BioC 3.5: CHECK report for psichomics on toluca2
This page was generated on 2017-04-23 14:42:17 -0400 (Sun, 23 Apr 2017).
psichomics 1.1.10 Nuno Saraiva-Agostinho
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/psichomics | Last Changed Rev: 129045 / Revision: 129046 | Last Changed Date: 2017-04-22 09:15:08 -0400 (Sat, 22 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | OK | | |
tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | OK | OK | |
toluca2 | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK | |
veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | OK | OK | |
Summary
Package: psichomics |
Version: 1.1.10 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.1.10.tar.gz |
StartedAt: 2017-04-23 08:17:55 -0400 (Sun, 23 Apr 2017) |
EndedAt: 2017-04-23 08:21:41 -0400 (Sun, 23 Apr 2017) |
EllapsedTime: 226.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: psichomics.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.1.10.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.1.10’
* package encoding: UTF-8
* 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 ‘psichomics’ 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
* 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 ... OK
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.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: OK
psichomics.Rcheck/00install.out:
* installing *source* package ‘psichomics’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (psichomics)
psichomics.Rcheck/psichomics-Ex.timings:
name | user | system | elapsed
|
createGroupByAttribute | 0.002 | 0.000 | 0.001 |
|
createJunctionsTemplate | 0.003 | 0.001 | 0.004 |
|
diffAnalyses | 0.691 | 0.033 | 0.726 |
|
downloadFiles | 0.000 | 0.000 | 0.001 |
|
ensemblToUniprot | 1.094 | 0.004 | 1.352 |
|
filterGroups | 0.001 | 0.000 | 0.001 |
|
getDownloadsFolder | 0.000 | 0.001 | 0.001 |
|
getFirebrowseCohorts | 0.175 | 0.001 | 0.334 |
|
getFirebrowseDataTypes | 0.033 | 0.001 | 0.034 |
|
getFirebrowseDateFormat | 0 | 0 | 0 |
|
getFirebrowseDates | 0.012 | 0.001 | 0.167 |
|
getMatchingSamples | 0.001 | 0.000 | 0.002 |
|
getNumerics | 0.004 | 0.000 | 0.005 |
|
getPatientFromSample | 0.001 | 0.001 | 0.001 |
|
getSplicingEventTypes | 0.000 | 0.000 | 0.001 |
|
getValidEvents | 0.006 | 0.001 | 0.007 |
|
groupPerPatient | 0.002 | 0.000 | 0.002 |
|
groupPerSample | 0.001 | 0.000 | 0.001 |
|
hchart.survfit | 0.832 | 0.060 | 0.899 |
|
isFirebrowseUp | 0.005 | 0.000 | 0.081 |
|
labelBasedOnCutoff | 0.021 | 0.001 | 0.021 |
|
leveneTest | 0.012 | 0.000 | 0.012 |
|
listAllAnnotations | 0.000 | 0.000 | 0.001 |
|
listSplicingAnnotations | 0.000 | 0.000 | 0.001 |
|
loadAnnotation | 0.001 | 0.000 | 0.001 |
|
loadFirebrowseData | 0.001 | 0.000 | 0.000 |
|
loadLocalFiles | 0.001 | 0.000 | 0.000 |
|
missingDataModal | 0.001 | 0.000 | 0.000 |
|
optimalPSIcutoff | 0.242 | 0.001 | 0.243 |
|
parseFirebrowseMetadata | 0.040 | 0.003 | 0.442 |
|
parseMatsEvent | 0.008 | 0.000 | 0.008 |
|
parseMatsGeneric | 0.033 | 0.001 | 0.035 |
|
parseMisoAnnotation | 0.461 | 0.006 | 0.467 |
|
parseMisoEvent | 0.005 | 0.000 | 0.005 |
|
parseMisoEventID | 0.006 | 0.000 | 0.006 |
|
parseMisoGeneric | 0.127 | 0.001 | 0.127 |
|
parseMisoId | 0.001 | 0.000 | 0.001 |
|
parseSampleGroups | 0.001 | 0.000 | 0.001 |
|
parseSplicingEvent | 0.004 | 0.000 | 0.004 |
|
parseSuppaEvent | 0.007 | 0.001 | 0.007 |
|
parseSuppaGeneric | 0.031 | 0.001 | 0.031 |
|
parseUrlsFromFirebrowseResponse | 0.018 | 0.000 | 0.215 |
|
parseVastToolsEvent | 0.008 | 0.000 | 0.008 |
|
parseVastToolsSE | 0.170 | 0.001 | 0.171 |
|
performPCA | 0.004 | 0.000 | 0.004 |
|
plotDistribution | 0.520 | 0.018 | 0.540 |
|
plotPCA | 0.278 | 0.049 | 0.332 |
|
plotProtein | 0.001 | 0.001 | 0.001 |
|
plotSurvivalCurves | 0.120 | 0.018 | 0.138 |
|
plotTranscripts | 0.021 | 0.001 | 0.580 |
|
plotVariance | 0.072 | 0.016 | 0.089 |
|
prepareAnnotationFromEvents | 0.470 | 0.003 | 0.474 |
|
prepareFirebrowseArchives | 0.001 | 0.000 | 0.001 |
|
processSurvTerms | 0.004 | 0.000 | 0.004 |
|
psichomics | 0.000 | 0.000 | 0.001 |
|
quantifySplicing | 0.032 | 0.000 | 0.031 |
|
queryEnsembl | 0.039 | 0.001 | 0.668 |
|
queryEnsemblByEvent | 0.105 | 0.003 | 1.045 |
|
queryEnsemblByGene | 0.113 | 0.004 | 1.381 |
|
queryFirebrowseData | 0.096 | 0.001 | 0.438 |
|
queryPubMed | 0.051 | 0.002 | 0.274 |
|
queryUniprot | 0.534 | 0.002 | 1.011 |
|
readFile | 0.001 | 0.000 | 0.002 |
|
renameDuplicated | 0.001 | 0.000 | 0.002 |
|
survdiff.survTerms | 0.010 | 0.001 | 0.011 |
|
survfit.survTerms | 0.033 | 0.001 | 0.033 |
|
testSurvival | 0.026 | 0.001 | 0.026 |
|
textSuggestions | 0.001 | 0.000 | 0.001 |
|
trimWhitespace | 0.001 | 0.000 | 0.001 |
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