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This page was generated on 2025-08-20 12:05 -0400 (Wed, 20 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4596
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4538
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4536
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 1628/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.35.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2025-08-19 13:45 -0400 (Tue, 19 Aug 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 lconway

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: /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_1.35.0.tar.gz
StartedAt: 2025-08-19 22:53:49 -0400 (Tue, 19 Aug 2025)
EndedAt: 2025-08-19 23:02:38 -0400 (Tue, 19 Aug 2025)
EllapsedTime: 528.6 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_1.35.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/psichomics.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.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 ... 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  17.357  1.174  19.400
listSplicingAnnotations 13.826  1.120  15.453
* 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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-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/4.5-x86_64/Resources/library’
* installing *source* package ‘psichomics’ ...
** this is package ‘psichomics’ version ‘1.35.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c progressBar.cpp -o progressBar.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c vastToolsParser.cpp -o vastToolsParser.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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/4.5-x86_64/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 version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 
  0.211   0.079   0.285 

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-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 1.35.0: 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 
 27.394   2.120  37.666 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0000.001
assignValuePerSubject0.0190.0130.033
blendColours0.0010.0010.001
calculateLoadingsContribution0.0100.0030.014
convertGeneIdentifiers17.357 1.17419.400
correlateGEandAS0.0160.0040.020
createGroupByAttribute0.0010.0010.002
createJunctionsTemplate0.0010.0000.002
customRowMeans0.0010.0000.002
diffAnalyses0.0670.0060.073
downloadFiles000
ensemblToUniprot0.0220.0020.828
filterGeneExpr0.0080.0020.009
filterGroups0.0020.0000.002
filterPSI0.0160.0050.020
getAttributesTime0.0030.0010.004
getDownloadsFolder0.0000.0000.001
getFirebrowseDateFormat000
getGeneList0.0040.0010.006
getGtexDataTypes0.0000.0010.001
getGtexTissues000
getNumerics0.0020.0010.002
getSampleFromSubject0.0010.0010.002
getSplicingEventFromGenes0.0040.0010.005
getSplicingEventTypes000
getSubjectFromSample0.0000.0010.001
getTCGAdataTypes0.0320.0030.280
getValidEvents0.0030.0010.004
groupPerElem000
hchart.survfit0.2840.1570.471
isFirebrowseUp0.0060.0000.026
labelBasedOnCutoff0.0010.0000.001
leveneTest0.0060.0000.007
listAllAnnotations2.9920.3033.419
listSplicingAnnotations13.826 1.12015.453
loadAnnotation3.3040.2583.659
loadGtexData0.0000.0000.001
loadLocalFiles000
loadSRAproject0.0000.0010.000
loadTCGAdata0.0080.0020.042
missingDataModal000
normaliseGeneExpression0.0230.0010.025
optimalSurvivalCutoff0.1170.0020.118
parseCategoricalGroups0.0010.0010.001
parseFirebrowseMetadata0.0380.0050.157
parseMatsEvent0.0060.0020.007
parseMatsGeneric0.0190.0030.021
parseMisoAnnotation0.1190.0180.140
parseMisoEvent0.0030.0000.004
parseMisoEventID0.0050.0010.006
parseMisoGeneric0.0290.0040.034
parseMisoId0.0010.0000.001
parseSplicingEvent0.0050.0020.007
parseSuppaEvent0.0040.0000.005
parseSuppaGeneric0.0180.0020.021
parseTcgaSampleInfo0.0040.0020.006
parseUrlsFromFirebrowseResponse0.0280.0010.132
parseVastToolsEvent0.0070.0010.007
parseVastToolsSE0.0230.0010.024
performICA0.0050.0030.009
performPCA0.0010.0000.001
plot.GEandAScorrelation0.5830.0110.597
plotDistribution0.7650.1010.870
plotGeneExprPerSample0.1010.0460.148
plotGroupIndependence0.2470.0020.252
plotICA0.1270.0150.144
plotLibrarySize0.2090.0470.258
plotPCA0.2850.1780.467
plotPCAvariance0.0610.0460.108
plotProtein0.7090.1051.749
plotRowStats0.5530.0110.567
plotSingleICA0.1930.1220.318
plotSplicingEvent0.0390.0010.040
plotSurvivalCurves0.0930.0420.136
plotSurvivalPvaluesByCutoff0.5670.0480.617
plotTranscripts0.0200.0011.130
prepareAnnotationFromEvents0.1750.0080.185
prepareFirebrowseArchives0.0010.0000.001
prepareJunctionQuantSTAR0.0000.0010.000
prepareSRAmetadata000
processSurvTerms0.0110.0010.012
psichomics0.0000.0010.000
quantifySplicing0.0120.0040.023
queryEnsembl0.0290.0030.595
queryEnsemblByGene0.1090.0172.973
queryFirebrowseData0.0390.0020.213
queryPubMed0.0300.0050.390
queryUniprot0.0600.0040.402
readFile0.0010.0010.002
renameDuplicated0.0010.0010.002
renderBoxplot0.0800.0480.129
survdiffTerms0.0080.0010.009
survfit.survTerms0.0290.0020.033
testGroupIndependence0.0040.0000.004
testSurvival0.0260.0010.027
textSuggestions0.0000.0000.001
trimWhitespace000