Multiple platform build/check report for BioC 3.20 - CHECK results for psichomics on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4764
palomino8	Windows Server 2022 Datacenter	x64	4.4.3 (2025-02-28 ucrt) -- "Trophy Case"	4495
merida1	macOS 12.7.5 Monterey	x86_64	4.4.3 (2025-02-28) -- "Trophy Case"	4522
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.3 (2025-02-28) -- "Trophy Case"	4449
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.3 (2025-02-28) -- "Trophy Case"	4420
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:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: psichomics

Version: 1.32.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings psichomics_1.32.0.tar.gz

StartedAt: 2025-03-25 01:19:08 -0400 (Tue, 25 Mar 2025)

EndedAt: 2025-03-25 01:27:41 -0400 (Tue, 25 Mar 2025)

EllapsedTime: 512.5 seconds

RetCode: 0

Status: OK

CheckDir: psichomics.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings psichomics_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.32.0’
* 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 ... 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
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* 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 code 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 whether startup messages can be suppressed ... 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 ... NOTE
Documented arguments not in \usage in Rd file 'createSparklines.Rd':
  ‘id’

Documented arguments not in \usage in Rd file 'renderGeneticInfo.Rd':
  ‘ns’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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  14.426  0.757  16.036
listSplicingAnnotations 11.295  0.375  12.268
* 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 ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck/00check.log’
for details.

Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c progressBar.cpp -o progressBar.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c psiFastCalc.cpp -o psiFastCalc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c vastToolsParser.cpp -o vastToolsParser.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-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 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.176   0.038   0.195

psichomics.Rcheck/tests/testthat.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 1.32.0: 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 4 | PASS 1418 ]

══ Skipped tests (4) ═══════════════════════════════════════════════════════════
• Couldn't resolve host name (1): 'testGeneInfo.R:99:5'
• On Bioconductor (2): 'testDiscardLowCoveragePSIs.R:62:5',
  'testGeneInfo.R:50:5'
• On CRAN (1): 'testSRAloading.R:4:5'

[ FAIL 0 | WARN 0 | SKIP 4 | PASS 1418 ]
> 
> proc.time()
   user  system elapsed 
 22.382   1.307  26.422

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0.001	0.000	0.000
assignValuePerSubject	0.011	0.006	0.018
blendColours	0.001	0.000	0.000
calculateLoadingsContribution	0.007	0.001	0.008
convertGeneIdentifiers	14.426	0.757	16.036
correlateGEandAS	0.015	0.001	0.015
createGroupByAttribute	0.001	0.000	0.000
createJunctionsTemplate	0.002	0.000	0.001
customRowMeans	0.001	0.000	0.000
diffAnalyses	0.061	0.003	0.064
downloadFiles	0	0	0
ensemblToUniprot	0.024	0.000	0.833
filterGeneExpr	0.006	0.000	0.006
filterGroups	0.001	0.000	0.001
filterPSI	0.012	0.000	0.012
getAttributesTime	0.002	0.000	0.002
getDownloadsFolder	0.000	0.001	0.000
getFirebrowseDateFormat	0	0	0
getGeneList	0.003	0.000	0.004
getGtexDataTypes	0.001	0.000	0.001
getGtexTissues	0	0	0
getNumerics	0.001	0.000	0.002
getSampleFromSubject	0.000	0.000	0.001
getSplicingEventFromGenes	0.003	0.000	0.003
getSplicingEventTypes	0	0	0
getSubjectFromSample	0	0	0
getTCGAdataTypes	0.033	0.003	0.109
getValidEvents	0.003	0.000	0.003
groupPerElem	0.000	0.000	0.001
hchart.survfit	0.212	0.025	0.238
isFirebrowseUp	0.005	0.000	0.017
labelBasedOnCutoff	0.001	0.000	0.000
leveneTest	0.005	0.000	0.006
listAllAnnotations	2.360	0.113	2.623
listSplicingAnnotations	11.295	0.375	12.268
loadAnnotation	2.903	0.091	3.145
loadGtexData	0	0	0
loadLocalFiles	0	0	0
loadSRAproject	0	0	0
loadTCGAdata	0.010	0.001	0.033
missingDataModal	0	0	0
normaliseGeneExpression	0.025	0.000	0.025
optimalSurvivalCutoff	0.1	0.0	0.1
parseCategoricalGroups	0.001	0.000	0.001
parseFirebrowseMetadata	0.046	0.001	0.123
parseMatsEvent	0.003	0.001	0.004
parseMatsGeneric	0.016	0.000	0.016
parseMisoAnnotation	0.153	0.006	0.162
parseMisoEvent	0.003	0.000	0.003
parseMisoEventID	0.005	0.000	0.004
parseMisoGeneric	0.022	0.003	0.024
parseMisoId	0.000	0.000	0.001
parseSplicingEvent	0.004	0.000	0.004
parseSuppaEvent	0.003	0.000	0.003
parseSuppaGeneric	0.014	0.001	0.014
parseTcgaSampleInfo	0.003	0.000	0.003
parseUrlsFromFirebrowseResponse	0.029	0.001	0.104
parseVastToolsEvent	0.005	0.000	0.004
parseVastToolsSE	0.015	0.000	0.014
performICA	0.006	0.000	0.005
performPCA	0.001	0.000	0.001
plot.GEandAScorrelation	0.485	0.004	0.490
plotDistribution	0.592	0.009	0.601
plotGeneExprPerSample	0.077	0.006	0.084
plotGroupIndependence	0.143	0.000	0.143
plotICA	0.109	0.002	0.112
plotLibrarySize	0.199	0.003	0.202
plotPCA	0.204	0.021	0.225
plotPCAvariance	0.042	0.004	0.047
plotProtein	0.546	0.014	1.426
plotRowStats	0.384	0.002	0.386
plotSingleICA	0.196	0.013	0.209
plotSplicingEvent	0.041	0.001	0.042
plotSurvivalCurves	0.073	0.008	0.082
plotSurvivalPvaluesByCutoff	0.405	0.006	0.410
plotTranscripts	0.017	0.000	1.551
prepareAnnotationFromEvents	0.14	0.00	0.14
prepareFirebrowseArchives	0	0	0
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0	0	0
processSurvTerms	0.008	0.000	0.007
psichomics	0	0	0
quantifySplicing	0.007	0.003	0.009
queryEnsembl	0.029	0.002	0.918
queryEnsemblByGene	0.148	0.001	4.932
queryFirebrowseData	0.068	0.000	0.205
queryPubMed	0.102	0.004	0.550
queryUniprot	0.092	0.001	0.427
readFile	0.001	0.001	0.002
renameDuplicated	0.001	0.000	0.001
renderBoxplot	0.102	0.007	0.110
survdiffTerms	0.004	0.001	0.006
survfit.survTerms	0.020	0.000	0.021
testGroupIndependence	0.003	0.000	0.002
testSurvival	0.020	0.000	0.019
textSuggestions	0.000	0.000	0.001
trimWhitespace	0	0	0