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This page was generated on 2021-10-15 15:06:47 -0400 (Fri, 15 Oct 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 1454/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.18.6  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_13
git_last_commit: 2ffd219
git_last_commit_date: 2021-10-04 13:47:26 -0400 (Mon, 04 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.2 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: 1.18.6
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psichomics_1.18.6.tar.gz
StartedAt: 2021-10-14 22:38:22 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 22:46:58 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 515.7 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psichomics_1.18.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/psichomics.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.18.6’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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 27.528   1.37  31.242
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/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 4.1.1 (2021-08-10) -- "Kick Things"
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   0.069   0.354 

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-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 1.18.6: 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 
 29.145   1.314  36.578 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0020.0010.002
assignValuePerSubject0.0260.0090.037
blendColours0.0020.0000.001
calculateLoadingsContribution0.0170.0050.023
convertGeneIdentifiers27.528 1.37031.242
correlateGEandAS0.0210.0060.026
createGroupByAttribute0.0020.0010.003
createJunctionsTemplate0.0040.0010.005
customRowMeans0.0000.0000.001
diffAnalyses0.1350.0100.146
downloadFiles0.0000.0010.001
ensemblToUniprot0.3160.0140.880
filterGeneExpr0.0110.0020.013
filterGroups0.0020.0000.003
filterPSI0.0210.0050.026
getAttributesTime0.0030.0010.003
getDownloadsFolder0.0010.0010.001
getFirebrowseDateFormat0.0000.0010.001
getGeneList0.0040.0010.005
getGtexDataTypes0.0890.0050.441
getGtexTissues0.0000.0000.001
getNumerics0.0050.0000.006
getSampleFromSubject0.0020.0000.002
getSplicingEventFromGenes0.0040.0010.004
getSplicingEventTypes0.0000.0010.001
getSubjectFromSample0.0010.0010.001
getTCGAdataTypes0.0990.0080.318
getValidEvents0.0060.0020.009
groupPerElem0.0010.0010.001
hchart.survfit0.4050.1380.555
isFirebrowseUp0.0080.0010.049
labelBasedOnCutoff0.0010.0010.001
leveneTest0.0120.0000.012
listAllAnnotations0.0010.0000.001
listSplicingAnnotations0.0020.0010.003
loadAnnotation0.0010.0000.001
loadGtexData0.0000.0000.001
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.0090.0010.054
missingDataModal0.0000.0000.001
normaliseGeneExpression0.0370.0020.039
optimalSurvivalCutoff0.1750.0010.176
parseCategoricalGroups0.0020.0000.001
parseFirebrowseMetadata0.0570.0050.315
parseMatsEvent0.0100.0010.011
parseMatsGeneric0.0410.0040.044
parseMisoAnnotation0.1790.0120.195
parseMisoEvent0.0080.0000.009
parseMisoEventID0.0060.0020.008
parseMisoGeneric0.0490.0040.053
parseMisoId0.0000.0000.001
parseSplicingEvent0.0090.0020.011
parseSuppaEvent0.0070.0010.008
parseSuppaGeneric0.0320.0020.033
parseTcgaSampleInfo0.0040.0010.005
parseUrlsFromFirebrowseResponse0.0350.0010.187
parseVastToolsEvent0.0120.0010.012
parseVastToolsSE0.0290.0020.031
performICA0.0110.0050.017
performPCA0.0020.0010.003
plot.GEandAScorrelation0.5290.0120.542
plotDistribution1.1440.0861.238
plotGeneExprPerSample0.1310.0430.181
plotGroupIndependence0.1890.0030.192
plotICA0.2090.0160.227
plotLibrarySize0.2500.0400.291
plotPCA0.3900.1630.570
plotPCAvariance0.0760.0440.238
plotProtein1.0660.1033.077
plotRowStats0.4730.0090.482
plotSingleICA0.3210.1260.459
plotSplicingEvent0.0910.0010.092
plotSurvivalCurves0.1470.0480.244
plotSurvivalPvaluesByCutoff0.6530.0480.705
plotTranscripts0.0280.0010.982
prepareAnnotationFromEvents0.1970.0060.203
prepareFirebrowseArchives0.0000.0000.001
prepareJunctionQuantSTAR000
prepareSRAmetadata0.0000.0010.001
processSurvTerms0.0120.0010.013
psichomics000
quantifySplicing0.0190.0090.029
queryEnsembl0.0470.0060.601
queryEnsemblByGene0.1770.0322.838
queryFirebrowseData0.0560.0020.353
queryPubMed0.0990.0150.612
queryUniprot0.0830.0051.501
readFile0.0010.0000.001
renameDuplicated0.0010.0000.001
renderBoxplot0.1070.0350.142
survdiffTerms0.0070.0020.009
survfit.survTerms0.0320.0010.034
testGroupIndependence0.0050.0000.006
testSurvival0.0260.0010.028
textSuggestions0.0010.0000.001
trimWhitespace0.0010.0010.001