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This page was generated on 2021-12-03 13:04:57 -0500 (Fri, 03 Dec 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 1480/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.20.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_14
git_last_commit: 84bcdbf
git_last_commit_date: 2021-10-26 12:30:49 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 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: 1.20.0
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_1.20.0.tar.gz
StartedAt: 2021-12-02 08:33:10 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 08:40:28 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 438.4 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_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/psichomics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.20.0’
* 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  20.632  1.189  23.246
listSplicingAnnotations 13.113  0.712  14.758
plotProtein              0.593  0.024   8.270
* 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

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##############################################################################
###
### 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 4.1.2 (2021-11-01) -- "Bird Hippie"
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 
  0.269   0.029   0.282 

psichomics.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
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 1.20.0: 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 
 21.067   1.664  40.175 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0020.0000.001
assignValuePerSubject0.0100.0080.018
blendColours0.0010.0000.001
calculateLoadingsContribution0.0090.0000.009
convertGeneIdentifiers20.632 1.18923.246
correlateGEandAS0.0150.0000.016
createGroupByAttribute0.0010.0000.001
createJunctionsTemplate0.0020.0000.001
customRowMeans0.0010.0000.000
diffAnalyses0.0590.0080.067
downloadFiles000
ensemblToUniprot0.0380.0001.063
filterGeneExpr0.0080.0000.008
filterGroups0.0020.0000.002
filterPSI0.0180.0000.018
getAttributesTime0.0030.0000.003
getDownloadsFolder000
getFirebrowseDateFormat000
getGeneList0.0040.0000.005
getGtexDataTypes0.0590.0000.332
getGtexTissues0.0010.0000.000
getNumerics0.0040.0000.005
getSampleFromSubject0.0010.0000.002
getSplicingEventFromGenes0.0050.0000.005
getSplicingEventTypes0.0000.0010.000
getSubjectFromSample0.0000.0010.001
getTCGAdataTypes0.0480.0050.166
getValidEvents0.0050.0000.005
groupPerElem0.0010.0000.001
hchart.survfit0.2500.0160.288
isFirebrowseUp0.0040.0000.012
labelBasedOnCutoff000
leveneTest0.0070.0000.007
listAllAnnotations3.0930.1763.647
listSplicingAnnotations13.113 0.71214.758
loadAnnotation3.5210.1793.888
loadGtexData000
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.0130.0000.028
missingDataModal0.0010.0000.000
normaliseGeneExpression0.0230.0000.024
optimalSurvivalCutoff0.0890.0000.089
parseCategoricalGroups0.0010.0000.001
parseFirebrowseMetadata0.0560.0040.113
parseMatsEvent0.0070.0000.007
parseMatsGeneric0.0140.0040.018
parseMisoAnnotation0.1420.0040.149
parseMisoEvent0.0030.0000.004
parseMisoEventID0.0050.0000.005
parseMisoGeneric0.0280.0000.027
parseMisoId0.0010.0000.000
parseSplicingEvent0.0040.0000.004
parseSuppaEvent0.0020.0000.002
parseSuppaGeneric0.0120.0040.016
parseTcgaSampleInfo0.0030.0000.003
parseUrlsFromFirebrowseResponse0.0480.0000.104
parseVastToolsEvent0.0100.0000.009
parseVastToolsSE0.0150.0000.015
performICA0.0060.0000.005
performPCA0.0010.0000.001
plot.GEandAScorrelation0.2940.0120.306
plotDistribution0.5380.0240.561
plotGeneExprPerSample0.0820.0040.086
plotGroupIndependence0.1390.0000.139
plotICA0.1030.0000.105
plotLibrarySize0.1540.0200.174
plotPCA0.2150.0080.223
plotPCAvariance0.0370.0080.045
plotProtein0.5930.0248.270
plotRowStats0.3850.0000.385
plotSingleICA0.1680.0200.188
plotSplicingEvent0.0380.0000.038
plotSurvivalCurves0.0750.0040.079
plotSurvivalPvaluesByCutoff0.4100.0280.438
plotTranscripts0.0390.0001.182
prepareAnnotationFromEvents0.2050.0000.206
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.0080.0000.008
psichomics000
quantifySplicing0.0050.0040.009
queryEnsembl0.0580.0000.859
queryEnsemblByGene0.1390.0084.383
queryFirebrowseData0.0700.0040.189
queryPubMed0.0570.0040.486
queryUniprot0.0830.0002.108
readFile0.0010.0000.002
renameDuplicated0.0010.0010.001
renderBoxplot0.1040.0150.120
survdiffTerms0.0060.0010.006
survfit.survTerms0.0230.0040.028
testGroupIndependence0.0000.0020.002
testSurvival0.0210.0000.020
textSuggestions0.0000.0000.001
trimWhitespace000