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CHECK report for psichomics on malbec1

This page was generated on 2019-04-16 11:52:24 -0400 (Tue, 16 Apr 2019).

Package 1211/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.8.2
Nuno Saraiva-Agostinho
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/psichomics
Branch: RELEASE_3_8
Last Commit: 5490eef
Last Changed Date: 2019-03-27 10:18:03 -0400 (Wed, 27 Mar 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: psichomics
Version: 1.8.2
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings psichomics_1.8.2.tar.gz
StartedAt: 2019-04-16 02:15:31 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 02:21:54 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 382.9 seconds
RetCode: 0
Status:  OK 
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings psichomics_1.8.2.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/psichomics.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (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
* 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
  ‘/home/biocbuild/bbs-3.8-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘psichomics’ ...
** libs
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c psiFastCalc.cpp -o psiFastCalc.o
psiFastCalc.cpp: In function ‘Rcpp::NumericMatrix psiFastCalc(const NumericMatrix&, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, Rcpp::NumericVector, int)’:
psiFastCalc.cpp:30:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t col=0; col < mat.ncol(); col++) {
                            ^
psiFastCalc.cpp:31:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t idx=0; idx < incA.length(); idx++) {
                                ^
psiFastCalc.cpp: In function ‘Rcpp::NumericMatrix psiFastCalc2(const NumericMatrix&, const List&, const List&, int)’:
psiFastCalc.cpp:62:28: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (size_t col=0; col < mat.ncol(); col++) {
                            ^
psiFastCalc.cpp:63:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (size_t idx=0; idx < inc.length(); idx++) {
                                ^
psiFastCalc.cpp:66:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t k=0; k < incIdx.length(); k++)
                                ^
psiFastCalc.cpp:71:32: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (size_t k=0; k < excIdx.length(); k++)
                                ^
g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o psiFastCalc.o -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/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

psichomics.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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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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: 1090 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 29.840   1.680  44.068 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs000
blendColours0.0040.0000.002
calculateLoadingsContribution0.0240.0000.025
convertGeneIdentifiers0.6240.0080.497
correlateGEandAS0.0160.0000.033
createGroupByAttribute0.0000.0000.001
createJunctionsTemplate0.0040.0000.002
diffAnalyses0.0720.0000.072
downloadFiles000
ensemblToUniprot0.3200.0000.758
filterGeneExpr0.0160.0000.013
filterGroups0.0000.0000.001
filterPSI0.0160.0000.013
getAttributesTime0.0040.0000.003
getDownloadsFolder0.0000.0000.001
getFirebrowseDataTypes0.0000.0000.001
getFirebrowseDateFormat0.0040.0000.000
getFirebrowseDates0.1400.0000.262
getGeneList0.0080.0040.031
getMatchingSamples0.0000.0000.001
getNumerics0.0040.0040.006
getPatientFromSample0.0000.0000.001
getSplicingEventFromGenes0.0000.0040.003
getSplicingEventTypes0.0000.0000.001
getValidEvents0.0040.0000.006
getValuePerPatient0.0080.0000.009
groupPerElem000
hchart.survfit0.3800.0680.665
isFirebrowseUp0.0080.0000.031
labelBasedOnCutoff0.0000.0000.001
leveneTest0.0120.0000.012
listAllAnnotations0.0000.0000.001
listSplicingAnnotations0.0000.0000.001
loadAnnotation000
loadFirebrowseData0.0040.0000.001
loadLocalFiles000
missingDataModal000
normaliseGeneExpression0.0280.0040.030
optimalSurvivalCutoff0.1840.0040.189
parseCategoricalGroups0.0040.0000.002
parseFirebrowseMetadata0.0840.0040.218
parseMatsEvent0.0080.0000.007
parseMatsGeneric0.0320.0000.033
parseMisoAnnotation0.4480.0000.491
parseMisoEvent0.0080.0000.007
parseMisoEventID0.0080.0000.010
parseMisoGeneric0.0480.0080.057
parseMisoId0.0000.0000.001
parseSampleGroups0.0040.0000.001
parseSplicingEvent0.0040.0000.003
parseSuppaEvent0.0080.0000.006
parseSuppaGeneric0.0200.0120.032
parseTcgaSampleInfo0.0040.0000.004
parseUrlsFromFirebrowseResponse0.0360.0040.116
parseVastToolsEvent0.0080.0000.010
parseVastToolsSE0.0240.0080.033
performICA0.0120.0000.011
performPCA0.0040.0000.003
plot.GEandAScorrelation0.5600.0080.568
plotDistribution0.1000.0120.110
plotGeneExprPerSample0.1920.0160.211
plotGroupIndependence0.2240.0000.224
plotICA0.1680.0280.224
plotPCA0.3240.0200.345
plotProtein1.4280.0324.977
plotRowStats1.9440.0001.950
plotSingleICA0.2880.0280.359
plotSurvivalCurves0.1280.0160.145
plotTranscripts0.0320.0000.899
plotVariance0.0600.0080.067
prepareAnnotationFromEvents0.2320.0000.235
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata0.0000.0000.001
processSurvTerms0.0040.0000.004
psichomics000
quantifySplicing0.0040.0040.008
queryEnsembl0.0560.0000.578
queryEnsemblByGene0.1520.0083.021
queryFirebrowseData0.0400.0040.208
queryPubMed0.1800.0200.632
queryUniprot0.1120.0003.398
readFile0.0040.0000.002
renameDuplicated0.0000.0000.001
renderBoxplot0.1400.0120.152
rowMeans000
sidebar0.0120.0000.013
survdiff.survTerms0.0080.0000.009
survfit.survTerms0.0240.0040.031
testGroupIndependence0.0040.0000.004
testSurvival0.0280.0040.031
textSuggestions0.0000.0000.001
trimWhitespace0.0040.0000.000