Multiple platform build/check report for BioC 3.20 - CHECK results for psichomics on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4358
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 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: 1.32.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings psichomics_1.32.0.tar.gz

StartedAt: 2025-01-03 01:16:44 -0500 (Fri, 03 Jan 2025)

EndedAt: 2025-01-03 01:25:13 -0500 (Fri, 03 Jan 2025)

EllapsedTime: 509.5 seconds

RetCode: 0

Status: OK

CheckDir: psichomics.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings psichomics_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.32.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... OK
* 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  14.469  1.477  16.772
listSplicingAnnotations 11.704  1.344  13.702
queryEnsemblByGene       0.135  0.030   6.281
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck/00check.log’
for details.

Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** 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-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c progressBar.cpp -o progressBar.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c psiFastCalc.cpp -o psiFastCalc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c vastToolsParser.cpp -o vastToolsParser.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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)
NULL
> 
> proc.time()
   user  system elapsed 
  0.152   0.026   0.168

psichomics.Rcheck/tests/testthat.Rout


R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 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 1.32.0: 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 
 22.483   2.065  27.011

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0.000	0.001	0.001
assignValuePerSubject	0.016	0.001	0.018
blendColours	0	0	0
calculateLoadingsContribution	0.007	0.001	0.009
convertGeneIdentifiers	14.469	1.477	16.772
correlateGEandAS	0.015	0.004	0.019
createGroupByAttribute	0.001	0.000	0.001
createJunctionsTemplate	0.001	0.001	0.002
customRowMeans	0.001	0.000	0.000
diffAnalyses	0.072	0.007	0.078
downloadFiles	0	0	0
ensemblToUniprot	0.022	0.007	0.600
filterGeneExpr	0.005	0.004	0.009
filterGroups	0.001	0.000	0.002
filterPSI	0.009	0.009	0.019
getAttributesTime	0.002	0.002	0.005
getDownloadsFolder	0	0	0
getFirebrowseDateFormat	0.000	0.001	0.001
getGeneList	0.003	0.002	0.007
getGtexDataTypes	0	0	0
getGtexTissues	0	0	0
getNumerics	0.000	0.002	0.003
getSampleFromSubject	0.001	0.000	0.001
getSplicingEventFromGenes	0.003	0.002	0.005
getSplicingEventTypes	0	0	0
getSubjectFromSample	0	0	0
getTCGAdataTypes	0.040	0.023	0.213
getValidEvents	0.003	0.000	0.004
groupPerElem	0	0	0
hchart.survfit	0.258	0.050	0.326
isFirebrowseUp	0.005	0.003	0.019
labelBasedOnCutoff	0.000	0.001	0.001
leveneTest	0.008	0.001	0.008
listAllAnnotations	2.660	0.358	4.669
listSplicingAnnotations	11.704	1.344	13.702
loadAnnotation	2.931	0.318	3.412
loadGtexData	0.000	0.001	0.000
loadLocalFiles	0	0	0
loadSRAproject	0	0	0
loadTCGAdata	0.007	0.012	0.038
missingDataModal	0	0	0
normaliseGeneExpression	0.033	0.005	0.038
optimalSurvivalCutoff	0.096	0.022	0.118
parseCategoricalGroups	0.001	0.000	0.001
parseFirebrowseMetadata	0.052	0.010	0.137
parseMatsEvent	0.003	0.002	0.005
parseMatsGeneric	0.017	0.002	0.019
parseMisoAnnotation	0.109	0.033	0.144
parseMisoEvent	0.004	0.000	0.004
parseMisoEventID	0.003	0.003	0.006
parseMisoGeneric	0.024	0.011	0.034
parseMisoId	0	0	0
parseSplicingEvent	0.002	0.002	0.005
parseSuppaEvent	0.003	0.001	0.004
parseSuppaGeneric	0.015	0.007	0.022
parseTcgaSampleInfo	0.004	0.000	0.005
parseUrlsFromFirebrowseResponse	0.031	0.005	0.108
parseVastToolsEvent	0.006	0.000	0.006
parseVastToolsSE	0.016	0.006	0.021
performICA	0.005	0.001	0.007
performPCA	0.001	0.001	0.001
plot.GEandAScorrelation	0.493	0.101	0.594
plotDistribution	0.637	0.077	0.714
plotGeneExprPerSample	0.076	0.007	0.083
plotGroupIndependence	0.224	0.045	0.270
plotICA	0.116	0.008	0.125
plotLibrarySize	0.172	0.011	0.183
plotPCA	0.211	0.025	0.236
plotPCAvariance	0.044	0.006	0.050
plotProtein	0.654	0.100	1.602
plotRowStats	0.446	0.062	0.508
plotSingleICA	0.172	0.023	0.195
plotSplicingEvent	0.037	0.001	0.038
plotSurvivalCurves	0.071	0.012	0.083
plotSurvivalPvaluesByCutoff	0.426	0.020	0.446
plotTranscripts	0.018	0.001	1.880
prepareAnnotationFromEvents	0.189	0.029	0.218
prepareFirebrowseArchives	0	0	0
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0.000	0.001	0.000
processSurvTerms	0.009	0.000	0.009
psichomics	0	0	0
quantifySplicing	0.010	0.001	0.010
queryEnsembl	0.030	0.002	0.872
queryEnsemblByGene	0.135	0.030	6.281
queryFirebrowseData	0.056	0.011	0.204
queryPubMed	0.088	0.050	0.652
queryUniprot	0.073	0.004	0.416
readFile	0.001	0.002	0.003
renameDuplicated	0.002	0.000	0.001
renderBoxplot	0.093	0.033	0.127
survdiffTerms	0.005	0.004	0.009
survfit.survTerms	0.022	0.013	0.035
testGroupIndependence	0.003	0.001	0.005
testSurvival	0.024	0.003	0.027
textSuggestions	0.001	0.000	0.001
trimWhitespace	0	0	0