Multiple platform build/check report for BioC 3.21 - CHECK results for psichomics on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4824
merida1	macOS 12.7.5 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4604
kjohnson1	macOS 13.6.6 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4545
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4579
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: 1.34.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings psichomics_1.34.0.tar.gz

StartedAt: 2025-08-21 01:39:56 -0400 (Thu, 21 Aug 2025)

EndedAt: 2025-08-21 01:48:39 -0400 (Thu, 21 Aug 2025)

EllapsedTime: 522.7 seconds

RetCode: 0

Status: OK

CheckDir: psichomics.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings psichomics_1.34.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/psichomics.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘1.34.0’
* 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  14.669  1.960  17.351
listSplicingAnnotations 11.757  2.291  14.747
* 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-3.21-bioc/meat/psichomics.Rcheck/00check.log’
for details.

Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** this is package ‘psichomics’ version ‘1.34.0’
** 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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-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 (2025-06-13) -- "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 
  0.154   0.037   0.178

psichomics.Rcheck/tests/testthat.Rout


R version 4.5.1 (2025-06-13) -- "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 1.34.0: 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 
 23.786   1.462  26.971

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0.001	0.000	0.001
assignValuePerSubject	0.017	0.003	0.020
blendColours	0.001	0.000	0.001
calculateLoadingsContribution	0.006	0.003	0.009
convertGeneIdentifiers	14.669	1.960	17.351
correlateGEandAS	0.016	0.006	0.022
createGroupByAttribute	0.001	0.000	0.001
createJunctionsTemplate	0.002	0.000	0.002
customRowMeans	0.000	0.001	0.001
diffAnalyses	0.073	0.008	0.081
downloadFiles	0	0	0
ensemblToUniprot	0.030	0.008	0.923
filterGeneExpr	0.008	0.001	0.010
filterGroups	0.001	0.000	0.002
filterPSI	0.014	0.002	0.016
getAttributesTime	0.001	0.001	0.003
getDownloadsFolder	0.000	0.000	0.001
getFirebrowseDateFormat	0.000	0.000	0.001
getGeneList	0.003	0.001	0.005
getGtexDataTypes	0.000	0.001	0.001
getGtexTissues	0	0	0
getNumerics	0.001	0.001	0.003
getSampleFromSubject	0.001	0.000	0.002
getSplicingEventFromGenes	0.004	0.000	0.005
getSplicingEventTypes	0.000	0.000	0.001
getSubjectFromSample	0.000	0.000	0.001
getTCGAdataTypes	0.047	0.028	0.383
getValidEvents	0.007	0.003	0.010
groupPerElem	0.000	0.001	0.001
hchart.survfit	0.260	0.115	0.394
isFirebrowseUp	0.006	0.000	0.022
labelBasedOnCutoff	0.001	0.000	0.001
leveneTest	0.009	0.002	0.010
listAllAnnotations	2.459	0.642	3.263
listSplicingAnnotations	11.757	2.291	14.747
loadAnnotation	2.956	0.528	3.646
loadGtexData	0.000	0.001	0.000
loadLocalFiles	0	0	0
loadSRAproject	0	0	0
loadTCGAdata	0.013	0.003	0.050
missingDataModal	0	0	0
normaliseGeneExpression	0.033	0.006	0.039
optimalSurvivalCutoff	0.113	0.011	0.123
parseCategoricalGroups	0.001	0.000	0.001
parseFirebrowseMetadata	0.054	0.012	0.166
parseMatsEvent	0.005	0.000	0.006
parseMatsGeneric	0.019	0.002	0.021
parseMisoAnnotation	0.123	0.014	0.142
parseMisoEvent	0.003	0.001	0.004
parseMisoEventID	0.005	0.002	0.006
parseMisoGeneric	0.028	0.003	0.031
parseMisoId	0	0	0
parseSplicingEvent	0.005	0.001	0.005
parseSuppaEvent	0.004	0.000	0.004
parseSuppaGeneric	0.017	0.004	0.020
parseTcgaSampleInfo	0.004	0.001	0.005
parseUrlsFromFirebrowseResponse	0.034	0.007	0.145
parseVastToolsEvent	0.004	0.004	0.008
parseVastToolsSE	0.020	0.013	0.032
performICA	0.005	0.009	0.015
performPCA	0.000	0.002	0.003
plot.GEandAScorrelation	0.581	0.172	0.753
plotDistribution	0.682	0.123	0.805
plotGeneExprPerSample	0.082	0.010	0.093
plotGroupIndependence	0.222	0.030	0.251
plotICA	0.115	0.016	0.133
plotLibrarySize	0.173	0.038	0.211
plotPCA	0.231	0.037	0.268
plotPCAvariance	0.047	0.011	0.058
plotProtein	0.671	0.142	1.880
plotRowStats	0.531	0.092	0.623
plotSingleICA	0.175	0.018	0.193
plotSplicingEvent	0.042	0.000	0.041
plotSurvivalCurves	0.087	0.023	0.109
plotSurvivalPvaluesByCutoff	0.533	0.075	0.608
plotTranscripts	0.024	0.007	0.965
prepareAnnotationFromEvents	0.165	0.025	0.190
prepareFirebrowseArchives	0.000	0.001	0.000
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0	0	0
processSurvTerms	0.006	0.003	0.009
psichomics	0	0	0
quantifySplicing	0.011	0.003	0.014
queryEnsembl	0.041	0.006	0.737
queryEnsemblByGene	0.141	0.034	3.348
queryFirebrowseData	0.060	0.004	0.230
queryPubMed	0.119	0.045	0.473
queryUniprot	0.087	0.013	0.611
readFile	0.002	0.001	0.003
renameDuplicated	0.000	0.003	0.002
renderBoxplot	0.084	0.019	0.102
survdiffTerms	0.006	0.002	0.008
survfit.survTerms	0.029	0.007	0.036
testGroupIndependence	0.004	0.000	0.004
testSurvival	0.031	0.009	0.040
textSuggestions	0.001	0.000	0.001
trimWhitespace	0	0	0