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This page was generated on 2021-10-21 12:04:28 -0400 (Thu, 21 Oct 2021).

CHECK results for psichomics on nebbiolo2

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 1475/2075HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.19.7  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2021-10-20 14:50:05 -0400 (Wed, 20 Oct 2021)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: master
git_last_commit: 68bbd6b
git_last_commit_date: 2021-10-19 12:30:37 -0400 (Tue, 19 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    NA  

Summary

Package: psichomics
Version: 1.19.7
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings psichomics_1.19.7.tar.gz
StartedAt: 2021-10-20 21:37:04 -0400 (Wed, 20 Oct 2021)
EndedAt: 2021-10-20 21:46:15 -0400 (Wed, 20 Oct 2021)
EllapsedTime: 550.6 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings psichomics_1.19.7.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-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 ‘1.19.7’
* 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  33.600  1.417  36.591
listSplicingAnnotations 22.629  1.140  25.078
listAllAnnotations       5.704  0.300   6.287
loadAnnotation           5.726  0.240   6.283
queryEnsemblByGene       0.216  0.000   5.157
* 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-3.14-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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 
  0.301   0.033   0.316 

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 1.19.7: 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 1396 ]
> 
> proc.time()
   user  system elapsed 
 31.809   1.881  39.685 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0000.0010.001
assignValuePerSubject0.0150.0070.023
blendColours0.0020.0000.001
calculateLoadingsContribution0.0090.0040.013
convertGeneIdentifiers33.600 1.41736.591
correlateGEandAS0.0250.0000.024
createGroupByAttribute0.0010.0000.002
createJunctionsTemplate0.0020.0000.002
customRowMeans0.0010.0000.000
diffAnalyses0.1040.0040.107
downloadFiles0.0000.0000.001
ensemblToUniprot0.0510.0002.559
filterGeneExpr0.0110.0000.011
filterGroups0.0030.0000.003
filterPSI0.0260.0000.026
getAttributesTime0.0050.0000.005
getDownloadsFolder0.0010.0000.001
getFirebrowseDateFormat0.0000.0000.001
getGeneList0.0060.0000.006
getGtexDataTypes0.0790.0000.313
getGtexTissues000
getNumerics0.0050.0000.006
getSampleFromSubject0.0000.0020.002
getSplicingEventFromGenes0.0050.0010.007
getSplicingEventTypes000
getSubjectFromSample000
getTCGAdataTypes0.0750.0521.270
getValidEvents0.0060.0000.006
groupPerElem0.0010.0000.001
hchart.survfit0.5610.0320.615
isFirebrowseUp0.0050.0040.016
labelBasedOnCutoff0.0010.0000.001
leveneTest0.0140.0000.013
listAllAnnotations5.7040.3006.287
listSplicingAnnotations22.629 1.14025.078
loadAnnotation5.7260.2406.283
loadGtexData0.0000.0000.001
loadLocalFiles0.0010.0000.000
loadSRAproject000
loadTCGAdata0.0210.0000.035
missingDataModal000
normaliseGeneExpression0.0300.0000.029
optimalSurvivalCutoff0.0970.0000.096
parseCategoricalGroups0.0010.0000.001
parseFirebrowseMetadata0.0610.0000.109
parseMatsEvent0.0010.0040.005
parseMatsGeneric0.0190.0000.019
parseMisoAnnotation0.1990.0000.201
parseMisoEvent0.0060.0000.006
parseMisoEventID0.0080.0000.008
parseMisoGeneric0.0480.0000.048
parseMisoId0.0000.0000.001
parseSplicingEvent0.0050.0000.005
parseSuppaEvent0.0030.0000.003
parseSuppaGeneric0.0170.0020.019
parseTcgaSampleInfo0.0020.0020.003
parseUrlsFromFirebrowseResponse0.0420.0000.096
parseVastToolsEvent0.0050.0000.004
parseVastToolsSE0.0160.0000.016
performICA0.0070.0000.007
performPCA0.0020.0000.002
plot.GEandAScorrelation0.3470.0040.352
plotDistribution0.6140.0120.626
plotGeneExprPerSample0.0960.0040.099
plotGroupIndependence0.1950.0000.195
plotICA0.1140.0080.124
plotLibrarySize0.1620.0080.170
plotPCA0.2370.0160.255
plotPCAvariance0.0500.0040.054
plotProtein1.0890.0203.205
plotRowStats0.7450.0040.749
plotSingleICA0.3830.0200.403
plotSplicingEvent0.0810.0000.081
plotSurvivalCurves0.2000.0080.208
plotSurvivalPvaluesByCutoff0.8240.0040.827
plotTranscripts0.0480.0001.941
prepareAnnotationFromEvents0.3280.0000.328
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.0190.0000.019
psichomics000
quantifySplicing0.0190.0000.019
queryEnsembl0.0600.0001.074
queryEnsemblByGene0.2160.0005.157
queryFirebrowseData0.1010.0000.308
queryPubMed0.0830.0000.606
queryUniprot0.0890.0081.876
readFile0.0020.0000.002
renameDuplicated0.0010.0000.002
renderBoxplot0.1960.0080.205
survdiffTerms0.0150.0000.015
survfit.survTerms0.0860.0040.089
testGroupIndependence0.0070.0000.007
testSurvival0.0680.0000.068
textSuggestions0.0010.0000.001
trimWhitespace0.0010.0000.001