Nuno Saraiva-Agostinho
| Snapshot Date: 2025-10-23 14:17 -0400 (Thu, 23 Oct 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) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-24 12:05 -0400 (Fri, 24 Oct 2025).
| 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" | 4898 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4688 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4634 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1660/2359 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.35.0 (landing page) Nuno Saraiva-Agostinho
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
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. |
| 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: 2025-10-23 23:23:21 -0400 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 23:33:49 -0400 (Thu, 23 Oct 2025) |
| EllapsedTime: 628.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: psichomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 Patched (2025-09-10 r88807)
* 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: ‘MacOSX11.3.1.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 ... 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 17.203 1.157 19.222
listSplicingAnnotations 13.513 0.984 14.925
listAllAnnotations 2.622 0.220 9.341
parseFirebrowseMetadata 0.039 0.006 10.368
queryFirebrowseData 0.040 0.002 10.484
queryPubMed 0.034 0.007 5.955
getTCGAdataTypes 0.029 0.004 8.341
parseUrlsFromFirebrowseResponse 0.031 0.002 6.257
* 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.
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: ‘MacOSX11.3.1.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)
psichomics.Rcheck/tests/spelling.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "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
0.222 0.085 0.301
psichomics.Rcheck/tests/testthat.Rout
R version 4.5.1 Patched (2025-09-10 r88807) -- "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")
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
Retrieving rMATS annotation...
Parsing rMATS annotation...
Retrieving rMATS annotation...
Parsing rMATS annotation...
Retrieving MISO annotation...
Parsing MISO annotation...
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
| | 0%
|======== | 20%
|================ | 40%
|======================== | 60%
|================================ | 80%
|========================================| 100%
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
29.167 2.260 80.493
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0 | 0 | 0 | |
| assignValuePerSubject | 0.016 | 0.008 | 0.025 | |
| blendColours | 0.000 | 0.000 | 0.001 | |
| calculateLoadingsContribution | 0.007 | 0.003 | 0.010 | |
| convertGeneIdentifiers | 17.203 | 1.157 | 19.222 | |
| correlateGEandAS | 0.023 | 0.006 | 0.030 | |
| createGroupByAttribute | 0.002 | 0.000 | 0.002 | |
| createJunctionsTemplate | 0.002 | 0.001 | 0.003 | |
| customRowMeans | 0.001 | 0.001 | 0.002 | |
| diffAnalyses | 0.092 | 0.010 | 0.101 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.026 | 0.002 | 0.463 | |
| filterGeneExpr | 0.006 | 0.001 | 0.009 | |
| filterGroups | 0.002 | 0.000 | 0.002 | |
| filterPSI | 0.013 | 0.003 | 0.017 | |
| getAttributesTime | 0.002 | 0.000 | 0.002 | |
| getDownloadsFolder | 0.000 | 0.001 | 0.000 | |
| getFirebrowseDateFormat | 0.000 | 0.000 | 0.001 | |
| getGeneList | 0.004 | 0.001 | 0.006 | |
| getGtexDataTypes | 0.000 | 0.001 | 0.001 | |
| getGtexTissues | 0 | 0 | 0 | |
