Multiple platform build/check report for BioC 3.7 - 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_1.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/psichomics.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.6.2’
* 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
File ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library/psichomics/libs/psichomics.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* 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-3.7-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
No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package ‘IRanges’ for request: ‘subset’ when loading ‘derfinder’
* DONE (psichomics)

Tests output


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
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)
No methods found in package 'IRanges' for request: 'subset' when loading 'derfinder'
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/RtmppQ10LN/viewhtml177d260d68c3a/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d22b5b3d7/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d211970f90/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d214bb7a75/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d227ec50d/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d28076c6b/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d271b0e177/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d25863df61/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d257de42e7/index.html.
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d25dfb268/index.html.

Retrieving protein annotation from UniProt...

Plotting protein domains...
LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d253444db5/index.html.

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving MISO annotation...

Parsing MISO annotation...
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LSOpenURLsWithRole() failed with error -10810 for the file /tmp/RtmppQ10LN/viewhtml177d2246930cd/index.html.

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 
 26.731   1.071  38.750

Example timings

name	user	system	elapsed
addObjectAttrs	0.002	0.000	0.003
blendColours	0.003	0.000	0.003
correlateGEandAS	0.023	0.005	0.028
createGroupByAttribute	0.003	0.000	0.004
createJunctionsTemplate	0.004	0.000	0.004
diffAnalyses	0.145	0.021	0.166
downloadFiles	0.001	0.000	0.001
ensemblToUniprot	0.087	0.010	0.618
filterGroups	0.002	0.000	0.002
getAttributesTime	0.005	0.001	0.006
getDownloadsFolder	0.001	0.000	0.001
getFirebrowseCohorts	1.637	0.004	1.728
getFirebrowseDataTypes	0.002	0.001	0.002
getFirebrowseDateFormat	0.002	0.000	0.003
getFirebrowseDates	0.014	0.001	0.073
getMatchingSamples	0.003	0.000	0.004
getNumerics	0.005	0.000	0.005
getPatientFromSample	0.003	0.001	0.003
getSplicingEventFromGenes	0.004	0.000	0.004
getSplicingEventTypes	0.001	0.000	0.002
getValidEvents	0.006	0.000	0.007
groupPerElem	0.002	0.001	0.002
hchart.survfit	0.325	0.058	0.397
isFirebrowseUp	0.006	0.000	0.035
labelBasedOnCutoff	0.002	0.001	0.002
leveneTest	0.015	0.000	0.016
listAllAnnotations	0.002	0.000	0.002
listSplicingAnnotations	0.001	0.000	0.002
loadAnnotation	0.001	0.000	0.002
loadFirebrowseData	0.001	0.000	0.001
loadLocalFiles	0.001	0.000	0.001
missingDataModal	0.001	0.001	0.001
normaliseGeneExpression	0.017	0.001	0.018
optimalSurvivalCutoff	0.117	0.002	0.119
parseCategoricalGroups	0.003	0.001	0.004
parseFirebrowseMetadata	0.048	0.002	0.206
parseMatsEvent	0.007	0.000	0.007
parseMatsGeneric	0.036	0.002	0.037
parseMisoAnnotation	0.197	0.011	0.213
parseMisoEvent	0.010	0.001	0.011
parseMisoEventID	0.007	0.000	0.009
parseMisoGeneric	0.063	0.003	0.067
parseMisoId	0.002	0.000	0.002
parseSampleGroups	0.003	0.001	0.004
parseSplicingEvent	0.004	0.000	0.003
parseSuppaEvent	0.005	0.001	0.005
parseSuppaGeneric	0.036	0.002	0.039
parseTcgaSampleInfo	0.005	0.000	0.006
parseUrlsFromFirebrowseResponse	0.020	0.001	0.114
parseVastToolsEvent	0.011	0.000	0.011
parseVastToolsSE	0.039	0.002	0.040
performICA	0.012	0.002	0.015
performPCA	0.003	0.000	0.003
plotCorrelation	0.802	0.023	0.828
plotDistribution	0.677	0.063	0.745
plotGroupIndependence	0.285	0.038	0.323
plotICA	0.216	0.026	0.248
plotPCA	0.308	0.120	0.434
plotProtein	0.002	0.000	0.001
plotSingleICA	0.294	0.068	0.373
plotSurvivalCurves	0.136	0.042	0.197
plotTranscripts	0.021	0.001	0.810
plotVariance	0.076	0.025	0.129
prepareAnnotationFromEvents	0.233	0.006	0.240
prepareFirebrowseArchives	0.003	0.000	0.003
prepareSRAmetadata	0.002	0.000	0.002
processSurvTerms	0.006	0.000	0.006
psichomics	0.001	0.000	0.001
quantifySplicing	0.008	0.001	0.009
queryEnsembl	0.050	0.003	0.527
queryEnsemblByEvent	0.111	0.006	1.336
queryEnsemblByGene	0.110	0.006	1.528
queryFirebrowseData	0.036	0.001	0.234
queryPubMed	0.067	0.006	0.496
queryUniprot	0.199	0.006	0.910
readFile	0.002	0.000	0.002
renameDuplicated	0.003	0.000	0.003
rowMeans	0.002	0.000	0.002
rowVars	0.002	0.000	0.002
sidebar	0.012	0.001	0.013
survdiff.survTerms	0.014	0.000	0.015
survfit.survTerms	0.025	0.000	0.026
testGroupIndependence	0.004	0.000	0.004
testSurvival	0.028	0.001	0.029
textSuggestions	0.002	0.000	0.002
trimWhitespace	0.002	0.000	0.002

CHECK report for psichomics on merida2

Summary

Command output

Installation output

Tests output

Example timings