Multiple platform build/check report for BioC 3.9 - CHECK report for psichomics on merida2

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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_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.9.2’
* 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’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  IR
  
  MERGE3m
  
  MIC
  
  EXSK
  
  MULTI
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1085 SKIPPED: 0 FAILED: 1
  1. Error: Plot transcripts (@testGeneInfo.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
* 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 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-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’ ...
** 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" -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" -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/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 Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 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/RtmpH6TqFW/viewhtml1831d2ff31667/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpH6TqFW/viewhtml1831d3ff75066/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpH6TqFW/viewhtml1831d4be6f4b8/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpH6TqFW/viewhtml1831d2c133233/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpH6TqFW/viewhtml1831d65c275d7/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpH6TqFW/viewhtml1831d1297350f/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpH6TqFW/viewhtml1831d759722ca/index.html.
── 1. Error: Plot transcripts (@testGeneInfo.R#64)  ────────────────────────────
argument of length 0
1: plotTranscripts(info, event = event) at testthat/testGeneInfo.R:64


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: 1085 SKIPPED: 0 FAILED: 1
1. Error: Plot transcripts (@testGeneInfo.R#64) 

Error: testthat unit tests failed
Execution halted

Example timings

name	user	system	elapsed
addObjectAttrs	0.001	0.000	0.001
blendColours	0.001	0.000	0.002
calculateLoadingsContribution	0.028	0.004	0.033
convertGeneIdentifiers	0.624	0.084	0.613
correlateGEandAS	0.089	0.095	0.026
createGroupByAttribute	0.009	0.009	0.002
createJunctionsTemplate	0.014	0.014	0.004
diffAnalyses	0.504	0.466	0.144
downloadFiles	0.001	0.000	0.001
ensemblToUniprot	0.513	0.009	1.006
filterGeneExpr	0.011	0.001	0.012
filterGroups	0.001	0.000	0.000
filterPSI	0.011	0.002	0.012
getAttributesTime	0.003	0.000	0.003
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseDataTypes	0.001	0.000	0.000
getFirebrowseDateFormat	0.001	0.000	0.001
getFirebrowseDates	1.637	0.009	1.810
getGeneList	0.013	0.007	0.020
getMatchingSamples	0.002	0.000	0.002
getNumerics	0.005	0.000	0.005
getPatientFromSample	0.001	0.000	0.001
getSplicingEventFromGenes	0.005	0.000	0.005
getSplicingEventTypes	0	0	0
getValidEvents	0.006	0.001	0.007
getValuePerPatient	0.009	0.002	0.012
groupPerElem	0.001	0.001	0.002
hchart.survfit	0.383	0.118	0.523
isFirebrowseUp	0.009	0.000	0.038
labelBasedOnCutoff	0.001	0.001	0.002
leveneTest	0.013	0.000	0.014
listAllAnnotations	0.000	0.000	0.001
listSplicingAnnotations	0.001	0.000	0.001
loadAnnotation	0	0	0
loadFirebrowseData	0.000	0.000	0.001
loadLocalFiles	0.000	0.001	0.000
missingDataModal	0.001	0.000	0.000
normaliseGeneExpression	0.826	0.003	0.832
optimalSurvivalCutoff	0.151	0.002	0.154
parseCategoricalGroups	0.003	0.000	0.003
parseFirebrowseMetadata	0.054	0.003	0.213
parseMatsEvent	0.009	0.001	0.009
parseMatsGeneric	0.036	0.002	0.038
parseMisoAnnotation	0.437	0.011	0.462
parseMisoEvent	0.007	0.000	0.008
parseMisoEventID	0.010	0.001	0.012
parseMisoGeneric	0.059	0.004	0.065
parseMisoId	0	0	0
parseSampleGroups	0.002	0.000	0.001
parseSplicingEvent	0.003	0.000	0.004
parseSuppaEvent	0.007	0.000	0.007
parseSuppaGeneric	0.036	0.003	0.038
parseTcgaSampleInfo	0.005	0.001	0.005
parseUrlsFromFirebrowseResponse	0.025	0.001	0.118
parseVastToolsEvent	0.007	0.001	0.007
parseVastToolsSE	0.037	0.002	0.040
performICA	0.012	0.003	0.013
performPCA	0.002	0.000	0.002
plot.GEandAScorrelation	0.613	0.073	0.688
plotDistribution	0.104	0.064	0.172
plotGeneExprPerSample	0.210	0.058	0.269
plotGroupIndependence	0.199	0.027	0.228
plotICA	0.183	0.036	0.224
plotPCA	0.331	0.107	0.445
plotProtein	1.044	0.086	1.450
plotRowStats	0.950	0.020	0.976
plotSingleICA	0.303	0.097	0.407
plotSurvivalCurves	0.120	0.038	0.162
plotTranscripts	0.025	0.001	1.168
plotVariance	0.079	0.038	0.119
prepareAnnotationFromEvents	0.244	0.003	0.248
prepareFirebrowseArchives	0	0	0
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0.000	0.001	0.000
processSurvTerms	0.004	0.000	0.005
psichomics	0.001	0.001	0.000
quantifySplicing	0.008	0.002	0.010
queryEnsembl	0.050	0.003	0.765
queryEnsemblByGene	0.212	0.013	4.575
queryFirebrowseData	0.039	0.001	0.237
queryPubMed	0.098	0.007	0.488
queryUniprot	0.133	0.004	0.443
readFile	0.001	0.000	0.001
renameDuplicated	0.001	0.000	0.000
renderBoxplot	0.093	0.024	0.119
rowMeans	0.000	0.000	0.001
sidebar	0.009	0.001	0.010
survdiff.survTerms	0.007	0.001	0.008
survfit.survTerms	0.017	0.001	0.018
testGroupIndependence	0.004	0.000	0.004
testSurvival	0.019	0.000	0.019
textSuggestions	0.001	0.000	0.001
trimWhitespace	0.000	0.000	0.001

CHECK report for psichomics on merida2

Summary

Command output

Installation output

Tests output

Example timings