Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-01-26 13:05:49 -0500 (Wed, 26 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.2 (2021-11-01) -- "Bird Hippie" 4329
tokay2Windows Server 2012 R2 Standardx644.1.2 (2021-11-01) -- "Bird Hippie" 4080
machv2macOS 10.14.6 Mojavex86_644.1.2 (2021-11-01) -- "Bird Hippie" 4141
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for psichomics on nebbiolo2


To the developers/maintainers of the psichomics package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/psichomics.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1480/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.20.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2022-01-25 01:55:07 -0500 (Tue, 25 Jan 2022)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_14
git_last_commit: 84bcdbf
git_last_commit_date: 2021-10-26 12:30:49 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: psichomics
Version: 1.20.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings psichomics_1.20.0.tar.gz
StartedAt: 2022-01-25 09:05:41 -0500 (Tue, 25 Jan 2022)
EndedAt: 2022-01-25 09:12:32 -0500 (Tue, 25 Jan 2022)
EllapsedTime: 411.5 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings psichomics_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/psichomics.Rcheck’
* using R version 4.1.2 (2021-11-01)
* 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 ‘1.20.0’
* 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 (user + system) or elapsed time > 5s
                          user system elapsed
convertGeneIdentifiers  19.779  0.661  23.146
listSplicingAnnotations 13.905  0.392  15.212
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  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-3.14-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c progressBar.cpp -o progressBar.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c psiFastCalc.cpp -o psiFastCalc.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c vastToolsParser.cpp -o vastToolsParser.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.14-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/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
*** copying figures
** 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

psichomics.Rcheck/tests/spelling.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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.

> if(requireNamespace('spelling', quietly = TRUE))
+   spelling::spell_check_test(vignettes = TRUE, error = FALSE,
+                              skip_on_cran = TRUE)
NULL
> 
> proc.time()
   user  system elapsed 
  0.252   0.030   0.267 

psichomics.Rcheck/tests/testthat.Rout


R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 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)

psichomics 1.20.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
> 
> test_check("psichomics")
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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

EXSK

IR

MERGE3m

MIC

MULTI
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1396 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (2)
• On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1396 ]
> 
> proc.time()
   user  system elapsed 
 20.883   1.524  29.790 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0000.001
assignValuePerSubject0.0170.0000.017
blendColours0.0010.0000.001
calculateLoadingsContribution0.0090.0000.008
convertGeneIdentifiers19.779 0.66123.146
correlateGEandAS0.0150.0000.016
createGroupByAttribute0.0010.0000.001
createJunctionsTemplate0.0020.0000.001
customRowMeans0.0010.0000.000
diffAnalyses0.0680.0000.068
downloadFiles000
ensemblToUniprot0.0390.0000.921
filterGeneExpr0.0050.0000.005
filterGroups0.0010.0000.002
filterPSI0.0110.0000.012
getAttributesTime0.0020.0000.003
getDownloadsFolder0.0000.0000.001
getFirebrowseDateFormat0.0010.0000.000
getGeneList0.0030.0000.004
getGtexDataTypes0.0450.0000.281
getGtexTissues000
getNumerics0.0050.0000.006
getSampleFromSubject0.0010.0010.001
getSplicingEventFromGenes0.0010.0020.003
getSplicingEventTypes000
getSubjectFromSample0.0010.0000.001
getTCGAdataTypes0.0400.0040.258
getValidEvents0.0020.0020.004
groupPerElem000
hchart.survfit0.2040.0390.266
isFirebrowseUp0.0060.0000.012
labelBasedOnCutoff0.0010.0000.001
leveneTest0.0080.0000.008
listAllAnnotations2.9400.0683.382
listSplicingAnnotations13.905 0.39215.212
loadAnnotation3.7020.1164.106
loadGtexData000
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.0120.0000.025
missingDataModal000
normaliseGeneExpression0.0330.0000.033
optimalSurvivalCutoff0.1160.0000.116
parseCategoricalGroups0.0000.0000.001
parseFirebrowseMetadata0.0560.0040.109
parseMatsEvent0.0050.0000.006
parseMatsGeneric0.0170.0000.017
parseMisoAnnotation0.1110.0040.118
parseMisoEvent0.0030.0000.004
parseMisoEventID0.0040.0000.005
parseMisoGeneric0.0260.0010.026
parseMisoId000
parseSplicingEvent0.0030.0000.004
parseSuppaEvent0.0030.0000.003
parseSuppaGeneric0.0130.0040.017
parseTcgaSampleInfo0.0030.0000.003
parseUrlsFromFirebrowseResponse0.0500.0000.151
parseVastToolsEvent0.0080.0000.008
parseVastToolsSE0.0260.0000.026
performICA0.0060.0040.010
performPCA0.0020.0000.002
plot.GEandAScorrelation0.3450.0000.345
plotDistribution0.5710.0080.579
plotGeneExprPerSample0.0850.0000.085
plotGroupIndependence0.1070.0000.107
plotICA0.0970.0030.102
plotLibrarySize0.1640.0040.168
plotPCA0.2350.0200.257
plotPCAvariance0.0450.0040.049
plotProtein0.6410.0163.120
plotRowStats0.3010.0000.302
plotSingleICA0.1700.0200.191
plotSplicingEvent0.0430.0000.043
plotSurvivalCurves0.0800.0040.085
plotSurvivalPvaluesByCutoff0.4330.0040.436
plotTranscripts0.0330.0001.454
prepareAnnotationFromEvents0.2870.0310.320
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.0060.0030.009
psichomics0.0010.0000.000
quantifySplicing0.0070.0030.011
queryEnsembl0.0390.0051.056
queryEnsemblByGene0.1350.0044.126
queryFirebrowseData0.0530.0000.161
queryPubMed0.0510.0040.555
queryUniprot0.0770.0041.738
readFile0.0010.0000.001
renameDuplicated0.0010.0000.000
renderBoxplot0.1070.0040.112
survdiffTerms0.0050.0040.009
survfit.survTerms0.0370.0000.037
testGroupIndependence0.0030.0000.002
testSurvival0.0250.0000.025
textSuggestions0.0000.0000.001
trimWhitespace000