Multiple platform build/check report for BioC 3.22 - CHECK results for psichomics on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"	4901
lconway	macOS 12.7.6 Monterey	x86_64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4691
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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: 1.36.0

Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings psichomics_1.36.0.tar.gz

StartedAt: 2025-11-01 03:04:31 -0400 (Sat, 01 Nov 2025)

EndedAt: 2025-11-01 03:13:20 -0400 (Sat, 01 Nov 2025)

EllapsedTime: 528.5 seconds

RetCode: 0

Status: OK

CheckDir: psichomics.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings psichomics_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/psichomics.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘1.36.0’
* 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 ... 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  15.417  1.598  17.957
listSplicingAnnotations 12.071  1.447  14.236
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/psichomics.Rcheck/00check.log’
for details.

Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** this is package ‘psichomics’ version ‘1.36.0’
** 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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-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-3.22-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-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 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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 
  0.144   0.038   0.172

psichomics.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
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 1.36.0: 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 
 25.152   1.878  28.825

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0.001	0.001	0.000
assignValuePerSubject	0.011	0.005	0.017
blendColours	0.001	0.000	0.001
calculateLoadingsContribution	0.008	0.001	0.008
convertGeneIdentifiers	15.417	1.598	17.957
correlateGEandAS	0.016	0.008	0.024
createGroupByAttribute	0.002	0.000	0.002
createJunctionsTemplate	0.003	0.000	0.003
customRowMeans	0.001	0.000	0.001
diffAnalyses	0.067	0.007	0.074
downloadFiles	0	0	0
ensemblToUniprot	0.038	0.006	0.515
filterGeneExpr	0.008	0.002	0.010
filterGroups	0.001	0.001	0.002
filterPSI	0.017	0.003	0.022
getAttributesTime	0.002	0.001	0.003
getDownloadsFolder	0.001	0.000	0.000
getFirebrowseDateFormat	0.001	0.000	0.000
getGeneList	0.006	0.000	0.006
getGtexDataTypes	0	0	0
getGtexTissues	0	0	0
getNumerics	0.002	0.000	0.003
getSampleFromSubject	0.001	0.000	0.001
getSplicingEventFromGenes	0.005	0.000	0.005
getSplicingEventTypes	0	0	0
getSubjectFromSample	0	0	0
getTCGAdataTypes	0.068	0.010	0.272
getValidEvents	0.003	0.001	0.003
groupPerElem	0.001	0.000	0.000
hchart.survfit	0.246	0.081	0.346
isFirebrowseUp	0.004	0.004	0.024
labelBasedOnCutoff	0.001	0.000	0.001
leveneTest	0.009	0.001	0.010
listAllAnnotations	2.524	0.483	3.198
listSplicingAnnotations	12.071	1.447	14.236
loadAnnotation	3.210	0.529	3.955
loadGtexData	0	0	0
loadLocalFiles	0	0	0
loadSRAproject	0	0	0
loadTCGAdata	0.011	0.008	0.049
missingDataModal	0	0	0
normaliseGeneExpression	0.029	0.018	0.048
optimalSurvivalCutoff	0.117	0.021	0.138
parseCategoricalGroups	0.001	0.000	0.001
parseFirebrowseMetadata	0.044	0.010	0.153
parseMatsEvent	0.005	0.000	0.005
parseMatsGeneric	0.015	0.007	0.021
parseMisoAnnotation	0.118	0.032	0.152
parseMisoEvent	0.004	0.000	0.004
parseMisoEventID	0.005	0.001	0.006
parseMisoGeneric	0.025	0.005	0.031
parseMisoId	0	0	0
parseSplicingEvent	0.004	0.001	0.004
parseSuppaEvent	0.004	0.000	0.003
parseSuppaGeneric	0.015	0.003	0.018
parseTcgaSampleInfo	0.003	0.001	0.004
parseUrlsFromFirebrowseResponse	0.030	0.005	0.127
parseVastToolsEvent	0.004	0.002	0.006
parseVastToolsSE	0.018	0.000	0.018
performICA	0.005	0.002	0.006
performPCA	0.002	0.000	0.002
plot.GEandAScorrelation	0.633	0.078	0.712
plotDistribution	0.628	0.182	0.811
plotGeneExprPerSample	0.077	0.009	0.085
plotGroupIndependence	0.397	0.031	0.427
plotICA	0.115	0.005	0.121
plotLibrarySize	0.166	0.005	0.170
plotPCA	0.221	0.032	0.254
plotPCAvariance	0.045	0.005	0.051
plotProtein	0.610	0.150	1.602
plotRowStats	0.596	0.076	0.672
plotSingleICA	0.185	0.034	0.220
plotSplicingEvent	0.040	0.006	0.047
plotSurvivalCurves	0.072	0.019	0.092
plotSurvivalPvaluesByCutoff	0.481	0.044	0.525
plotTranscripts	0.023	0.006	0.695
prepareAnnotationFromEvents	0.143	0.003	0.146
prepareFirebrowseArchives	0.001	0.000	0.000
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0	0	0
processSurvTerms	0.008	0.001	0.008
psichomics	0	0	0
quantifySplicing	0.009	0.001	0.010
queryEnsembl	0.031	0.000	0.448
queryEnsemblByGene	0.175	0.030	2.732
queryFirebrowseData	0.061	0.008	0.226
queryPubMed	0.153	0.014	0.654
queryUniprot	0.049	0.008	0.399
readFile	0.002	0.000	0.002
renameDuplicated	0.001	0.000	0.001
renderBoxplot	0.085	0.033	0.119
survdiffTerms	0.006	0.003	0.009
survfit.survTerms	0.028	0.014	0.042
testGroupIndependence	0.004	0.000	0.004
testSurvival	0.027	0.002	0.028
textSuggestions	0.000	0.001	0.001
trimWhitespace	0.000	0.000	0.001