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This page was generated on 2021-10-15 15:05:49 -0400 (Fri, 15 Oct 2021).

CHECK results for psichomics on nebbiolo1

To the developers/maintainers of the psichomics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psichomics.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.

raw results

Package 1454/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.18.6  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_13
git_last_commit: 2ffd219
git_last_commit_date: 2021-10-04 13:47:26 -0400 (Mon, 04 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: psichomics
Version: 1.18.6
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings psichomics_1.18.6.tar.gz
StartedAt: 2021-10-14 11:08:32 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 11:16:02 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 450.0 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings psichomics_1.18.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/psichomics.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.18.6’
* 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 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
convertGeneIdentifiers 19.443  0.915  21.692
queryEnsemblByGene      0.116  0.024  21.660
getTCGAdataTypes        0.044  0.008   5.826
ensemblToUniprot        0.030  0.008  12.223
queryEnsembl            0.024  0.000  12.673
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c progressBar.cpp -o progressBar.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c psiFastCalc.cpp -o psiFastCalc.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c vastToolsParser.cpp -o vastToolsParser.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.13-bioc/R/library/00LOCK-psichomics/00new/psichomics/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a generic function for ‘colSums’ from package ‘base’ in package ‘psichomics’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (psichomics)

Tests output

psichomics.Rcheck/tests/spelling.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.202   0.043   0.231 

psichomics.Rcheck/tests/testthat.Rout


R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(psichomics)
Loading required package: shiny
Loading required package: shinyBS
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

psichomics 1.18.6: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
> 
> test_check("psichomics")
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Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving MISO annotation...

Parsing MISO annotation...
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Retrieving SUPPA annotation...

Parsing SUPPA annotation...

Retrieving VAST-TOOLS annotation...

Parsing VAST-TOOLS annotation...

ALT3

ALT5

COMBI

EXSK

IR

MERGE3m

MIC

MULTI
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (2)
• On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1378 ]
> 
> proc.time()
   user  system elapsed 
 21.510   1.504  39.868 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0010.001
assignValuePerSubject0.0140.0080.022
blendColours0.0010.0000.001
calculateLoadingsContribution0.0060.0030.010
convertGeneIdentifiers19.443 0.91521.692
correlateGEandAS0.0250.0040.029
createGroupByAttribute0.0010.0000.001
createJunctionsTemplate0.0040.0000.004
customRowMeans0.0010.0000.002
diffAnalyses0.0620.0160.078
downloadFiles0.0010.0000.001
ensemblToUniprot 0.030 0.00812.223
filterGeneExpr0.0020.0080.011
filterGroups0.0030.0000.002
filterPSI0.0170.0080.026
getAttributesTime0.0010.0030.005
getDownloadsFolder0.0010.0000.000
getFirebrowseDateFormat0.0000.0010.001
getGeneList0.0030.0020.006
getGtexDataTypes0.0450.0040.281
getGtexTissues0.0010.0000.000
getNumerics0.0030.0000.003
getSampleFromSubject0.0010.0000.001
getSplicingEventFromGenes0.0040.0000.004
getSplicingEventTypes0.0000.0000.001
getSubjectFromSample0.0000.0000.001
getTCGAdataTypes0.0440.0085.826
getValidEvents0.0050.0000.005
groupPerElem0.0000.0020.002
hchart.survfit0.2980.0380.361
isFirebrowseUp0.0050.0000.013
labelBasedOnCutoff0.0010.0000.001
leveneTest0.0040.0040.009
listAllAnnotations0.0010.0000.002
listSplicingAnnotations0.0030.0000.003
loadAnnotation0.0010.0000.001
loadGtexData0.0010.0000.000
loadLocalFiles0.0010.0000.000
loadSRAproject000
loadTCGAdata0.0180.0000.031
missingDataModal000
normaliseGeneExpression0.0350.0000.035
optimalSurvivalCutoff0.1620.0040.166
parseCategoricalGroups0.0010.0000.001
parseFirebrowseMetadata0.0780.0280.155
parseMatsEvent0.0050.0040.009
parseMatsGeneric0.0200.0040.024
parseMisoAnnotation0.1750.0160.196
parseMisoEvent0.0070.0000.007
parseMisoEventID0.0060.0040.010
parseMisoGeneric0.0420.0080.050
parseMisoId0.0010.0000.001
parseSplicingEvent0.0020.0080.009
parseSuppaEvent0.0050.0000.005
parseSuppaGeneric0.030.000.03
parseTcgaSampleInfo0.0050.0000.005
parseUrlsFromFirebrowseResponse0.0480.0000.109
parseVastToolsEvent0.0010.0080.008
parseVastToolsSE0.0260.0040.030
performICA0.0080.0080.016
performPCA0.0030.0000.003
plot.GEandAScorrelation0.3310.0160.346
plotDistribution0.5930.0280.621
plotGeneExprPerSample0.0930.0040.096
plotGroupIndependence0.0960.0040.100
plotICA0.1060.0040.111
plotLibrarySize0.1620.0040.165
plotPCA0.2200.0240.244
plotPCAvariance0.0420.0080.050
plotProtein0.5540.0443.461
plotRowStats0.2720.0000.272
plotSingleICA0.1780.0280.206
plotSplicingEvent0.0510.0000.051
plotSurvivalCurves0.0740.0080.082
plotSurvivalPvaluesByCutoff0.3940.0120.406
plotTranscripts0.0250.0042.545
prepareAnnotationFromEvents0.1550.0040.159
prepareFirebrowseArchives0.0000.0010.001
prepareJunctionQuantSTAR0.0000.0010.001
prepareSRAmetadata0.0000.0010.000
processSurvTerms0.0080.0010.009
psichomics000
quantifySplicing0.0130.0000.013
queryEnsembl 0.024 0.00012.673
queryEnsemblByGene 0.116 0.02421.660
queryFirebrowseData0.0520.0040.157
queryPubMed0.0490.0080.539
queryUniprot0.0680.0002.109
readFile0.0000.0010.002
renameDuplicated0.0000.0010.001
renderBoxplot0.1060.0120.124
survdiffTerms0.0090.0000.009
survfit.survTerms0.0320.0040.036
testGroupIndependence0.0040.0000.004
testSurvival0.0320.0000.032
textSuggestions0.0010.0000.001
trimWhitespace0.0010.0000.000