Multiple platform build/check report for BioC 3.11 - CHECK report for psichomics on celaya2

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### Running command:
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###   /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_1.13.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.13.0’
* 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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  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-3.11-bioc/meat/psichomics.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL psichomics
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -std=gnu++11 -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 psiFastCalc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/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
** 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


R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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)
Start the visual interface by running the function psichomics()

Attaching package: 'psichomics'

The following object is masked from 'package:base':

    rowMeans

> 
> test_check("psichomics")
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Retrieving protein annotation from UniProt...

Plotting protein domains...

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

IR

MERGE3m

MIC

EXSK

MULTI
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 1078 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 34.004   2.590  50.854

Example timings

name	user	system	elapsed
addObjectAttrs	0	0	0
blendColours	0.001	0.000	0.001
calculateLoadingsContribution	0.020	0.003	0.023
convertGeneIdentifiers	0.684	0.053	0.659
correlateGEandAS	0.096	0.074	0.038
createGroupByAttribute	0.010	0.008	0.004
createJunctionsTemplate	0.016	0.014	0.005
diffAnalyses	0.402	0.281	0.154
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.562	0.003	1.020
filterGeneExpr	0.015	0.001	0.016
filterGroups	0.001	0.001	0.001
filterPSI	0.012	0.003	0.015
getAttributesTime	0.003	0.001	0.003
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseDataTypes	0.001	0.000	0.001
getFirebrowseDateFormat	0	0	0
getFirebrowseDates	0.082	0.004	0.178
getGeneList	0.019	0.014	0.035
getMatchingSamples	0.002	0.001	0.003
getNumerics	0.006	0.000	0.007
getPatientFromSample	0.001	0.000	0.002
getSplicingEventFromGenes	0.005	0.001	0.006
getSplicingEventTypes	0.000	0.001	0.001
getValidEvents	0.009	0.002	0.011
getValuePerPatient	0.012	0.006	0.018
groupPerElem	0.001	0.001	0.001
hchart.survfit	0.504	0.276	0.812
isFirebrowseUp	0.007	0.001	0.026
labelBasedOnCutoff	0.001	0.001	0.002
leveneTest	0.014	0.001	0.014
listAllAnnotations	0.001	0.000	0.001
listSplicingAnnotations	0	0	0
loadAnnotation	0.000	0.000	0.001
loadFirebrowseData	0.000	0.000	0.001
loadLocalFiles	0.000	0.001	0.000
missingDataModal	0.000	0.001	0.001
normaliseGeneExpression	0.087	0.005	0.092
optimalSurvivalCutoff	0.224	0.004	0.229
parseCategoricalGroups	0.003	0.001	0.003
parseFirebrowseMetadata	0.060	0.006	0.167
parseMatsEvent	0.013	0.002	0.014
parseMatsGeneric	0.044	0.003	0.047
parseMisoAnnotation	0.280	0.016	0.307
parseMisoEvent	0.010	0.001	0.011
parseMisoEventID	0.011	0.002	0.014
parseMisoGeneric	0.078	0.006	0.084
parseMisoId	0.001	0.000	0.002
parseSampleGroups	0.002	0.001	0.003
parseSplicingEvent	0.003	0.000	0.004
parseSuppaEvent	0.007	0.000	0.008
parseSuppaGeneric	0.045	0.003	0.048
parseTcgaSampleInfo	0.005	0.001	0.007
parseUrlsFromFirebrowseResponse	0.030	0.002	0.096
parseVastToolsEvent	0.014	0.001	0.014
parseVastToolsSE	0.043	0.002	0.045
performICA	0.018	0.008	0.025
performPCA	0.004	0.000	0.005
plot.GEandAScorrelation	0.963	0.072	1.035
plotDistribution	0.121	0.062	0.184
plotGeneExprPerSample	0.273	0.066	0.338
plotGroupIndependence	0.229	0.002	0.232
plotICA	0.263	0.020	0.292
plotPCA	0.333	0.178	0.513
plotProtein	1.914	0.363	3.814
plotRowStats	2.428	0.100	2.531
plotSingleICA	0.345	0.167	0.513
plotSurvivalCurves	0.163	0.058	0.222
plotTranscripts	0.030	0.002	1.407
plotVariance	0.080	0.056	0.137
prepareAnnotationFromEvents	0.283	0.013	0.296
prepareFirebrowseArchives	0.000	0.000	0.001
prepareJunctionQuantSTAR	0.000	0.001	0.001
prepareSRAmetadata	0.000	0.000	0.001
processSurvTerms	0.004	0.000	0.004
psichomics	0.001	0.000	0.001
quantifySplicing	0.012	0.006	0.019
queryEnsembl	0.052	0.005	1.073
queryEnsemblByGene	0.228	0.034	3.839
queryFirebrowseData	0.043	0.005	0.180
queryPubMed	0.098	0.015	0.535
queryUniprot	0.138	0.006	0.978
readFile	0.001	0.000	0.002
renameDuplicated	0.002	0.001	0.001
renderBoxplot	0.143	0.068	0.212
rowMeans	0.000	0.001	0.001
sidebar	0.018	0.001	0.018
survdiffTerms	0.015	0.003	0.018
survfit.survTerms	0.055	0.005	0.061
testGroupIndependence	0.005	0.002	0.007
testSurvival	0.051	0.001	0.052
textSuggestions	0.002	0.000	0.001
trimWhitespace	0.001	0.000	0.001

CHECK report for psichomics on celaya2

Summary

Command output

Installation output

Tests output

Example timings