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This page was generated on 2022-04-13 12:08:34 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

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? 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 1.20.2  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_14
git_last_commit: fcc6503
git_last_commit_date: 2022-03-13 06:14:54 -0400 (Sun, 13 Mar 2022)
nebbiolo2Linux (Ubuntu 20.04.4 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: 1.20.2
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_1.20.2.tar.gz
StartedAt: 2022-04-12 17:04:30 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:15:28 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 658.4 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_1.20.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/psichomics.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.20.2’
* 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  35.538  1.837  41.008
listSplicingAnnotations 28.885  1.457  32.263
loadAnnotation           6.899  0.283   7.666
listAllAnnotations       6.423  0.386   7.381
* 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 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 
  0.336   0.083   0.390 

psichomics.Rcheck/tests/testthat.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 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 1.20.2: 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
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1396 ]

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

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1396 ]
> 
> proc.time()
   user  system elapsed 
 35.279   1.560  44.316 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0010.002
assignValuePerSubject0.0230.0100.034
blendColours0.0010.0000.002
calculateLoadingsContribution0.0170.0040.021
convertGeneIdentifiers35.538 1.83741.008
correlateGEandAS0.0300.0090.039
createGroupByAttribute0.0020.0010.002
createJunctionsTemplate0.0040.0010.005
customRowMeans0.0010.0010.002
diffAnalyses0.1430.0120.155
downloadFiles0.0000.0000.001
ensemblToUniprot0.0740.0041.398
filterGeneExpr0.0110.0020.013
filterGroups0.0020.0000.003
filterPSI0.0280.0070.035
getAttributesTime0.0050.0000.006
getDownloadsFolder0.0010.0000.001
getFirebrowseDateFormat0.0010.0000.000
getGeneList0.0050.0010.006
getGtexDataTypes0.1090.0080.486
getGtexTissues0.0010.0000.001
getNumerics0.0050.0010.006
getSampleFromSubject0.0010.0000.002
getSplicingEventFromGenes0.0070.0020.008
getSplicingEventTypes000
getSubjectFromSample0.0000.0000.001
getTCGAdataTypes0.0950.0070.304
getValidEvents0.0060.0020.008
groupPerElem0.0010.0000.002
hchart.survfit0.3780.1720.572
isFirebrowseUp0.0080.0010.050
labelBasedOnCutoff0.0010.0010.002
leveneTest0.0140.0010.015
listAllAnnotations6.4230.3867.381
listSplicingAnnotations28.885 1.45732.263
loadAnnotation6.8990.2837.666
loadGtexData0.0000.0010.001
loadLocalFiles0.0000.0000.001
loadSRAproject0.0010.0000.001
loadTCGAdata0.0150.0040.099
missingDataModal0.0000.0010.001
normaliseGeneExpression0.0370.0030.039
optimalSurvivalCutoff0.1710.0020.173
parseCategoricalGroups0.0020.0000.003
parseFirebrowseMetadata0.0520.0070.274
parseMatsEvent0.0090.0020.010
parseMatsGeneric0.0320.0040.036
parseMisoAnnotation0.2150.0150.235
parseMisoEvent0.0080.0010.009
parseMisoEventID0.0100.0030.013
parseMisoGeneric0.0560.0060.063
parseMisoId0.0010.0000.001
parseSplicingEvent0.0090.0040.014
parseSuppaEvent0.0070.0010.008
parseSuppaGeneric0.0380.0050.042
parseTcgaSampleInfo0.0050.0020.007
parseUrlsFromFirebrowseResponse0.0360.0020.189
parseVastToolsEvent0.0110.0020.012
parseVastToolsSE0.0350.0030.037
performICA0.0100.0050.016
performPCA0.0020.0000.003
plot.GEandAScorrelation0.6230.0150.639
plotDistribution1.1240.1011.229
plotGeneExprPerSample0.1710.0520.227
plotGroupIndependence0.1620.0020.163
plotICA0.2590.0150.276
plotLibrarySize0.3370.0520.395
plotPCA0.4860.2150.717
plotPCAvariance0.0990.0520.154
plotProtein1.2990.1103.084
plotRowStats0.6290.0090.643
plotSingleICA0.3680.1590.543
plotSplicingEvent0.1040.0020.105
plotSurvivalCurves0.1480.0560.209
plotSurvivalPvaluesByCutoff0.8490.0660.923
plotTranscripts0.0290.0021.342
prepareAnnotationFromEvents0.3050.0070.311
prepareFirebrowseArchives0.0000.0000.001
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.0160.0010.016
psichomics0.0000.0010.000
quantifySplicing0.0160.0040.020
queryEnsembl0.0420.0040.916
queryEnsemblByGene0.1590.0233.170
queryFirebrowseData0.0600.0030.360
queryPubMed0.1050.0160.690
queryUniprot0.0950.0041.877
readFile0.0020.0000.002
renameDuplicated0.0020.0000.001
renderBoxplot0.1710.0560.229
survdiffTerms0.0100.0010.010
survfit.survTerms0.0430.0020.044
testGroupIndependence0.0050.0000.006
testSurvival0.0350.0010.036
textSuggestions0.0010.0000.001
trimWhitespace0.0010.0000.001