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This page was generated on 2021-12-01 17:18:29 -0500 (Wed, 01 Dec 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: 2021-11-30 04:15:05 -0500 (Tue, 30 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: 2021-11-30 20:08:29 -0500 (Tue, 30 Nov 2021)
EndedAt: 2021-11-30 20:18:43 -0500 (Tue, 30 Nov 2021)
EllapsedTime: 614.4 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  32.676  1.607  36.819
listSplicingAnnotations 25.672  1.327  29.042
loadAnnotation           5.986  0.297   6.742
listAllAnnotations       5.127  0.316   6.099
* 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

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##############################################################################
###
### 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 
  0.309   0.071   0.358 

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 
 31.723   1.495  41.597 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0000.002
assignValuePerSubject0.0240.0070.031
blendColours0.0010.0010.002
calculateLoadingsContribution0.0150.0040.019
convertGeneIdentifiers32.676 1.60736.819
correlateGEandAS0.0320.0090.041
createGroupByAttribute0.0020.0000.002
createJunctionsTemplate0.0040.0010.005
customRowMeans0.0010.0000.002
diffAnalyses0.1500.0120.164
downloadFiles0.0000.0000.001
ensemblToUniprot0.0700.0050.747
filterGeneExpr0.0110.0020.013
filterGroups0.0020.0010.003
filterPSI0.0200.0050.026
getAttributesTime0.0050.0010.005
getDownloadsFolder000
getFirebrowseDateFormat0.0010.0010.001
getGeneList0.0040.0000.005
getGtexDataTypes0.1020.0070.427
getGtexTissues0.0000.0000.001
getNumerics0.0040.0010.005
getSampleFromSubject0.0020.0010.002
getSplicingEventFromGenes0.0060.0020.007
getSplicingEventTypes0.0010.0000.001
getSubjectFromSample0.0010.0010.001
getTCGAdataTypes0.0930.0070.301
getValidEvents0.0070.0010.009
groupPerElem0.0010.0010.002
hchart.survfit0.4390.1740.724
isFirebrowseUp0.0080.0000.113
labelBasedOnCutoff0.0000.0010.001
leveneTest0.0150.0010.015
listAllAnnotations5.1270.3166.099
listSplicingAnnotations25.672 1.32729.042
loadAnnotation5.9860.2976.742
loadGtexData000
loadLocalFiles0.0000.0000.001
loadSRAproject000
loadTCGAdata0.0120.0030.094
missingDataModal0.0000.0000.001
normaliseGeneExpression0.0260.0020.027
optimalSurvivalCutoff0.1700.0010.172
parseCategoricalGroups0.0020.0010.002
parseFirebrowseMetadata0.0530.0080.271
parseMatsEvent0.0080.0010.011
parseMatsGeneric0.0360.0040.041
parseMisoAnnotation0.1940.0120.211
parseMisoEvent0.0080.0010.009
parseMisoEventID0.0060.0020.008
parseMisoGeneric0.0500.0050.056
parseMisoId0.0010.0010.001
parseSplicingEvent0.0060.0040.010
parseSuppaEvent0.0070.0010.008
parseSuppaGeneric0.0370.0040.040
parseTcgaSampleInfo0.0600.0250.086
parseUrlsFromFirebrowseResponse0.0360.0010.186
parseVastToolsEvent0.0110.0010.012
parseVastToolsSE0.0300.0020.033
performICA0.0120.0080.019
performPCA0.0020.0010.002
plot.GEandAScorrelation0.5350.0130.548
plotDistribution1.1420.0971.272
plotGeneExprPerSample0.1520.0450.203
plotGroupIndependence0.2080.0030.210
plotICA0.2350.0180.255
plotLibrarySize0.3980.0450.450
plotPCA0.4230.1990.717
plotPCAvariance0.0750.0450.121
plotProtein1.1350.0992.918
plotRowStats0.5350.0090.545
plotSingleICA0.3780.1320.518
plotSplicingEvent0.0880.0020.089
plotSurvivalCurves0.1360.0500.187
plotSurvivalPvaluesByCutoff0.7280.0500.779
plotTranscripts0.0260.0011.199
prepareAnnotationFromEvents0.3020.0080.310
prepareFirebrowseArchives0.0000.0010.001
prepareJunctionQuantSTAR000
prepareSRAmetadata0.0000.0000.001
processSurvTerms0.0130.0010.014
psichomics0.0010.0000.001
quantifySplicing0.0180.0080.025
queryEnsembl0.0410.0050.582
queryEnsemblByGene0.1550.0202.739
queryFirebrowseData0.0590.0030.352
queryPubMed0.0930.0111.485
queryUniprot0.0860.0031.662
readFile0.0010.0010.002
renameDuplicated0.0010.0010.001
renderBoxplot0.1340.0400.174
survdiffTerms0.0100.0020.012
survfit.survTerms0.0350.0020.037
testGroupIndependence0.0050.0000.006
testSurvival0.0310.0010.032
textSuggestions0.0000.0010.001
trimWhitespace000