Package: psichomics

Version: 1.10.2

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_1.10.2.tar.gz

StartedAt: 2019-10-16 05:48:57 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 05:58:36 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 579.4 seconds

RetCode: 0

Status:  OK

CheckDir: psichomics.Rcheck

Warnings: 0

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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_1.10.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/psichomics.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.10.2’
* 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
* 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-3.9-bioc/meat/psichomics.Rcheck/00check.log’
for details.

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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
** 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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
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 
 31.649   2.582  48.485 

name	user	system	elapsed
addObjectAttrs	0.001	0.000	0.002
blendColours	0.002	0.001	0.003
calculateLoadingsContribution	1.048	0.007	1.055
convertGeneIdentifiers	0.598	0.061	0.580
correlateGEandAS	0.098	0.085	0.040
createGroupByAttribute	0.012	0.010	0.004
createJunctionsTemplate	0.014	0.013	0.005
diffAnalyses	0.385	0.251	0.169
downloadFiles	0.000	0.001	0.001
ensemblToUniprot	0.485	0.008	1.042
filterGeneExpr	0.019	0.002	0.022
filterGroups	0.001	0.001	0.002
filterPSI	0.013	0.004	0.017
getAttributesTime	0.003	0.001	0.004
getDownloadsFolder	0.001	0.000	0.001
getFirebrowseDataTypes	0.001	0.000	0.002
getFirebrowseDateFormat	0.000	0.000	0.001
getFirebrowseDates	0.086	0.004	0.181
getGeneList	0.021	0.015	0.039
getMatchingSamples	0.002	0.000	0.003
getNumerics	0.006	0.001	0.007
getPatientFromSample	0.001	0.001	0.002
getSplicingEventFromGenes	0.005	0.001	0.006
getSplicingEventTypes	0.000	0.000	0.002
getValidEvents	0.008	0.001	0.010
getValuePerPatient	0.011	0.005	0.015
groupPerElem	0.001	0.001	0.002
hchart.survfit	0.451	0.213	0.771
isFirebrowseUp	0.009	0.000	0.027
labelBasedOnCutoff	0.002	0.001	0.002
leveneTest	0.013	0.001	0.014
listAllAnnotations	0.001	0.000	0.002
listSplicingAnnotations	0.000	0.000	0.001
loadAnnotation	0.000	0.000	0.001
loadFirebrowseData	0.001	0.000	0.001
loadLocalFiles	0	0	0
missingDataModal	0.000	0.000	0.001
normaliseGeneExpression	0.038	0.004	0.043
optimalSurvivalCutoff	0.172	0.011	0.183
parseCategoricalGroups	0.002	0.001	0.002
parseFirebrowseMetadata	0.060	0.006	0.168
parseMatsEvent	0.013	0.002	0.014
parseMatsGeneric	0.044	0.005	0.049
parseMisoAnnotation	0.720	0.156	0.891
parseMisoEvent	0.009	0.003	0.012
parseMisoEventID	0.017	0.005	0.023
parseMisoGeneric	0.088	0.022	0.110
parseMisoId	0.000	0.000	0.002
parseSampleGroups	0.002	0.001	0.004
parseSplicingEvent	0.006	0.002	0.006
parseSuppaEvent	0.007	0.002	0.009
parseSuppaGeneric	0.041	0.009	0.051
parseTcgaSampleInfo	0.006	0.002	0.009
parseUrlsFromFirebrowseResponse	0.033	0.006	0.101
parseVastToolsEvent	0.014	0.004	0.018
parseVastToolsSE	0.058	0.014	0.072
performICA	0.018	0.008	0.027
performPCA	0.004	0.001	0.006
plot.GEandAScorrelation	0.734	0.026	0.761
plotDistribution	0.124	0.061	0.185
plotGeneExprPerSample	0.260	0.065	0.324
plotGroupIndependence	0.295	0.004	0.299
plotICA	0.256	0.026	0.285
plotPCA	0.330	0.178	0.509
plotProtein	1.921	0.377	4.318
plotRowStats	1.131	0.037	1.169
plotSingleICA	0.342	0.172	0.513
plotSurvivalCurves	0.161	0.063	0.224
plotTranscripts	0.031	0.002	0.987
plotVariance	0.072	0.058	0.130
prepareAnnotationFromEvents	0.340	0.011	0.351
prepareFirebrowseArchives	0.000	0.000	0.001
prepareJunctionQuantSTAR	0.001	0.000	0.001
prepareSRAmetadata	0.000	0.001	0.001
processSurvTerms	0.004	0.000	0.004
psichomics	0.000	0.000	0.001
quantifySplicing	0.010	0.004	0.015
queryEnsembl	0.058	0.008	0.845
queryEnsemblByGene	0.236	0.026	4.179
queryFirebrowseData	0.045	0.003	0.177
queryPubMed	0.089	0.019	0.550
queryUniprot	0.153	0.005	1.286
readFile	0.001	0.000	0.002
renameDuplicated	0.001	0.000	0.002
renderBoxplot	0.173	0.063	0.237
rowMeans	0.000	0.000	0.001
sidebar	0.016	0.000	0.017
survdiffTerms	0.014	0.001	0.016
survfit.survTerms	0.050	0.002	0.052
testGroupIndependence	0.007	0.001	0.008
testSurvival	0.041	0.001	0.042
textSuggestions	0.001	0.000	0.002
trimWhitespace	0.001	0.000	0.002