 | 0.02 | 0.01 | |
| clusVarAnalysis | 0.07 | 0.01 | 0.36 | |
| clusterFastICARuns | 0.86 | 0.15 | 29.32 | |
| clusterSamplesByComp | 1.32 | 0.01 | 1.57 | |
| clusterSamplesByComp_multiple | 0.14 | 0.02 | 0.47 | |
| compareAn | 0.32 | 0.06 | 0.58 | |
| compareAn2graphfile | 0.22 | 0.00 | 0.41 | |
| compareGenes | 0 | 0 | 0 | |
| cor2An | 0.02 | 0.00 | 0.01 | |
| getProj | 0.01 | 0.01 | 0.03 | |
| getSdExpr | 0 | 0 | 0 | |
| hypergeoAn | 0 | 0 | 0 | |
| nbOccByGeneInComp | 0.02 | 0.00 | 0.02 | |
| nbOccInComp | 0.11 | 0.00 | 0.41 | |
| nbOccInComp_simple | 0.01 | 0.00 | 0.32 | |
| nodeAttrs | 0.02 | 0.00 | 0.02 | |
| plotAllMix | 0.75 | 0.00 | 0.77 | |
| plotCorGraph | 0.48 | 0.07 | 0.84 | |
| plotDensAllAnnotInAllComp | 0 | 0 | 0 | |
| plotDensOneAnnotInAllComp | 0 | 0 | 0 | |
| plotMclust | 0.13 | 0.00 | 0.12 | |
| plotMix | 0.11 | 0.00 | 0.11 | |
| plotPosAnnotInComp | 0 | 0 | 0 | |
| plotPosSamplesInComp | 0 | 0 | 0 | |
| plot_heatmapsOnSel | 0 | 0 | 0 | |
| qualVarAnalysis | 0.09 | 0.00 | 0.41 | |
| quantVarAnalysis | 0.07 | 0.01 | 0.42 | |
| relativePath | 0 | 0 | 0 | |
| runAn | 0 | 0 | 0 | |
| runCompareIcaSets | 0.45 | 0.00 | 0.63 | |
| runEnrich | 0 | 0 | 0 | |
| runICA | 0.03 | 0.00 | 0.03 | |
| selectContrib | 0 | 0 | 0 | |
| selectFeatures_IQR | 0.08 | 0.00 | 0.08 | |
| selectWitnessGenes | 0.08 | 0.02 | 0.37 | |
| writeGenes | 0 | 0 | 0 | |
| writeGostatsHtmltable | 0 | 0 | 0 | |
| writeProjByComp | 0 | 0 | 0 | |