| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-04 11:57 -0400 (Sat, 04 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4897 |
| 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 1662/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.36.1 (landing page) Nuno Saraiva-Agostinho
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for psichomics in R Universe. | ||||||||||||||
|
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: 1.36.1 |
| 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_1.36.1.tar.gz |
| StartedAt: 2026-04-04 02:45:38 -0400 (Sat, 04 Apr 2026) |
| EndedAt: 2026-04-04 02:55:06 -0400 (Sat, 04 Apr 2026) |
| EllapsedTime: 568.6 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: psichomics.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### 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_1.36.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/psichomics.Rcheck’
* using R version 4.5.2 (2025-10-31)
* 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 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.36.1’
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 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 ... ERROR
Running examples in ‘psichomics-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: queryPubMed
> ### Title: Query the PubMed REST API
> ### Aliases: queryPubMed
> ### Keywords: internal
>
> ### ** Examples
>
> psichomics:::queryPubMed("BRCA1", "cancer", "adrenocortical carcinoma")
Error in curl::curl_fetch_memory(url, handle = handle) :
SSL connect error [eutils.ncbi.nlm.nih.gov]:
gnutls_handshake() failed: The TLS connection was non-properly terminated.
Calls: <Anonymous> ... request_fetch.write_memory -> <Anonymous> -> raise_libcurl_error
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
convertGeneIdentifiers 14.133 1.498 16.537
listSplicingAnnotations 11.131 0.959 12.854
* 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: 1 ERROR, 4 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/psichomics.Rcheck/00check.log’
for details.
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 ‘1.36.1’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 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)
psichomics.Rcheck/tests/spelling.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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
0.139 0.037 0.167
psichomics.Rcheck/tests/testthat.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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 1.36.1: 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
24.842 2.233 69.800
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0.001 | 0.000 | 0.001 | |
| assignValuePerSubject | 0.015 | 0.003 | 0.018 | |
| blendColours | 0.000 | 0.001 | 0.001 | |
| calculateLoadingsContribution | 0.007 | 0.003 | 0.010 | |
| convertGeneIdentifiers | 14.133 | 1.498 | 16.537 | |
| correlateGEandAS | 0.015 | 0.001 | 0.015 | |
| createGroupByAttribute | 0.001 | 0.000 | 0.001 | |
| createJunctionsTemplate | 0.002 | 0.000 | 0.001 | |
| customRowMeans | 0.001 | 0.000 | 0.001 | |
| diffAnalyses | 0.061 | 0.001 | 0.062 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.039 | 0.000 | 1.035 | |
| filterGeneExpr | 0.010 | 0.001 | 0.011 | |
| filterGroups | 0.002 | 0.000 | 0.002 | |