| getNumerics | 0.002 | 0.001 | 0.002 | |
| getSampleFromSubject | 0.001 | 0.001 | 0.002 | |
| getSplicingEventFromGenes | 0.003 | 0.001 | 0.005 | |
| getSplicingEventTypes | 0.000 | 0.000 | 0.001 | |
| getSubjectFromSample | 0.001 | 0.000 | 0.000 | |
| getTCGAdataTypes | 0.029 | 0.004 | 8.341 | |
| getValidEvents | 0.003 | 0.000 | 0.003 | |
| groupPerElem | 0.000 | 0.001 | 0.001 | |
| hchart.survfit | 0.281 | 0.157 | 0.464 | |
| isFirebrowseUp | 0.006 | 0.001 | 2.069 | |
| labelBasedOnCutoff | 0.001 | 0.000 | 0.001 | |
| leveneTest | 0.007 | 0.001 | 0.007 | |
| listAllAnnotations | 2.622 | 0.220 | 9.341 | |
| listSplicingAnnotations | 13.513 | 0.984 | 14.925 | |
| loadAnnotation | 3.301 | 0.234 | 3.622 | |
| loadGtexData | 0.001 | 0.001 | 0.001 | |
| loadLocalFiles | 0 | 0 | 0 | |
| loadSRAproject | 0 | 0 | 0 | |
| loadTCGAdata | 0.010 | 0.003 | 2.087 | |
| missingDataModal | 0 | 0 | 0 | |
| normaliseGeneExpression | 0.028 | 0.002 | 0.030 | |
| optimalSurvivalCutoff | 0.114 | 0.002 | 0.116 | |
| parseCategoricalGroups | 0.001 | 0.000 | 0.002 | |
| parseFirebrowseMetadata | 0.039 | 0.006 | 10.368 | |
| parseMatsEvent | 0.004 | 0.001 | 0.005 | |
| parseMatsGeneric | 0.018 | 0.003 | 0.021 | |
| parseMisoAnnotation | 0.135 | 0.019 | 0.160 | |
| parseMisoEvent | 0.003 | 0.000 | 0.005 | |
| parseMisoEventID | 0.006 | 0.003 | 0.009 | |
| parseMisoGeneric | 0.031 | 0.004 | 0.036 | |
| parseMisoId | 0 | 0 | 0 | |
| parseSplicingEvent | 0.005 | 0.002 | 0.007 | |
| parseSuppaEvent | 0.004 | 0.001 | 0.005 | |
| parseSuppaGeneric | 0.022 | 0.002 | 0.024 | |
| parseTcgaSampleInfo | 0.006 | 0.002 | 0.008 | |
| parseUrlsFromFirebrowseResponse | 0.031 | 0.002 | 6.257 | |
| parseVastToolsEvent | 0.007 | 0.000 | 0.007 | |
| parseVastToolsSE | 0.022 | 0.001 | 0.024 | |
| performICA | 0.007 | 0.004 | 0.012 | |
| performPCA | 0.002 | 0.001 | 0.002 | |
| plot.GEandAScorrelation | 0.788 | 0.013 | 0.803 | |
| plotDistribution | 0.722 | 0.114 | 0.841 | |
| plotGeneExprPerSample | 0.105 | 0.052 | 0.158 | |
| plotGroupIndependence | 0.568 | 0.014 | 0.588 | |
| plotICA | 0.130 | 0.015 | 0.147 | |
| plotLibrarySize | 0.201 | 0.044 | 0.247 | |
| plotPCA | 0.324 | 0.216 | 0.554 | |
| plotPCAvariance | 0.063 | 0.059 | 0.133 | |
| plotProtein | 0.663 | 0.099 | 1.786 | |
| plotRowStats | 0.719 | 0.010 | 0.733 | |
| plotSingleICA | 0.230 | 0.161 | 0.463 | |
| plotSplicingEvent | 0.052 | 0.002 | 0.054 | |
| plotSurvivalCurves | 0.107 | 0.054 | 0.186 | |
| plotSurvivalPvaluesByCutoff | 0.593 | 0.061 | 0.660 | |
| plotTranscripts | 0.021 | 0.001 | 1.668 | |
| prepareAnnotationFromEvents | 0.237 | 0.011 | 0.250 | |
| prepareFirebrowseArchives | 0 | 0 | 0 | |
| prepareJunctionQuantSTAR | 0.000 | 0.000 | 0.001 | |
| prepareSRAmetadata | 0 | 0 | 0 | |
| processSurvTerms | 0.011 | 0.001 | 0.012 | |
| psichomics | 0.001 | 0.000 | 0.000 | |
| quantifySplicing | 0.016 | 0.007 | 0.023 | |
| queryEnsembl | 0.029 | 0.004 | 0.484 | |
| queryEnsemblByGene | 0.103 | 0.019 | 2.773 | |
| queryFirebrowseData | 0.040 | 0.002 | 10.484 | |
| queryPubMed | 0.034 | 0.007 | 5.955 | |
| queryUniprot | 0.061 | 0.002 | 0.408 | |
| readFile | 0.001 | 0.000 | 0.002 | |
| renameDuplicated | 0.001 | 0.000 | 0.002 | |
| renderBoxplot | 0.092 | 0.051 | 0.144 | |
| survdiffTerms | 0.007 | 0.001 | 0.009 | |
| survfit.survTerms | 0.026 | 0.002 | 0.028 | |
| testGroupIndependence | 0.004 | 0.000 | 0.005 | |
| testSurvival | 0.026 | 0.001 | 0.027 | |
| textSuggestions | 0.001 | 0.000 | 0.001 | |
| trimWhitespace | 0.001 | 0.000 | 0.001 | |