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This page was generated on 2022-01-14 11:06:31 -0500 (Fri, 14 Jan 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4159
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4055
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2021-12-21 r81400 ucrt) -- "Unsuffered Consequences" 3997
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences" 4114
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? 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 1474/2074HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.21.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2022-01-13 13:55:14 -0500 (Thu, 13 Jan 2022)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: master
git_last_commit: 9ecda58
git_last_commit_date: 2021-10-26 12:30:49 -0500 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  NO, package depends on 'AnnotationDbi' which is not available
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: psichomics
Version: 1.21.0
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_1.21.0.tar.gz
StartedAt: 2022-01-13 20:40:58 -0500 (Thu, 13 Jan 2022)
EndedAt: 2022-01-13 20:47:42 -0500 (Thu, 13 Jan 2022)
EllapsedTime: 404.1 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_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* 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 ‘1.21.0’
* 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  14.544  0.797  16.713
listSplicingAnnotations  9.855  0.505  11.489
* 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-3.15-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 Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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 
  0.151   0.048   0.187 

psichomics.Rcheck/tests/testthat.Rout


R Under development (unstable) (2022-01-05 r81451) -- "Unsuffered Consequences"
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 1.21.0: 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
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (2)
• On CRAN (1)

[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1396 ]
> 
> proc.time()
   user  system elapsed 
 20.219   1.482  29.508 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0020.0010.002
assignValuePerSubject0.0170.0040.021
blendColours0.0010.0000.001
calculateLoadingsContribution0.0060.0040.010
convertGeneIdentifiers14.544 0.79716.713
correlateGEandAS0.0140.0040.018
createGroupByAttribute0.0010.0000.001
createJunctionsTemplate0.0020.0000.002
customRowMeans0.0010.0000.001
diffAnalyses0.0550.0150.070
downloadFiles0.0010.0000.001
ensemblToUniprot0.0290.0041.470
filterGeneExpr0.0090.0000.009
filterGroups0.0020.0000.002
filterPSI0.0120.0080.020
getAttributesTime0.0030.0000.004
getDownloadsFolder0.0010.0000.000
getFirebrowseDateFormat0.0000.0000.001
getGeneList0.0040.0000.005
getGtexDataTypes0.0610.0000.304
getGtexTissues000
getNumerics0.0050.0000.004
getSampleFromSubject0.0020.0000.002
getSplicingEventFromGenes0.0060.0000.006
getSplicingEventTypes0.0000.0010.000
getSubjectFromSample0.0000.0010.001
getTCGAdataTypes0.0450.0050.150
getValidEvents0.0060.0000.006
groupPerElem0.0020.0000.002
hchart.survfit0.2170.0390.281
isFirebrowseUp0.0050.0000.014
labelBasedOnCutoff0.0010.0000.001
leveneTest0.0080.0000.007
listAllAnnotations2.0820.1522.673
listSplicingAnnotations 9.855 0.50511.489
loadAnnotation2.5020.1282.914
loadGtexData0.0010.0000.000
loadLocalFiles000
loadSRAproject0.0010.0000.000
loadTCGAdata0.0140.0000.031
missingDataModal0.0010.0000.000
normaliseGeneExpression0.0240.0000.024
optimalSurvivalCutoff0.0810.0070.087
parseCategoricalGroups0.0010.0010.001
parseFirebrowseMetadata0.0390.0120.105
parseMatsEvent0.0060.0000.006
parseMatsGeneric0.0180.0000.019
parseMisoAnnotation0.1050.0160.127
parseMisoEvent0.0040.0000.004
parseMisoEventID0.0020.0040.006
parseMisoGeneric0.0230.0040.027
parseMisoId0.0010.0000.000
parseSplicingEvent0.0060.0000.005
parseSuppaEvent0.0040.0000.003
parseSuppaGeneric0.0080.0090.017
parseTcgaSampleInfo0.0020.0020.004
parseUrlsFromFirebrowseResponse0.0380.0000.096
parseVastToolsEvent0.0050.0000.006
parseVastToolsSE0.0160.0000.016
performICA0.0050.0040.009
performPCA0.0010.0000.002
plot.GEandAScorrelation0.3840.0040.388
plotDistribution0.5960.0480.643
plotGeneExprPerSample0.0820.0160.098
plotGroupIndependence0.1070.0200.127
plotICA0.0880.0320.121
plotLibrarySize0.1980.0360.234
plotPCA0.2190.0200.239
plotPCAvariance0.0450.0040.049
plotProtein0.5930.0354.072
plotRowStats0.3270.0040.331
plotSingleICA0.2240.0400.266
plotSplicingEvent0.0430.0040.047
plotSurvivalCurves0.0800.0000.081
plotSurvivalPvaluesByCutoff0.3840.0120.396
plotTranscripts0.0260.0001.319
prepareAnnotationFromEvents0.1570.0040.160
prepareFirebrowseArchives0.0010.0000.000
prepareJunctionQuantSTAR0.0000.0010.000
prepareSRAmetadata0.0000.0010.000
processSurvTerms0.0070.0020.009
psichomics0.0000.0000.001
quantifySplicing0.0050.0080.013
queryEnsembl0.0470.0000.851
queryEnsemblByGene0.1650.0244.327
queryFirebrowseData0.0640.0040.166
queryPubMed0.0660.0081.376
queryUniprot0.0600.0201.783
readFile0.0010.0000.002
renameDuplicated0.0020.0000.001
renderBoxplot0.1120.0160.128
survdiffTerms0.0090.0000.009
survfit.survTerms0.0350.0000.035
testGroupIndependence0.0040.0000.004
testSurvival0.0300.0040.034
textSuggestions0.0000.0010.001
trimWhitespace000