| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-02-27 02:34:37 -0000 (Mon, 27 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4259 |
| 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? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1194/2169 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MineICA 1.39.0 (landing page) Anne Biton
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: MineICA |
| Version: 1.39.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MineICA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MineICA_1.39.0.tar.gz |
| StartedAt: 2023-02-24 14:13:22 -0000 (Fri, 24 Feb 2023) |
| EndedAt: 2023-02-24 14:19:42 -0000 (Fri, 24 Feb 2023) |
| EllapsedTime: 380.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: MineICA.Rcheck |
| Warnings: NA |
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### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:MineICA.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings MineICA_1.39.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/MineICA.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘MineICA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MineICA’ version ‘1.39.0’
* 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 ... 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 dependencies in R code ... WARNING
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.
Missing or unexported object: ‘GOstats::geneIdsByCategory’
':::' 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
‘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 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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘MineICA.Rnw’... failed
ERROR
Errors in running code in vignettes:
when running code in ‘MineICA.Rnw’
...
[25] "hgu133aPFAM" "hgu133aPMID" "hgu133aPMID2PROBE"
[28] "hgu133aPROSITE" "hgu133aREFSEQ" "hgu133aSYMBOL"
[31] "hgu133aUNIPROT" "hgu133a_dbInfo" "hgu133a_dbconn"
[34] "hgu133a_dbfile" "hgu133a_dbschema"
> mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
When sourcing ‘MineICA.R’:
Error: Timeout was reached: [www.ensembl.org:443] Operation timed out after 10000 milliseconds with 117181 bytes received
Execution halted
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘MineICA.Rnw’ using Sweave
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: Category
Loading required package: stats4
Loading required package: AnnotationDbi
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:plyr’:
rename
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Attaching package: ‘IRanges’
The following object is masked from ‘package:plyr’:
desc
Loading required package: Matrix
Attaching package: ‘Matrix’
The following object is masked from ‘package:S4Vectors’:
expand
Loading required package: graph
Attaching package: ‘graph’
The following object is masked from ‘package:plyr’:
join
Attaching package: ‘GOstats’
The following object is masked from ‘package:AnnotationDbi’:
makeGOGraph
Loading required package: limma
Attaching package: ‘limma’
The following object is masked from ‘package:BiocGenerics’:
plotMA
Package 'mclust' version 6.0.0
Type 'citation("mclust")' for citing this R package in publications.
Attaching package: ‘igraph’
The following objects are masked from ‘package:graph’:
degree, edges, intersection, union
The following object is masked from ‘package:IRanges’:
union
The following object is masked from ‘package:S4Vectors’:
union
The following objects are masked from ‘package:BiocGenerics’:
normalize, path, union
The following objects are masked from ‘package:stats’:
decompose, spectrum
The following object is masked from ‘package:base’:
union
Loading required package: grid
Attaching package: ‘Rgraphviz’
The following objects are masked from ‘package:IRanges’:
from, to
The following objects are masked from ‘package:S4Vectors’:
from, to
Loading required package: XML
Attaching package: ‘XML’
The following object is masked from ‘package:graph’:
addNode
Attaching package: ‘annotate’
The following object is masked from ‘package:Rgraphviz’:
toFile
Attaching package: ‘gtools’
The following object is masked from ‘package:igraph’:
permute
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Attaching package: ‘Hmisc’
The following object is masked from ‘package:AnnotationDbi’:
contents
The following objects are masked from ‘package:xtable’:
label, label<-
The following objects are masked from ‘package:plyr’:
is.discrete, summarize
The following object is masked from ‘package:Biobase’:
contents
The following objects are masked from ‘package:base’:
format.pval, units
Loading required package: fastICA
Loading required package: JADE
Number of selected genes is 10000
Max IQR is 0.89
Loading required package: org.Hs.eg.db
Error: processing vignette 'MineICA.Rnw' failed with diagnostics:
chunk 10 (label = mart)
Error in curl::curl_fetch_memory(url, handle = handle) :
Timeout was reached: [www.ensembl.org:443] Operation timed out after 10001 milliseconds with 0 bytes received
--- failed re-building ‘MineICA.Rnw’
SUMMARY: processing the following file failed:
‘MineICA.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 3 WARNINGs, 4 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/MineICA.Rcheck/00check.log’
for details.
