Multiple platform build/check report for BioC 3.9 - 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_1.9.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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
Examples with CPU or elapsed time > 5s
                  user system elapsed
ensemblToUniprot 0.217  0.016  10.346
* 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.

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" -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/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) (2019-03-18 r76245) -- "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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LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld7825ab0726a/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld7823abcac64/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld782759f1b1e/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld78215684113/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld78265d9d5de/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld7821ffef88e/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld78273cf3c84/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld78213097f3/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld78267e33805/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld78273505564/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld7821a154a61/index.html.

Retrieving protein annotation from UniProt...

Plotting protein domains...
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmpWmI2lS/viewhtmld7829119dab/index.html.

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: 1090 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 38.300   2.639  55.240

Example timings

name	user	system	elapsed
addObjectAttrs	0.001	0.001	0.002
blendColours	0.002	0.001	0.002
calculateLoadingsContribution	0.035	0.008	0.042
convertGeneIdentifiers	0.781	0.067	0.845
correlateGEandAS	0.307	0.017	0.043
createGroupByAttribute	0.012	0.001	0.002
createJunctionsTemplate	0.099	0.001	0.009
diffAnalyses	1.273	0.012	0.190
downloadFiles	0.000	0.001	0.000
ensemblToUniprot	0.217	0.016	10.346
filterGeneExpr	0.019	0.002	0.021
filterGroups	0.001	0.001	0.001
filterPSI	0.019	0.005	0.023
getAttributesTime	0.005	0.001	0.006
getDownloadsFolder	0.001	0.001	0.001
getFirebrowseDataTypes	0.001	0.001	0.002
getFirebrowseDateFormat	0.001	0.001	0.001
getFirebrowseDates	0.108	0.005	0.231
getGeneList	0.023	0.018	0.041
getMatchingSamples	0.002	0.001	0.002
getNumerics	0.005	0.001	0.007
getPatientFromSample	0.002	0.001	0.002
getSplicingEventFromGenes	0.005	0.001	0.006
getSplicingEventTypes	0.001	0.001	0.001
getValidEvents	0.010	0.002	0.012
getValuePerPatient	0.012	0.005	0.017
groupPerElem	0.002	0.000	0.003
hchart.survfit	0.471	0.247	0.741
isFirebrowseUp	0.009	0.004	0.036
labelBasedOnCutoff	0.002	0.000	0.001
leveneTest	0.015	0.001	0.016
listAllAnnotations	0.001	0.001	0.002
listSplicingAnnotations	0.001	0.000	0.001
loadAnnotation	0.001	0.000	0.000
loadFirebrowseData	0.000	0.000	0.001
loadLocalFiles	0.000	0.001	0.001
missingDataModal	0.001	0.001	0.001
normaliseGeneExpression	1.135	0.010	1.189
optimalSurvivalCutoff	0.244	0.004	0.249
parseCategoricalGroups	0.003	0.001	0.004
parseFirebrowseMetadata	0.064	0.007	0.202
parseMatsEvent	0.011	0.002	0.012
parseMatsGeneric	0.046	0.003	0.048
parseMisoAnnotation	0.642	0.022	0.687
parseMisoEvent	0.009	0.001	0.009
parseMisoEventID	0.010	0.002	0.013
parseMisoGeneric	0.076	0.006	0.083
parseMisoId	0.000	0.000	0.001
parseSampleGroups	0.001	0.000	0.004
parseSplicingEvent	0.004	0.000	0.004
parseSuppaEvent	0.008	0.000	0.008
parseSuppaGeneric	0.046	0.009	0.056
parseTcgaSampleInfo	0.006	0.001	0.007
parseUrlsFromFirebrowseResponse	0.027	0.002	0.109
parseVastToolsEvent	0.014	0.001	0.015
parseVastToolsSE	0.048	0.004	0.052
performICA	0.017	0.007	0.023
performPCA	0.003	0.000	0.004
plot.GEandAScorrelation	0.918	0.134	1.081
plotDistribution	0.148	0.105	0.256
plotGeneExprPerSample	0.319	0.118	0.438
plotGroupIndependence	0.363	0.070	0.453
plotICA	0.315	0.090	0.459
plotPCA	0.465	0.235	0.705
plotProtein	1.139	0.180	1.734
plotRowStats	0.969	0.040	1.009
plotSingleICA	0.328	0.205	0.544
plotSurvivalCurves	0.183	0.071	0.262
plotTranscripts	0.024	0.001	1.014
plotVariance	0.083	0.061	0.150
prepareAnnotationFromEvents	0.227	0.010	0.236
prepareFirebrowseArchives	0.001	0.001	0.000
prepareJunctionQuantSTAR	0.000	0.000	0.001
prepareSRAmetadata	0.000	0.001	0.000
processSurvTerms	0.003	0.000	0.003
psichomics	0	0	0
quantifySplicing	0.008	0.004	0.011
queryEnsembl	0.050	0.004	0.676
queryEnsemblByGene	0.246	0.028	3.565
queryFirebrowseData	0.040	0.002	0.207
queryPubMed	0.155	0.016	0.564
queryUniprot	0.149	0.007	0.439
readFile	0.002	0.001	0.002
renameDuplicated	0.001	0.001	0.002
renderBoxplot	0.148	0.055	0.207
rowMeans	0.000	0.001	0.001
sidebar	0.016	0.002	0.019
survdiff.survTerms	0.014	0.002	0.015
survfit.survTerms	0.046	0.002	0.048
testGroupIndependence	0.006	0.000	0.006
testSurvival	0.039	0.001	0.040
textSuggestions	0.000	0.001	0.001
trimWhitespace	0.001	0.001	0.001

CHECK report for psichomics on celaya2

Summary

Command output

Installation output

Tests output

Example timings