regionReport 1.8.2
Leonardo Collado-Torres
| Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/regionReport | | Last Changed Rev: 127200 / Revision: 128728 | | Last Changed Date: 2017-03-06 13:01:40 -0500 (Mon, 06 Mar 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ ERROR ] | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf regionReport.buildbin-libdir regionReport.Rcheck && mkdir regionReport.buildbin-libdir regionReport.Rcheck && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=regionReport.buildbin-libdir regionReport_1.8.2.tar.gz >regionReport.Rcheck\00install.out 2>&1 && cp regionReport.Rcheck\00install.out regionReport-install.out && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD check --library=regionReport.buildbin-libdir --install="check:regionReport-install.out" --force-multiarch --no-vignettes --timings regionReport_1.8.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'C:/Users/biocbuild/bbs-3.4-bioc/meat/regionReport.Rcheck'
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'regionReport/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'regionReport' version '1.8.2'
* 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 whether package 'regionReport' can be installed ... OK
* 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
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'DESeq2:::pvalueAdjustment'
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 ... OK
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
renderReport 71.25 4.09 76.19
DESeq2Report 26.48 1.52 35.72
derfinderReport 21.21 3.65 29.80
edgeReport 11.02 1.21 14.31
** running examples for arch 'x64' ... ERROR
Running examples in 'regionReport-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: derfinderReport
> ### Title: Generate a HTML/PDF report exploring the basic results from
> ### derfinder
> ### Aliases: derfinderReport
>
> ### ** Examples
>
>
> ## Load derfinder
> library('derfinder')
>
> ## The output will be saved in the 'derfinderReport-example' directory
> dir.create('derfinderReport-example', showWarnings = FALSE, recursive = TRUE)
>
> ## For convenience, the derfinder output has been pre-computed
> file.copy(system.file(file.path('extdata', 'chr21'), package='derfinder',
+ mustWork=TRUE), 'derfinderReport-example', recursive = TRUE)
[1] TRUE
>
> ## Not run:
> ##D ## If you prefer, you can generate the output from derfinder
> ##D initialPath <- getwd()
> ##D setwd(file.path(initialPath, 'derfinderReport-example'))
> ##D
> ##D ## Collapse the coverage information
> ##D collapsedFull <- collapseFullCoverage(list(genomeData$coverage),
> ##D verbose=TRUE)
> ##D
> ##D ## Calculate library size adjustments
> ##D sampleDepths <- sampleDepth(collapsedFull, probs=c(0.5), nonzero=TRUE,
> ##D verbose=TRUE)
> ##D
> ##D ## Build the models
> ##D group <- genomeInfo$pop
> ##D adjustvars <- data.frame(genomeInfo$gender)
> ##D models <- makeModels(sampleDepths, testvars=group, adjustvars=adjustvars)
> ##D
> ##D ## Analyze chromosome 21
> ##D analyzeChr(chr='21', coverageInfo=genomeData, models=models,
> ##D cutoffFstat=1, cutoffType='manual', seeds=20140330, groupInfo=group,
> ##D mc.cores=1, writeOutput=TRUE, returnOutput=FALSE)
> ##D
> ##D ## Change the directory back to the original one
> ##D setwd(initialPath)
> ## End(Not run)
>
> ## Merge the results from the different chromosomes. In this case, there's
> ## only one: chr21
> mergeResults(chrs = '21', prefix = 'derfinderReport-example',
+ genomicState = genomicState$fullGenome)
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
2017-04-15 00:34:52 mergeResults: Saving options used
2017-04-15 00:34:52 Loading chromosome chr21
Neither 'cutoffFstatUsed' nor 'optionsStats' were supplied, so the FWER calculation step will be skipped.
2017-04-15 00:34:52 mergeResults: Saving fullNullSummary
2017-04-15 00:34:53 mergeResults: Re-calculating the p-values
2017-04-15 00:34:53 mergeResults: Saving fullRegions
2017-04-15 00:34:53 mergeResults: assigning genomic states
2017-04-15 00:34:53 annotateRegions: counting
2017-04-15 00:34:53 annotateRegions: annotating
2017-04-15 00:34:53 mergeResults: Saving fullAnnotatedRegions
2017-04-15 00:34:53 mergeResults: Saving fullFstats
2017-04-15 00:34:53 mergeResults: Saving fullTime
>
> ## Load the options used for calculating the statistics
> load(file.path('derfinderReport-example', 'chr21', 'optionsStats.Rdata'))
>
> ## Generate the HTML report
> report <- derfinderReport(prefix='derfinderReport-example', browse=FALSE,
+ nBestRegions=1, makeBestClusters=FALSE,
+ fullCov=list('21'=genomeDataRaw$coverage), optionsStats=optionsStats)
Writing 9 Bibtex entries ... OK
Results written to file 'derfinderReport-example/basicExploration/basicExploration.bib'
extendedMapSeqlevels: sequence names mapped from NCBI to UCSC for species homo_sapiens
processing file: basicExploration.Rmd
inline R code fragments
Quitting from lines 2-28 (basicExploration.Rmd)
Error in strrep(char, width - nchar(x)) : reached elapsed time limit
Calls: derfinderReport ... vapply -> FUN -> paste -> strlpad -> paste0 -> strrep
Execution halted
* 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 NOTE
See
'C:/Users/biocbuild/bbs-3.4-bioc/meat/regionReport.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'regionReport' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'regionReport' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'regionReport' as regionReport_1.8.2.zip
* DONE (regionReport)