Multiple platform build/check report for BioC 3.23 - CHECK results for psichomics on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4877
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"	4570
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 kjohnson3

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: 1.37.1

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.37.1.tar.gz

StartedAt: 2026-02-27 21:51:00 -0500 (Fri, 27 Feb 2026)

EndedAt: 2026-02-27 21:55:21 -0500 (Fri, 27 Feb 2026)

EllapsedTime: 260.4 seconds

RetCode: 0

Status: OK

CheckDir: psichomics.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.37.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.23-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 16.0.0 (clang-1600.0.26.6)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Sonoma 14.8.3
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.37.1’
* 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: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.1.sdk’
* 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 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          7.405  0.448   9.017
listSplicingAnnotations         6.350  0.564   7.567
parseFirebrowseMetadata         0.025  0.004  10.361
getTCGAdataTypes                0.017  0.003   8.515
parseUrlsFromFirebrowseResponse 0.017  0.001   6.251
queryFirebrowseData             0.013  0.002  10.424
* 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 running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.23-bioc/meat/psichomics.Rcheck/00check.log’
for details.

Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library’
* installing *source* package ‘psichomics’ ...
** this is package ‘psichomics’ version ‘1.37.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.1.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c progressBar.cpp -o progressBar.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c vastToolsParser.cpp -o vastToolsParser.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/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) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 
  0.093   0.030   0.118

psichomics.Rcheck/tests/testthat.Rout


R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20

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 1.37.1: 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 (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 
 10.030   0.590  12.866

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0	0	0
assignValuePerSubject	0.006	0.003	0.010
blendColours	0.000	0.000	0.001
calculateLoadingsContribution	0.003	0.001	0.004
convertGeneIdentifiers	7.405	0.448	9.017
correlateGEandAS	0.007	0.002	0.009
createGroupByAttribute	0.001	0.000	0.002
createJunctionsTemplate	0.001	0.001	0.002
customRowMeans	0.000	0.001	0.001
diffAnalyses	0.029	0.006	0.034
downloadFiles	0	0	0
ensemblToUniprot	0.014	0.002	0.660
filterGeneExpr	0.005	0.001	0.006
filterGroups	0.001	0.000	0.002
filterPSI	0.012	0.004	0.015
getAttributesTime	0.002	0.000	0.003
getDownloadsFolder	0.001	0.000	0.000
getFirebrowseDateFormat	0	0	0
getGeneList	0.002	0.001	0.003
getGtexDataTypes	0.001	0.000	0.001
getGtexTissues	0.000	0.000	0.001
getNumerics	0.002	0.001	0.002
getSampleFromSubject	0.001	0.001	0.001
getSplicingEventFromGenes	0.002	0.001	0.003
getSplicingEventTypes	0	0	0
getSubjectFromSample	0.001	0.001	0.001
getTCGAdataTypes	0.017	0.003	8.515
getValidEvents	0.001	0.001	0.001
groupPerElem	0.001	0.000	0.000
hchart.survfit	0.097	0.053	0.165
isFirebrowseUp	0.002	0.001	2.065
labelBasedOnCutoff	0.001	0.000	0.000
leveneTest	0.002	0.000	0.003
listAllAnnotations	1.233	0.126	1.675
listSplicingAnnotations	6.350	0.564	7.567
loadAnnotation	1.537	0.115	1.803
loadGtexData	0	0	0
loadLocalFiles	0.001	0.000	0.000
loadSRAproject	0	0	0
loadTCGAdata	0.003	0.001	2.082
missingDataModal	0	0	0
normaliseGeneExpression	0.012	0.000	0.013
optimalSurvivalCutoff	0.040	0.000	0.041
parseCategoricalGroups	0.000	0.001	0.000
parseFirebrowseMetadata	0.025	0.004	10.361
parseMatsEvent	0.003	0.001	0.004
parseMatsGeneric	0.013	0.003	0.017
parseMisoAnnotation	0.068	0.012	0.085
parseMisoEvent	0.001	0.000	0.002
parseMisoEventID	0.004	0.002	0.006
parseMisoGeneric	0.013	0.003	0.016
parseMisoId	0	0	0
parseSplicingEvent	0.001	0.001	0.004
parseSuppaEvent	0.001	0.000	0.002
parseSuppaGeneric	0.005	0.001	0.006
parseTCGAsampleInfo	0.003	0.001	0.004
parseUrlsFromFirebrowseResponse	0.017	0.001	6.251
parseVastToolsEvent	0.004	0.001	0.005
parseVastToolsSE	0.005	0.001	0.006
performICA	0.001	0.003	0.004
performPCA	0.001	0.001	0.002
plot.GEandAScorrelation	0.315	0.012	0.331
plotDistribution	0.242	0.038	0.319
plotGeneExprPerSample	0.025	0.013	0.041
plotGroupIndependence	0.131	0.002	0.146
plotICA	0.036	0.005	0.048
plotLibrarySize	0.064	0.013	0.082
plotPCA	0.077	0.048	0.141
plotPCAvariance	0.014	0.011	0.029
plotProtein	0.205	0.031	1.323
plotRowStats	0.188	0.004	0.202
plotSingleICA	0.058	0.039	0.105
plotSplicingEvent	0.015	0.000	0.017
plotSurvivalCurves	0.029	0.013	0.043
plotSurvivalPvaluesByCutoff	0.154	0.014	0.179
plotTranscripts	0.006	0.001	1.186
prepareAnnotationFromEvents	0.048	0.003	0.052
prepareFirebrowseArchives	0	0	0
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0	0	0
processSurvTerms	0.003	0.000	0.003
psichomics	0	0	0
quantifySplicing	0.003	0.002	0.005
queryEnsembl	0.010	0.002	1.064
queryEnsemblByGene	0.036	0.009	3.567
queryFirebrowseData	0.013	0.002	10.424
queryPubMed	0.011	0.003	0.461
queryUniprot	0.026	0.002	0.619
readFile	0.001	0.000	0.001
renameDuplicated	0	0	0
renderBoxplot	0.023	0.013	0.034
survdiffTerms	0.002	0.000	0.002
survfit.survTerms	0.01	0.00	0.01
testGroupIndependence	0.001	0.000	0.001
testSurvival	0.008	0.001	0.009
textSuggestions	0.000	0.000	0.001
trimWhitespace	0	0	0