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This page was generated on 2022-10-19 13:20:42 -0400 (Wed, 19 Oct 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.5 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4386
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4138
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4205
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 nebbiolo1


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? 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 1518/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.22.1  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2022-10-18 13:55:19 -0400 (Tue, 18 Oct 2022)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_15
git_last_commit: 07747f4
git_last_commit_date: 2022-07-14 16:42:35 -0400 (Thu, 14 Jul 2022)
nebbiolo1Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: psichomics
Version: 1.22.1
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings psichomics_1.22.1.tar.gz
StartedAt: 2022-10-18 21:15:45 -0400 (Tue, 18 Oct 2022)
EndedAt: 2022-10-18 21:23:01 -0400 (Tue, 18 Oct 2022)
EllapsedTime: 435.5 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings psichomics_1.22.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/psichomics.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.22.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .devcontainer
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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  15.460  2.512  19.293
listSplicingAnnotations 12.412  2.396  15.706
queryEnsemblByGene       0.148  0.044   5.471
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.15-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-3.15-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-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 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 
  0.162   0.027   0.174 

psichomics.Rcheck/tests/testthat.Rout


R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 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 1.22.1: 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 4 | PASS 1418 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• Couldn't resolve host name (1)
• On Bioconductor (2)
• On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 1418 ]
> 
> proc.time()
   user  system elapsed 
 21.952   2.288  28.017 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0000.001
assignValuePerSubject0.0190.0120.031
blendColours0.0000.0010.001
calculateLoadingsContribution0.0090.0010.011
convertGeneIdentifiers15.460 2.51219.293
correlateGEandAS0.0170.0040.021
createGroupByAttribute0.0020.0000.002
createJunctionsTemplate0.0020.0000.002
customRowMeans0.0000.0000.001
diffAnalyses0.0710.0140.085
downloadFiles000
ensemblToUniprot0.0290.0111.357
filterGeneExpr0.0070.0000.008
filterGroups0.0020.0000.002
filterPSI0.0090.0080.017
getAttributesTime0.0000.0030.003
getDownloadsFolder000
getFirebrowseDateFormat000
getGeneList0.0030.0020.005
getGtexDataTypes0.0420.0150.256
getGtexTissues0.0010.0000.001
getNumerics0.0040.0030.012
getSampleFromSubject0.0020.0000.002
getSplicingEventFromGenes0.0020.0030.005
getSplicingEventTypes0.0000.0000.001
getSubjectFromSample0.0000.0000.001
getTCGAdataTypes0.0450.0240.246
getValidEvents0.0050.0000.006
groupPerElem0.0010.0000.001
hchart.survfit0.2750.0670.364
isFirebrowseUp0.0070.0000.014
labelBasedOnCutoff0.0010.0000.001
leveneTest0.0110.0000.011
listAllAnnotations2.5370.6663.575
listSplicingAnnotations12.412 2.39615.706
loadAnnotation3.3250.5514.089
loadGtexData0.0000.0000.001
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.0170.0050.035
missingDataModal0.0010.0000.001
normaliseGeneExpression0.0310.0040.035
optimalSurvivalCutoff0.1060.0000.106
parseCategoricalGroups0.0010.0000.001
parseFirebrowseMetadata0.0810.0040.131
parseMatsEvent0.0010.0080.008
parseMatsGeneric0.0400.0040.044
parseMisoAnnotation0.1220.0320.160
parseMisoEvent0.0010.0040.004
parseMisoEventID0.0030.0040.007
parseMisoGeneric0.0300.0030.034
parseMisoId000
parseSplicingEvent0.0000.0070.006
parseSuppaEvent0.0030.0010.003
parseSuppaGeneric0.0170.0050.021
parseTcgaSampleInfo0.0020.0020.004
parseUrlsFromFirebrowseResponse0.0420.0130.104
parseVastToolsEvent0.0120.0000.012
parseVastToolsSE0.0150.0080.022
performICA0.0080.0040.012
performPCA0.0030.0000.002
plot.GEandAScorrelation0.4500.0550.505
plotDistribution0.6320.0920.724
plotGeneExprPerSample0.1120.0110.123
plotGroupIndependence0.1330.0240.157
plotICA0.1050.0300.138
plotLibrarySize0.2140.0560.269
plotPCA0.2050.0400.245
plotPCAvariance0.0420.0040.046
plotProtein0.6030.1201.635
plotRowStats0.3990.1480.547
plotSingleICA0.2030.0950.298
plotSplicingEvent0.0470.0280.075
plotSurvivalCurves0.220.080.30
plotSurvivalPvaluesByCutoff0.4420.0280.469
plotTranscripts0.0340.0071.527
prepareAnnotationFromEvents0.2630.0320.296
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.0090.0040.013
psichomics000
quantifySplicing0.0120.0040.016
queryEnsembl0.0480.0070.622
queryEnsemblByGene0.1480.0445.471
queryFirebrowseData0.0550.0160.158
queryPubMed0.0670.0200.613
queryUniprot0.0550.0120.549
readFile0.0020.0010.001
renameDuplicated0.0010.0000.002
renderBoxplot0.1220.0190.141
survdiffTerms0.0080.0000.008
survfit.survTerms0.0340.0090.043
testGroupIndependence0.0040.0000.003
testSurvival0.0270.0000.026
textSuggestions0.0010.0000.001
trimWhitespace000