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This page was generated on 2021-11-29 15:06:07 -0500 (Mon, 29 Nov 2021).

CHECK results for psichomics on machv2

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: 2021-11-28 04:15:06 -0500 (Sun, 28 Nov 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.20.0.tar.gz
StartedAt: 2021-11-28 19:57:42 -0500 (Sun, 28 Nov 2021)
EndedAt: 2021-11-28 20:07:45 -0500 (Sun, 28 Nov 2021)
EllapsedTime: 603.1 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/psichomics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* using platform: x86_64-apple-darwin17.0 (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  31.065  1.385  35.188
listSplicingAnnotations 24.704  1.277  27.680
loadAnnotation           5.818  0.239   6.638
listAllAnnotations       5.266  0.347   6.214
* 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
  ‘/Users/biocbuild/bbs-3.14-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c progressBar.cpp -o progressBar.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c vastToolsParser.cpp -o vastToolsParser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/Resources/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-apple-darwin17.0 (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 
  0.247   0.064   0.285 

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-apple-darwin17.0 (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 
 30.602   1.460  40.889 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0010.002
assignValuePerSubject0.0220.0080.030
blendColours0.0010.0000.002
calculateLoadingsContribution0.0100.0030.013
convertGeneIdentifiers31.065 1.38535.188
correlateGEandAS0.0300.0090.039
createGroupByAttribute0.0010.0010.002
createJunctionsTemplate0.0030.0010.003
customRowMeans0.0010.0010.002
diffAnalyses0.1210.0090.130
downloadFiles000
ensemblToUniprot0.3060.0102.721
filterGeneExpr0.0100.0010.011
filterGroups0.0020.0010.003
filterPSI0.0230.0060.029
getAttributesTime0.0050.0000.005
getDownloadsFolder0.0010.0000.001
getFirebrowseDateFormat000
getGeneList0.0040.0000.004
getGtexDataTypes0.1050.0060.441
getGtexTissues000
getNumerics0.0040.0010.006
getSampleFromSubject0.0020.0000.003
getSplicingEventFromGenes0.0060.0010.008
getSplicingEventTypes0.0000.0000.001
getSubjectFromSample0.0010.0000.001
getTCGAdataTypes0.0890.0100.299
getValidEvents0.0060.0020.008
groupPerElem0.0010.0010.002
hchart.survfit0.4130.1600.597
isFirebrowseUp0.0080.0010.048
labelBasedOnCutoff0.0010.0010.001
leveneTest0.0140.0010.014
listAllAnnotations5.2660.3476.214
listSplicingAnnotations24.704 1.27727.680
loadAnnotation5.8180.2396.638
loadGtexData0.0000.0010.001
loadLocalFiles0.0000.0010.001
loadSRAproject0.0000.0010.001
loadTCGAdata0.0150.0030.102
missingDataModal0.0000.0010.001
normaliseGeneExpression0.0280.0030.030
optimalSurvivalCutoff0.1690.0020.170
parseCategoricalGroups0.0010.0000.001
parseFirebrowseMetadata0.0570.0080.277
parseMatsEvent0.0100.0020.011
parseMatsGeneric0.0300.0030.034
parseMisoAnnotation0.1990.0130.219
parseMisoEvent0.0050.0010.006
parseMisoEventID0.0090.0040.013
parseMisoGeneric0.0620.0080.069
parseMisoId0.0000.0010.002
parseSplicingEvent0.0100.0040.014
parseSuppaEvent0.0070.0010.009
parseSuppaGeneric0.0350.0040.038
parseTcgaSampleInfo0.0040.0010.005
parseUrlsFromFirebrowseResponse0.0310.0020.190
parseVastToolsEvent0.0490.0140.064
parseVastToolsSE0.0300.0020.033
performICA0.0090.0080.017
performPCA0.0030.0000.003
plot.GEandAScorrelation0.4830.0130.497
plotDistribution1.1600.0881.257
plotGeneExprPerSample0.1450.0400.186
plotGroupIndependence0.1980.0020.200
plotICA0.2300.0160.250
plotLibrarySize0.3290.0480.384
plotPCA0.4190.1920.625
plotPCAvariance0.0850.0460.135
plotProtein0.9500.0852.635
plotRowStats0.4010.0090.412
plotSingleICA0.3150.1270.448
plotSplicingEvent0.0730.0010.075
plotSurvivalCurves0.1260.0390.170
plotSurvivalPvaluesByCutoff0.6790.0520.734
plotTranscripts0.0280.0011.374
prepareAnnotationFromEvents0.2390.0060.245
prepareFirebrowseArchives0.0000.0000.001
prepareJunctionQuantSTAR000
prepareSRAmetadata0.0000.0010.000
processSurvTerms0.0100.0010.011
psichomics0.0000.0000.001
quantifySplicing0.0130.0050.017
queryEnsembl0.0360.0060.737
queryEnsemblByGene0.1600.0213.160
queryFirebrowseData0.0580.0020.352
queryPubMed0.0990.0160.626
queryUniprot0.0840.0041.480
readFile0.0010.0010.001
renameDuplicated0.0010.0000.001
renderBoxplot0.1280.0460.192
survdiffTerms0.0070.0010.008
survfit.survTerms0.0290.0010.029
testGroupIndependence0.0050.0010.005
testSurvival0.0320.0020.033
textSuggestions0.0020.0010.002
trimWhitespace0.0000.0000.001