| filterPSI | 0.018 | 0.003 | 0.021 | |
| getAttributesTime | 0.003 | 0.000 | 0.003 | |
| getDownloadsFolder | 0 | 0 | 0 | |
| getFirebrowseDateFormat | 0.001 | 0.000 | 0.000 | |
| getGeneList | 0.004 | 0.001 | 0.004 | |
| getGtexDataTypes | 0.001 | 0.000 | 0.001 | |
| getGtexTissues | 0 | 0 | 0 | |
| getNumerics | 0.002 | 0.000 | 0.002 | |
| getSampleFromSubject | 0.001 | 0.000 | 0.001 | |
| getSplicingEventFromGenes | 0.003 | 0.000 | 0.004 | |
| getSplicingEventTypes | 0 | 0 | 0 | |
| getSubjectFromSample | 0.000 | 0.000 | 0.001 | |
| getTCGAdataTypes | 0.065 | 0.037 | 0.439 | |
| getValidEvents | 0.008 | 0.002 | 0.010 | |
| groupPerElem | 0.001 | 0.000 | 0.001 | |
| hchart.survfit | 0.245 | 0.058 | 0.323 | |
| isFirebrowseUp | 0.006 | 0.000 | 0.022 | |
| labelBasedOnCutoff | 0.000 | 0.000 | 0.001 | |
| leveneTest | 0.007 | 0.000 | 0.007 | |
| listAllAnnotations | 2.436 | 0.491 | 3.117 | |
| listSplicingAnnotations | 11.131 | 0.959 | 12.854 | |
| loadAnnotation | 2.802 | 0.141 | 3.164 | |
| loadGtexData | 0 | 0 | 0 | |
| loadLocalFiles | 0.001 | 0.000 | 0.000 | |
| loadSRAproject | 0 | 0 | 0 | |
| loadTCGAdata | 0.012 | 0.001 | 0.047 | |
| missingDataModal | 0 | 0 | 0 | |
| normaliseGeneExpression | 0.030 | 0.001 | 0.030 | |
| optimalSurvivalCutoff | 0.135 | 0.007 | 0.142 | |
| parseCategoricalGroups | 0.001 | 0.000 | 0.001 | |
| parseFirebrowseMetadata | 0.047 | 0.001 | 0.148 | |
| parseMatsEvent | 0.005 | 0.000 | 0.005 | |
| parseMatsGeneric | 0.018 | 0.002 | 0.020 | |
| parseMisoAnnotation | 0.111 | 0.008 | 0.121 | |
| parseMisoEvent | 0.004 | 0.000 | 0.004 | |
| parseMisoEventID | 0.005 | 0.000 | 0.006 | |
| parseMisoGeneric | 0.025 | 0.001 | 0.026 | |
| parseMisoId | 0.000 | 0.000 | 0.001 | |
| parseSplicingEvent | 0.004 | 0.000 | 0.004 | |
| parseSuppaEvent | 0.003 | 0.000 | 0.003 | |
| parseSuppaGeneric | 0.016 | 0.000 | 0.016 | |
| parseTCGAsampleInfo | 0.004 | 0.000 | 0.003 | |
| parseUrlsFromFirebrowseResponse | 0.029 | 0.002 | 0.135 | |
| parseVastToolsEvent | 0.006 | 0.000 | 0.005 | |
| parseVastToolsSE | 0.016 | 0.001 | 0.016 | |
| performICA | 0.005 | 0.001 | 0.006 | |
| performPCA | 0.001 | 0.000 | 0.002 | |
| plot.GEandAScorrelation | 0.586 | 0.036 | 0.623 | |
| plotDistribution | 0.628 | 0.109 | 0.737 | |
| plotGeneExprPerSample | 0.074 | 0.015 | 0.089 | |
| plotGroupIndependence | 0.391 | 0.034 | 0.426 | |
| plotICA | 0.109 | 0.002 | 0.113 | |
| plotLibrarySize | 0.165 | 0.014 | 0.179 | |
| plotPCA | 0.223 | 0.027 | 0.250 | |
| plotPCAvariance | 0.043 | 0.005 | 0.049 | |
| plotProtein | 0.636 | 0.061 | 1.769 | |
| plotRowStats | 0.605 | 0.025 | 0.630 | |
| plotSingleICA | 0.188 | 0.024 | 0.212 | |
| plotSplicingEvent | 0.043 | 0.006 | 0.049 | |
| plotSurvivalCurves | 0.080 | 0.017 | 0.097 | |
| plotSurvivalPvaluesByCutoff | 0.477 | 0.029 | 0.506 | |
| plotTranscripts | 0.024 | 0.001 | 1.027 | |
| prepareAnnotationFromEvents | 0.153 | 0.003 | 0.156 | |
| prepareFirebrowseArchives | 0 | 0 | 0 | |
| prepareJunctionQuantSTAR | 0 | 0 | 0 | |
| prepareSRAmetadata | 0 | 0 | 0 | |
| processSurvTerms | 0.008 | 0.001 | 0.008 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.01 | 0.00 | 0.01 | |
| queryEnsembl | 0.038 | 0.007 | 0.501 | |
| queryEnsemblByGene | 0.163 | 0.013 | 2.810 | |
| queryFirebrowseData | 0.066 | 0.004 | 0.254 | |