Multiple platform build/check report for BioC 3.8 - 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_1.8.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/psichomics.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.8.2’
* 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 or elapsed time > 5s
             user system elapsed
plotProtein 1.047  0.097   5.106
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘psichomics’ ...
** libs
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++  -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -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/3.5/Resources/library/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
* DONE (psichomics)

Tests output


R version 3.5.3 (2019-03-11) -- "Great Truth"
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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LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml14768730d18fe/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml147684765c223/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml14768a8d92b/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml147685f458e9d/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml1476817ff4024/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml1476842536df4/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml147681221e323/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml147682f0d7bf4/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml1476830afa39c/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml14768601c16cb/index.html.

Retrieving protein annotation from UniProt...
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml14768adbb11d/index.html.

Plotting protein domains...

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving rMATS annotation...

Parsing rMATS annotation...
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpEefIh9/viewhtml147685327f72b/index.html.

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: 1090 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 29.317   1.280  42.931

Example timings

name	user	system	elapsed
addObjectAttrs	0.001	0.000	0.001
blendColours	0.001	0.000	0.001
calculateLoadingsContribution	0.024	0.004	0.028
convertGeneIdentifiers	0.542	0.289	0.474
correlateGEandAS	0.076	0.125	0.024
createGroupByAttribute	0.007	0.012	0.002
createJunctionsTemplate	0.012	0.020	0.004
diffAnalyses	0.359	0.503	0.140
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.051	0.006	0.486
filterGeneExpr	0.015	0.001	0.017
filterGroups	0.001	0.000	0.001
filterPSI	0.014	0.003	0.018
getAttributesTime	0.004	0.000	0.004
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseDataTypes	0.001	0.000	0.002
getFirebrowseDateFormat	0.001	0.001	0.000
getFirebrowseDates	1.660	0.004	1.810
getGeneList	0.014	0.007	0.020
getMatchingSamples	0.002	0.000	0.002
getNumerics	0.004	0.000	0.003
getPatientFromSample	0.001	0.000	0.001
getSplicingEventFromGenes	0.003	0.000	0.003
getSplicingEventTypes	0.001	0.000	0.001
getValidEvents	0.005	0.000	0.004
getValuePerPatient	0.007	0.002	0.009
groupPerElem	0.001	0.000	0.001
hchart.survfit	0.368	0.116	0.508
isFirebrowseUp	0.009	0.000	0.037
labelBasedOnCutoff	0.001	0.001	0.001
leveneTest	0.014	0.000	0.014
listAllAnnotations	0.001	0.000	0.002
listSplicingAnnotations	0	0	0
loadAnnotation	0	0	0
loadFirebrowseData	0.000	0.000	0.001
loadLocalFiles	0.001	0.001	0.000
missingDataModal	0.000	0.000	0.001
normaliseGeneExpression	0.031	0.002	0.033
optimalSurvivalCutoff	0.148	0.005	0.153
parseCategoricalGroups	0.002	0.001	0.003
parseFirebrowseMetadata	0.051	0.003	0.212
parseMatsEvent	0.007	0.001	0.008
parseMatsGeneric	0.030	0.002	0.032
parseMisoAnnotation	0.507	0.010	0.529
parseMisoEvent	0.005	0.000	0.006
parseMisoEventID	0.009	0.001	0.009
parseMisoGeneric	0.062	0.003	0.066
parseMisoId	0.001	0.001	0.000
parseSampleGroups	0.001	0.000	0.001
parseSplicingEvent	0.003	0.001	0.004
parseSuppaEvent	0.005	0.000	0.005
parseSuppaGeneric	0.022	0.001	0.023
parseTcgaSampleInfo	0.003	0.000	0.003
parseUrlsFromFirebrowseResponse	0.022	0.000	0.117
parseVastToolsEvent	0.009	0.000	0.009
parseVastToolsSE	0.027	0.001	0.028
performICA	0.009	0.002	0.010
performPCA	0.003	0.001	0.003
plot.GEandAScorrelation	1.343	0.031	1.378
plotDistribution	0.082	0.034	0.118
plotGeneExprPerSample	0.185	0.030	0.217
plotGroupIndependence	0.174	0.001	0.175
plotICA	0.173	0.011	0.187
plotPCA	0.289	0.100	0.391
plotProtein	1.047	0.097	5.106
plotRowStats	1.102	0.024	1.158
plotSingleICA	0.344	0.112	0.459
plotSurvivalCurves	0.140	0.041	0.184
plotTranscripts	0.027	0.001	0.946
plotVariance	0.079	0.038	0.117
prepareAnnotationFromEvents	0.301	0.006	0.307
prepareFirebrowseArchives	0	0	0
prepareJunctionQuantSTAR	0.001	0.000	0.000
prepareSRAmetadata	0.001	0.000	0.000
processSurvTerms	0.005	0.000	0.005
psichomics	0	0	0
quantifySplicing	0.007	0.002	0.009
queryEnsembl	0.052	0.003	0.551
queryEnsemblByGene	0.255	0.015	2.879
queryFirebrowseData	0.044	0.002	0.241
queryPubMed	0.079	0.009	0.534
queryUniprot	0.180	0.003	3.140
readFile	0.001	0.000	0.002
renameDuplicated	0.001	0.000	0.001
renderBoxplot	0.139	0.031	0.171
rowMeans	0.000	0.000	0.001
sidebar	0.014	0.002	0.016
survdiff.survTerms	0.011	0.001	0.011
survfit.survTerms	0.027	0.001	0.029
testGroupIndependence	0.005	0.000	0.005
testSurvival	0.024	0.001	0.025
textSuggestions	0.001	0.000	0.001
trimWhitespace	0.001	0.000	0.001

CHECK report for psichomics on merida1

Summary

Command output

Installation output

Tests output

Example timings