Package: psichomics

Version: 1.4.5

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings psichomics_1.4.5.tar.gz

StartedAt: 2018-04-12 07:58:53 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 08:03:10 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 257.2 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 --no-vignettes --timings psichomics_1.4.5.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.4.5’
* 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 ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
* 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 loading without being on the library search path ... 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
File ‘psichomics/libs/psichomics.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘psiFastCalc.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘psiFastCalc.o’
  Found ‘_putchar’, possibly from ‘putchar’ (C)
    Object: ‘psiFastCalc.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
ensemblToUniprot 0.19  0.002  10.588
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck/00check.log’
for details.

* installing *source* package ‘psichomics’ ...
** libs
clang++  -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/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/3.4/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 /Users/biocbuild/bbs-3.6-bioc/meat/psichomics.Rcheck/psichomics/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (psichomics)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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
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: 1071 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 10.606   0.274  24.282 

name	user	system	elapsed
blendColours	0.001	0.000	0.001
correlateGEandAS	0.395	0.003	0.402
createGroupByAttribute	0.002	0.001	0.002
createJunctionsTemplate	0.003	0.000	0.004
diffAnalyses	0.274	0.018	0.293
downloadFiles	0.001	0.000	0.001
ensemblToUniprot	0.190	0.002	10.588
filterGroups	0.000	0.000	0.001
getAttributesTime	0.003	0.001	0.003
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseCohorts	1.709	0.006	1.816
getFirebrowseDataTypes	0.001	0.000	0.002
getFirebrowseDateFormat	0.001	0.000	0.002
getFirebrowseDates	0.011	0.000	0.068
getMatchingSamples	0.002	0.001	0.003
getNumerics	0.005	0.000	0.005
getPatientFromSample	0.002	0.000	0.002
getSplicingEventFromGenes	0.037	0.000	0.037
getSplicingEventTypes	0.001	0.000	0.001
getValidEvents	0.007	0.000	0.007
groupPerElem	0.001	0.000	0.002
hchart.survfit	0.688	0.058	0.769
isFirebrowseUp	0.005	0.000	0.033
labelBasedOnCutoff	0.015	0.001	0.015
leveneTest	0.007	0.000	0.007
listAllAnnotations	0.001	0.000	0.001
listSplicingAnnotations	0.001	0.000	0.001
loadAnnotation	0	0	0
loadFirebrowseData	0.001	0.000	0.001
loadLocalFiles	0.000	0.000	0.001
missingDataModal	0.000	0.000	0.001
normaliseGeneExpression	0.064	0.000	0.064
optimalSurvivalCutoff	0.210	0.000	0.211
parseCategoricalGroups	0.002	0.000	0.002
parseFirebrowseMetadata	0.033	0.002	0.190
parseMatsEvent	0.007	0.001	0.008
parseMatsGeneric	0.025	0.001	0.027
parseMisoAnnotation	0.457	0.006	0.467
parseMisoEvent	0.006	0.000	0.006
parseMisoEventID	0.005	0.000	0.006
parseMisoGeneric	0.127	0.003	0.130
parseMisoId	0.001	0.000	0.001
parseSampleGroups	0.001	0.000	0.002
parseSplicingEvent	0.002	0.000	0.003
parseSuppaEvent	0.005	0.000	0.006
parseSuppaGeneric	0.028	0.001	0.029
parseTcgaSampleInfo	0.004	0.000	0.005
parseUrlsFromFirebrowseResponse	0.015	0.001	0.121
parseVastToolsEvent	0.007	0.000	0.007
parseVastToolsSE	0.118	0.002	0.121
performICA	0.010	0.002	0.012
performPCA	0.045	0.001	0.045
plotCorrelation	1.957	0.028	2.016
plotDistribution	0.328	0.020	0.353
plotGroupIndependence	0.143	0.002	0.147
plotICA	0.284	0.009	0.303
plotPCA	0.243	0.044	0.297
plotProtein	0.001	0.000	0.000
plotSingleICA	0.228	0.041	0.274
plotSurvivalCurves	0.086	0.017	0.105
plotTranscripts	0.015	0.001	2.106
plotVariance	0.052	0.017	0.076
prepareAnnotationFromEvents	0.297	0.004	0.309
prepareFirebrowseArchives	0	0	0
processSurvTerms	0.004	0.001	0.004
psichomics	0.001	0.000	0.000
quantifySplicing	0.004	0.000	0.004
queryEnsembl	0.026	0.002	0.826
queryEnsemblByEvent	0.064	0.004	3.167
queryEnsemblByGene	0.078	0.005	4.275
queryFirebrowseData	0.070	0.001	0.273
queryPubMed	0.069	0.003	0.335
queryUniprot	0.454	0.002	1.470
readFile	0.001	0.001	0.001
renameDuplicated	0.001	0.000	0.000
rowMeans	0.000	0.000	0.001
rowVars	0	0	0
survdiff.survTerms	0.006	0.001	0.007
survfit.survTerms	0.021	0.000	0.021
testGroupIndependence	0.04	0.00	0.04
testSurvival	0.016	0.000	0.017
textSuggestions	0.001	0.000	0.001
trimWhitespace	0	0	0