Multiple platform build/check report for BioC 3.10 - CHECK report for psichomics on merida1

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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_1.12.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/psichomics.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.12.1’
* 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 ‘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-3.10-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/3.6/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/3.6/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/3.6/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/3.6/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


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.211   0.061   0.251


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 1240 | SKIPPED: 2 | WARNINGS: 1 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 38.180   3.239  43.394

Example timings

name	user	system	elapsed
addObjectAttrs	0	0	0
assignValuePerSubject	0.011	0.003	0.015
blendColours	0.001	0.001	0.001
calculateLoadingsContribution	0.021	0.003	0.024
convertGeneIdentifiers	1.658	0.847	1.275
correlateGEandAS	0.015	0.003	0.017
createGroupByAttribute	0.003	0.000	0.003
createJunctionsTemplate	0.003	0.001	0.004
diffAnalyses	0.111	0.004	0.114
downloadFiles	0	0	0
ensemblToUniprot	0.054	0.002	0.481
filterGeneExpr	0.014	0.002	0.015
filterGroups	0	0	0
filterPSI	0.016	0.003	0.018
getAttributesTime	0.003	0.000	0.004
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseDateFormat	0.001	0.000	0.001
getGeneList	0.015	0.009	0.023
getGtexDataTypes	0.000	0.000	0.001
getGtexTissues	0	0	0
getMatchingSamples	0.001	0.001	0.002
getNumerics	0.005	0.000	0.005
getSplicingEventFromGenes	0.004	0.000	0.006
getSplicingEventTypes	0.001	0.000	0.001
getSubjectFromSample	0.001	0.000	0.001
getTCGAdataTypes	1.684	0.007	1.845
getValidEvents	0.005	0.001	0.006
groupPerElem	0.001	0.000	0.001
hchart.survfit	0.451	0.111	0.579
isFirebrowseUp	0.006	0.001	0.034
labelBasedOnCutoff	0.001	0.000	0.000
leveneTest	0.008	0.000	0.009
listAllAnnotations	0.001	0.000	0.001
listSplicingAnnotations	0.165	0.002	0.020
loadAnnotation	0.003	0.003	0.002
loadGtexData	0.001	0.002	0.000
loadLocalFiles	0.001	0.001	0.001
loadTCGAdata	0.003	0.003	0.001
missingDataModal	0.001	0.002	0.001
normaliseGeneExpression	0.117	0.141	0.038
optimalSurvivalCutoff	0.533	0.556	0.234
parseCategoricalGroups	0.002	0.000	0.003
parseFirebrowseMetadata	0.059	0.008	0.219
parseMatsEvent	0.011	0.002	0.013
parseMatsGeneric	0.044	0.007	0.051
parseMisoAnnotation	0.512	0.074	0.628
parseMisoEvent	0.008	0.001	0.010
parseMisoEventID	0.009	0.002	0.011
parseMisoGeneric	0.049	0.008	0.059
parseMisoId	0.001	0.000	0.000
parseSplicingEvent	0.003	0.000	0.003
parseSuppaEvent	0.006	0.001	0.007
parseSuppaGeneric	0.033	0.006	0.040
parseTcgaSampleInfo	0.004	0.001	0.005
parseUrlsFromFirebrowseResponse	0.023	0.003	0.111
parseVastToolsEvent	0.007	0.002	0.010
parseVastToolsSE	0.030	0.005	0.035
performICA	0.008	0.002	0.011
performPCA	0.002	0.000	0.003
plot.GEandAScorrelation	0.596	0.036	0.644
plotDistribution	2.718	0.171	2.926
plotGeneExprPerSample	0.252	0.036	0.290
plotGroupIndependence	0.223	0.002	0.225
plotICA	0.209	0.012	0.224
plotPCA	0.493	0.090	0.596
plotProtein	0.890	0.074	1.318
plotRowStats	0.819	0.022	0.848
plotSingleICA	0.365	0.108	0.474
plotSplicingEvent	0.086	0.001	0.088
plotSurvivalCurves	0.095	0.032	0.130
plotSurvivalPvaluesByCutoff	0.915	0.035	0.955
plotTranscripts	0.025	0.001	1.053
plotVariance	0.063	0.057	0.121
prepareAnnotationFromEvents	0.235	0.005	0.245
prepareFirebrowseArchives	0.000	0.000	0.001
prepareJunctionQuantSTAR	0.001	0.000	0.000
prepareSRAmetadata	0	0	0
processSurvTerms	0.011	0.001	0.011
psichomics	0.001	0.000	0.000
quantifySplicing	0.007	0.002	0.009
queryEnsembl	0.048	0.003	0.906
queryEnsemblByGene	0.222	0.012	3.741
queryFirebrowseData	0.037	0.002	0.228
queryPubMed	0.094	0.008	0.489
queryUniprot	0.137	0.005	0.436
readFile	0.001	0.000	0.001
renameDuplicated	0.001	0.000	0.001
renderBoxplot	0.189	0.035	0.228
rowMeans	0.000	0.001	0.001
sidebar	0.005	0.000	0.005
survdiffTerms	0.041	0.002	0.042
survfit.survTerms	0.022	0.001	0.023
testGroupIndependence	0.004	0.000	0.004
testSurvival	0.017	0.000	0.018
textSuggestions	0.001	0.000	0.001
trimWhitespace	0	0	0

CHECK report for psichomics on merida1

Summary

Command output

Installation output

Tests output

Example timings