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This page was generated on 2025-09-06 12:04 -0400 (Sat, 06 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4823
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4618
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4565
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4544
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

Package 1632/2322HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.35.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2025-09-05 13:45 -0400 (Fri, 05 Sep 2025)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: devel
git_last_commit: bfacab9
git_last_commit_date: 2025-04-15 11:06:18 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


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: 1.35.0
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_1.35.0.tar.gz
StartedAt: 2025-09-06 02:57:05 -0400 (Sat, 06 Sep 2025)
EndedAt: 2025-09-06 03:05:36 -0400 (Sat, 06 Sep 2025)
EllapsedTime: 510.5 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_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-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 ‘1.35.0’
* 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  14.024  0.523  15.410
listSplicingAnnotations 11.016  0.430  12.047
* 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 ‘1.35.0’
** 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 (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 
  0.144   0.038   0.170 

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 1.35.0: 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 
 23.443   1.136  26.572 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0000.0010.000
assignValuePerSubject0.0130.0050.018
blendColours0.0000.0000.001
calculateLoadingsContribution0.0080.0000.010
convertGeneIdentifiers14.024 0.52315.410
correlateGEandAS0.0150.0000.015
createGroupByAttribute0.0000.0010.001
createJunctionsTemplate0.0010.0000.001
customRowMeans000
diffAnalyses0.0610.0020.064
downloadFiles000
ensemblToUniprot0.0260.0010.344
filterGeneExpr0.0050.0000.006
filterGroups0.0010.0000.002
filterPSI0.0110.0000.012
getAttributesTime0.0020.0000.002
getDownloadsFolder000
getFirebrowseDateFormat000
getGeneList0.0020.0010.003
getGtexDataTypes0.0000.0000.001
getGtexTissues0.0000.0010.000
getNumerics0.0000.0010.002
getSampleFromSubject0.0000.0000.001
getSplicingEventFromGenes0.0030.0000.003
getSplicingEventTypes000
getSubjectFromSample000
getTCGAdataTypes0.0290.0010.127
getValidEvents0.0030.0000.002
groupPerElem0.0010.0000.000
hchart.survfit0.2060.0170.243
isFirebrowseUp0.0050.0000.021
labelBasedOnCutoff0.0000.0000.001
leveneTest0.0060.0000.007
listAllAnnotations2.4170.1642.739
listSplicingAnnotations11.016 0.43012.047
loadAnnotation2.8620.0963.106
loadGtexData000
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.0100.0000.042
missingDataModal000
normaliseGeneExpression0.0240.0000.024
optimalSurvivalCutoff0.0980.0000.098
parseCategoricalGroups0.0010.0000.001
parseFirebrowseMetadata0.0450.0010.169
parseMatsEvent0.0030.0010.004
parseMatsGeneric0.0200.0000.019
parseMisoAnnotation0.1130.0030.118
parseMisoEvent0.0030.0000.004
parseMisoEventID0.0050.0000.007
parseMisoGeneric0.0250.0000.025
parseMisoId0.0000.0000.001
parseSplicingEvent0.0030.0000.004
parseSuppaEvent0.0030.0000.003
parseSuppaGeneric0.0150.0000.016
parseTcgaSampleInfo0.0040.0010.004
parseUrlsFromFirebrowseResponse0.0290.0010.121
parseVastToolsEvent0.0050.0000.005
parseVastToolsSE0.0170.0000.017
performICA0.0040.0010.005
performPCA0.0000.0010.001
plot.GEandAScorrelation0.4980.0070.505
plotDistribution0.5960.0090.605
plotGeneExprPerSample0.0820.0050.086
plotGroupIndependence0.1940.0010.194
plotICA0.1090.0020.113
plotLibrarySize0.1690.0040.174
plotPCA0.2170.0220.239
plotPCAvariance0.0440.0050.049
plotProtein0.6120.0151.520
plotRowStats0.5150.0000.515
plotSingleICA0.1640.0120.177
plotSplicingEvent0.0380.0000.038
plotSurvivalCurves0.0690.0050.074
plotSurvivalPvaluesByCutoff0.4550.0050.461
plotTranscripts0.0310.0010.752
prepareAnnotationFromEvents0.1790.0020.181
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.0070.0000.007
psichomics000
quantifySplicing0.0090.0000.009
queryEnsembl0.0270.0000.491
queryEnsemblByGene0.1250.0022.617
queryFirebrowseData0.0400.0010.206
queryPubMed0.0790.0040.603
queryUniprot0.0430.0010.388
readFile0.0010.0000.001
renameDuplicated0.0010.0000.001
renderBoxplot0.0630.0050.068
survdiffTerms0.0050.0010.006
survfit.survTerms0.020.000.02
testGroupIndependence0.0030.0000.003
testSurvival0.0170.0000.017
textSuggestions0.0010.0000.001
trimWhitespace000