Build/check report for BioC 3.23 - CHECK results for psichomics on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"	4428
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:
- 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: 1.37.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings psichomics_1.37.0.tar.gz

StartedAt: 2025-10-30 23:31:59 -0400 (Thu, 30 Oct 2025)

EndedAt: 2025-10-30 23:40:54 -0400 (Thu, 30 Oct 2025)

EllapsedTime: 534.8 seconds

RetCode: 0

Status: OK

CheckDir: psichomics.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings psichomics_1.37.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.37.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 33 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  colSums-EList-method.Rd: EList-class
  renderDataTableSparklines.Rd: renderDataTable
  showAlert.Rd: showModal
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 ... INFO
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  14.590  2.579  18.275
listSplicingAnnotations 11.188  2.070  13.856
* 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-3.23-bioc/meat/psichomics.Rcheck/00check.log’
for details.

Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** this is package ‘psichomics’ version ‘1.37.0’
** 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-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c progressBar.cpp -o progressBar.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c psiFastCalc.cpp -o psiFastCalc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -Werror=format-security  -c vastToolsParser.cpp -o vastToolsParser.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-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 Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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)
All Done!
> 
> proc.time()
   user  system elapsed 
  0.149   0.035   0.172

psichomics.Rcheck/tests/testthat.Rout


R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
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 1.37.0: 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 
 24.217   1.653  27.758

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0.001	0.000	0.000
assignValuePerSubject	0.015	0.004	0.020
blendColours	0.000	0.000	0.001
calculateLoadingsContribution	0.007	0.002	0.011
convertGeneIdentifiers	14.590	2.579	18.275
correlateGEandAS	0.013	0.007	0.020
createGroupByAttribute	0.001	0.000	0.001
createJunctionsTemplate	0.001	0.001	0.002
customRowMeans	0.001	0.000	0.001
diffAnalyses	0.066	0.010	0.075
downloadFiles	0.000	0.001	0.000
ensemblToUniprot	0.028	0.003	0.422
filterGeneExpr	0.004	0.003	0.007
filterGroups	0.002	0.000	0.002
filterPSI	0.013	0.003	0.016
getAttributesTime	0.003	0.000	0.002
getDownloadsFolder	0.000	0.001	0.000
getFirebrowseDateFormat	0	0	0
getGeneList	0.004	0.000	0.005
getGtexDataTypes	0.046	0.033	0.080
getGtexTissues	0.000	0.000	0.001
getNumerics	0.008	0.000	0.008
getSampleFromSubject	0.001	0.000	0.001
getSplicingEventFromGenes	0.004	0.000	0.004
getSplicingEventTypes	0	0	0
getSubjectFromSample	0	0	0
getTCGAdataTypes	0.030	0.007	0.204
getValidEvents	0.003	0.001	0.003
groupPerElem	0.000	0.001	0.001
hchart.survfit	0.226	0.026	0.260
isFirebrowseUp	0.005	0.000	0.024
labelBasedOnCutoff	0.000	0.001	0.001
leveneTest	0.007	0.000	0.006
listAllAnnotations	2.410	0.599	3.159
listSplicingAnnotations	11.188	2.070	13.856
loadAnnotation	2.817	0.457	3.423
loadGtexData	0	0	0
loadLocalFiles	0.001	0.000	0.000
loadSRAproject	0	0	0
loadTCGAdata	0.012	0.001	0.050
missingDataModal	0	0	0
normaliseGeneExpression	0.027	0.004	0.030
optimalSurvivalCutoff	0.094	0.008	0.102
parseCategoricalGroups	0.001	0.000	0.001
parseFirebrowseMetadata	0.045	0.003	0.154
parseMatsEvent	0.001	0.003	0.005
parseMatsGeneric	0.015	0.003	0.018
parseMisoAnnotation	0.106	0.017	0.127
parseMisoEvent	0.003	0.001	0.004
parseMisoEventID	0.004	0.002	0.006
parseMisoGeneric	0.023	0.007	0.031
parseMisoId	0.000	0.000	0.001
parseSplicingEvent	0.002	0.004	0.006
parseSuppaEvent	0.004	0.000	0.004
parseSuppaGeneric	0.017	0.005	0.022
parseTcgaSampleInfo	0.004	0.001	0.004
parseUrlsFromFirebrowseResponse	0.061	0.009	0.164
parseVastToolsEvent	0.006	0.000	0.006
parseVastToolsSE	0.018	0.001	0.020
performICA	0.006	0.003	0.009
performPCA	0.001	0.000	0.002
plot.GEandAScorrelation	0.573	0.034	0.607
plotDistribution	0.560	0.075	0.636
plotGeneExprPerSample	0.077	0.018	0.095
plotGroupIndependence	0.417	0.063	0.481
plotICA	0.106	0.014	0.121
plotLibrarySize	0.161	0.026	0.186
plotPCA	0.219	0.022	0.240
plotPCAvariance	0.042	0.007	0.048
plotProtein	0.628	0.115	1.727
plotRowStats	0.574	0.021	0.595
plotSingleICA	0.195	0.028	0.223
plotSplicingEvent	0.041	0.004	0.046
plotSurvivalCurves	0.077	0.016	0.094
plotSurvivalPvaluesByCutoff	0.446	0.029	0.475
plotTranscripts	0.019	0.003	0.688
prepareAnnotationFromEvents	0.210	0.033	0.243
prepareFirebrowseArchives	0.000	0.000	0.001
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0	0	0
processSurvTerms	0.013	0.000	0.013
psichomics	0	0	0
quantifySplicing	0.011	0.005	0.017
queryEnsembl	0.029	0.012	0.462
queryEnsemblByGene	0.140	0.053	2.614
queryFirebrowseData	0.054	0.014	0.236
queryPubMed	0.117	0.029	0.732
queryUniprot	0.087	0.005	0.530
readFile	0.003	0.000	0.003
renameDuplicated	0.000	0.001	0.001
renderBoxplot	0.083	0.012	0.095
survdiffTerms	0.005	0.002	0.007
survfit.survTerms	0.019	0.003	0.022
testGroupIndependence	0.002	0.002	0.003
testSurvival	0.020	0.001	0.021
textSuggestions	0.000	0.001	0.001
trimWhitespace	0.000	0.000	0.001