inSilicoMerging 1.16.0
InSilico DB
| Snapshot Date: 2016-10-12 17:20:15 -0700 (Wed, 12 Oct 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_3/madman/Rpacks/inSilicoMerging | | Last Changed Rev: 117079 / Revision: 122332 | | Last Changed Date: 2016-05-03 14:20:18 -0700 (Tue, 03 May 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ ERROR ] | | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | ERROR | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | ERROR | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings inSilicoMerging_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/inSilicoMerging.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘inSilicoMerging/DESCRIPTION’ ... OK
* this is package ‘inSilicoMerging’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘inSilicoMerging’ can be installed ... WARNING
Found the following significant warnings:
Warning: Package 'inSilicoDb' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.3-bioc/meat/inSilicoMerging.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘Biobase’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘BiocGenerics:::testPackage’
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
aprior: no visible global function definition for ‘var’
bprior: no visible global function definition for ‘var’
commonGenes : <anonymous>: no visible global function definition for
‘exprs’
geneBMCESet: no visible global function definition for ‘exprs<-’
geneBMCESet: no visible global function definition for ‘exprs’
geneNormESet: no visible global function definition for ‘exprs<-’
geneNormESet: no visible global function definition for ‘exprs’
geneNormESet : <anonymous>: no visible global function definition for
‘sd’
identify_common_genes: no visible global function definition for
‘exprs’
makeColorMap: no visible global function definition for ‘pData’
makeColorVec: no visible global function definition for ‘pData’
matchExprsPheno: no visible global function definition for ‘exprs’
matchExprsPheno: no visible global function definition for ‘pData<-’
matchExprsPheno: no visible global function definition for ‘pData’
mergeCOMBAT: no visible global function definition for ‘pData’
mergeCOMBAT: no visible global function definition for ‘exprs’
mergeCOMBAT: no visible binding for global variable ‘var’
mergeCOMBAT: no visible global function definition for ‘exprs<-’
mergeNONE: no visible global function definition for ‘annotation’
mergeNONE: no visible global function definition for ‘exprs’
mergeNONE: no visible global function definition for ‘new’
mergeNONE: no visible global function definition for ‘exprs<-’
mergeNONE: no visible global function definition for ‘pData<-’
mergeNONE: no visible global function definition for ‘fData<-’
mergeNONE: no visible global function definition for ‘annotation<-’
plotGeneWiseBoxPlot: no visible global function definition for ‘pdf’
plotGeneWiseBoxPlot: no visible global function definition for ‘exprs’
plotGeneWiseBoxPlot: no visible global function definition for ‘par’
plotGeneWiseBoxPlot: no visible global function definition for ‘pData’
plotGeneWiseBoxPlot: no visible global function definition for ‘plot’
plotGeneWiseBoxPlot: no visible global function definition for
‘boxplot’
plotGeneWiseBoxPlot: no visible global function definition for ‘rect’
plotGeneWiseBoxPlot: no visible global function definition for ‘axis’
plotGeneWiseBoxPlot: no visible global function definition for
‘dev.off’
plotMDS: no visible global function definition for ‘pdf’
plotMDS: no visible global function definition for ‘cmdscale’
plotMDS: no visible global function definition for ‘dist’
plotMDS: no visible global function definition for ‘exprs’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘plot’
plotMDS: no visible global function definition for ‘pData’
plotMDS: no visible global function definition for ‘rect’
plotMDS: no visible global function definition for ‘dev.off’
plotRLE: no visible global function definition for ‘pdf’
plotRLE: no visible global function definition for ‘exprs’
plotRLE: no visible global function definition for ‘rowMedians’
plotRLE: no visible global function definition for ‘par’
plotRLE: no visible global function definition for ‘plot’
plotRLE: no visible global function definition for ‘lines’
plotRLE: no visible global function definition for ‘rect’
plotRLE: no visible global function definition for ‘boxplot.matrix’
plotRLE: no visible global function definition for ‘dev.off’
xpn: no visible global function definition for ‘exprs’
xpn: no visible global function definition for ‘sd’
xpn: no visible global function definition for ‘exprs<-’
xpn: no visible global function definition for ‘median’
xpn: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
annotation annotation<- axis boxplot boxplot.matrix cmdscale dev.off
dist exprs exprs<- fData<- kmeans lines median new pData pData<- par
pdf plot rect rowMedians sd var
Consider adding
importFrom("grDevices", "dev.off", "pdf")
importFrom("graphics", "axis", "boxplot", "boxplot.matrix", "lines",
"par", "plot", "rect")
importFrom("methods", "new")
importFrom("stats", "cmdscale", "dist", "kmeans", "median", "sd",
"var")
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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘inSilicoMerging-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotGeneWiseBoxPlot
> ### Title: Create gene-wise boxplot from (merged) ExpressionSet
> ### Aliases: plotGeneWiseBoxPlot
>
> ### ** Examples
>
>
> # retrieve two datasets:
> library(inSilicoDb);
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
Warning: Package 'inSilicoDb' is deprecated and will be removed from
Bioconductor version 3.3
> InSilicoLogin("rpackage_tester@insilicodb.com", "5c4d0b231e5cba4a0bc54783b385cc9a");
INSILICODB: Welcome RPackage Tester
[1] 5296
> eset1 = getDataset("GSE18842", "GPL570", norm="FRMA", features="gene");
INSILICODB: The dataset you requested is available for download.
INSILICODB: Dataset GSE18842, GPL570, CURESET, GENE, FRMA, 37369, RNA, Gene expression analysis of human lung cancer and control samples, finished, GSE18842GPL570_RNA_FRMAGENE_37369.RData
INSILICODB: Requested dataset found in local file: cache/GSE18842GPL570_RNA_FRMAGENE_37369.RData
> eset2 = getDataset("GSE31547", "GPL96", norm="FRMA", features="gene");
INSILICODB: The dataset you requested is available for download.
INSILICODB: Dataset GSE31547, GPL96, CURESET, GENE, FRMA, 38206, RNA, MSKCC-A Primary Lung Cancer Specimens, finished, GSE31547GPL96_RNA_FRMAGENE_38206.RData
INSILICODB: Requested dataset found in local file: cache/GSE31547GPL96_RNA_FRMAGENE_38206.RData
> esets = list(eset1,eset2);
>
> # merge them using no additional merging technique and the 'COMBAT' method:
> library(inSilicoMerging)
> eset_FRMA = merge(esets);
INSILICOMERGING: Run with no additional merging technique...
> eset_COMBAT = merge(esets, method="COMBAT");
INSILICOMERGING: Run COMBAT...
INSILICOMERGING: => Found 2 batches
INSILICOMERGING: => Found 0 covariate(s)
>
> # check available annotations:
> colnames(pData(eset_FRMA))
[1] "DiseaseState" "characteristics" "source_name" "title"
> table(pData(eset_FRMA)[,"Disease"]);
Error in `[.data.frame`(pData(eset_FRMA), , "Disease") :
undefined columns selected
Calls: table ... standardGeneric -> eval -> eval -> eval -> [ -> [.data.frame
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘inSilicoMerging_unit_tests.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.3-bioc/meat/inSilicoMerging.Rcheck/00check.log’
for details.