MineICA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL MineICA ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-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 ** 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)
MineICA.Rcheck/MineICA-Ex.timings
| name | user | system | elapsed | |
| annotFeatures | 0.991 | 0.064 | 1.054 | |
| annotFeaturesComp | 2.992 | 0.015 | 3.008 | |
| annotFeaturesWithBiomaRt | 0.001 | 0.000 | 0.001 | |
| annotInGene | 1.432 | 0.076 | 1.507 | |
| annotReciprocal | 0.006 | 0.000 | 0.006 | |
| buildIcaSet | 0.403 | 0.014 | 0.417 | |
| buildMineICAParams | 0.007 | 0.009 | 0.016 | |
| class-IcaSet | 0.242 | 0.024 | 2.757 | |
| class-MineICAParams | 0.003 | 0.000 | 0.003 | |
| clusVarAnalysis | 0.091 | 0.019 | 0.109 | |
| clusterFastICARuns | 0.444 | 0.035 | 0.480 | |
| clusterSamplesByComp | 0.887 | 0.032 | 0.919 | |
| clusterSamplesByComp_multiple | 0.219 | 0.030 | 0.249 | |
| compareAn | 0.605 | 0.020 | 0.625 | |
| compareAn2graphfile | 0.505 | 0.000 | 0.504 | |
| compareGenes | 0.001 | 0.000 | 0.000 | |
| cor2An | 0.012 | 0.008 | 0.019 | |
| getProj | 0.024 | 0.002 | 0.026 | |
| getSdExpr | 0.000 | 0.001 | 0.002 | |
| hypergeoAn | 0.000 | 0.000 | 0.001 | |
| nbOccByGeneInComp | 0.014 | 0.000 | 0.015 | |
| nbOccInComp | 0.151 | 0.003 | 0.153 | |
| nbOccInComp_simple | 0.039 | 0.007 | 0.044 | |
| nodeAttrs | 0.005 | 0.000 | 0.006 | |
| plotAllMix | 0.555 | 0.003 | 0.558 | |
| plotCorGraph | 0.829 | 0.013 | 0.843 | |
| plotDensAllAnnotInAllComp | 0 | 0 | 0 | |
| plotDensOneAnnotInAllComp | 0 | 0 | 0 | |
| plotMclust | 0.076 | 0.003 | 0.078 | |
| plotMix | 0.075 | 0.004 | 0.079 | |
| plotPosAnnotInComp | 0 | 0 | 0 | |
| plotPosSamplesInComp | 0.001 | 0.000 | 0.000 | |
| plot_heatmapsOnSel | 0.001 | 0.000 | 0.000 | |
| qualVarAnalysis | 0.100 | 0.007 | 0.107 | |
| quantVarAnalysis | 0.137 | 0.004 | 0.140 | |
| relativePath | 0 | 0 | 0 | |
| runAn | 0 | 0 | 0 | |
| runCompareIcaSets | 0.592 | 0.001 | 0.593 | |
| runEnrich | 0.001 | 0.000 | 0.000 | |
| runICA | 0.081 | 0.000 | 0.080 | |
| selectContrib | 0 | 0 | 0 | |
| selectFeatures_IQR | 0.157 | 0.003 | 0.161 | |
| selectWitnessGenes | 0.164 | 0.002 | 0.166 | |
| writeGenes | 0.001 | 0.000 | 0.001 | |
| writeGostatsHtmltable | 0.009 | 0.000 | 0.008 | |
| writeProjByComp | 0.001 | 0.000 | 0.000 | |