Multiple platform build/check report for BioC 3.19 - CHECK results for psichomics on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4757
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4491
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 nebbiolo1

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: 1.30.0

Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings psichomics_1.30.0.tar.gz

StartedAt: 2024-06-13 02:27:59 -0400 (Thu, 13 Jun 2024)

EndedAt: 2024-06-13 02:36:42 -0400 (Thu, 13 Jun 2024)

EllapsedTime: 523.1 seconds

RetCode: 0

Status: OK

CheckDir: psichomics.Rcheck

Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings psichomics_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.30.0’
* 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 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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  13.637  2.076  16.852
listSplicingAnnotations 10.803  1.870  13.385
* 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-3.19-bioc/meat/psichomics.Rcheck/00check.log’
for details.

Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 
  0.159   0.029   0.179

psichomics.Rcheck/tests/testthat.Rout


R version 4.4.0 (2024-04-24) -- "Puppy Cup"
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 1.30.0: 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 
 22.517   1.693  29.506

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0.000	0.001	0.001
assignValuePerSubject	0.019	0.002	0.021
blendColours	0.000	0.001	0.001
calculateLoadingsContribution	0.008	0.002	0.011
convertGeneIdentifiers	13.637	2.076	16.852
correlateGEandAS	0.013	0.008	0.021
createGroupByAttribute	0.001	0.000	0.001
createJunctionsTemplate	0.000	0.002	0.002
customRowMeans	0.000	0.001	0.001
diffAnalyses	0.056	0.024	0.080
downloadFiles	0	0	0
ensemblToUniprot	0.019	0.006	0.359
filterGeneExpr	0.008	0.000	0.007
filterGroups	0.002	0.000	0.002
filterPSI	0.008	0.008	0.016
getAttributesTime	0.003	0.000	0.003
getDownloadsFolder	0.000	0.001	0.001
getFirebrowseDateFormat	0.000	0.001	0.001
getGeneList	0.003	0.002	0.004
getGtexDataTypes	0.001	0.000	0.001
getGtexTissues	0.000	0.001	0.000
getNumerics	0.000	0.002	0.002
getSampleFromSubject	0.000	0.001	0.001
getSplicingEventFromGenes	0.002	0.002	0.004
getSplicingEventTypes	0.001	0.000	0.000
getSubjectFromSample	0	0	0
getTCGAdataTypes	0.055	0.009	3.255
getValidEvents	0.002	0.007	0.008
groupPerElem	0.001	0.001	0.002
hchart.survfit	0.217	0.080	0.311
isFirebrowseUp	0.007	0.000	0.043
labelBasedOnCutoff	0.001	0.000	0.001
leveneTest	0.007	0.000	0.007
listAllAnnotations	2.395	0.587	3.192
listSplicingAnnotations	10.803	1.870	13.385
loadAnnotation	2.807	0.468	3.457
loadGtexData	0	0	0
loadLocalFiles	0	0	0
loadSRAproject	0	0	0
loadTCGAdata	0.013	0.000	0.072
missingDataModal	0.001	0.000	0.001
normaliseGeneExpression	0.018	0.012	0.030
optimalSurvivalCutoff	0.097	0.004	0.102
parseCategoricalGroups	0.001	0.000	0.001
parseFirebrowseMetadata	0.053	0.003	0.289
parseMatsEvent	0.002	0.004	0.005
parseMatsGeneric	0.014	0.007	0.020
parseMisoAnnotation	0.110	0.022	0.135
parseMisoEvent	0.003	0.000	0.004
parseMisoEventID	0.001	0.005	0.006
parseMisoGeneric	0.025	0.007	0.032
parseMisoId	0.000	0.000	0.001
parseSplicingEvent	0.005	0.000	0.006
parseSuppaEvent	0.000	0.004	0.003
parseSuppaGeneric	0.015	0.003	0.017
parseTcgaSampleInfo	0.005	0.000	0.005
parseUrlsFromFirebrowseResponse	0.035	0.000	0.211
parseVastToolsEvent	0.006	0.000	0.006
parseVastToolsSE	0.019	0.000	0.020
performICA	0.009	0.000	0.010
performPCA	0.002	0.000	0.001
plot.GEandAScorrelation	0.501	0.059	0.560
plotDistribution	0.592	0.036	0.627
plotGeneExprPerSample	0.072	0.011	0.084
plotGroupIndependence	0.182	0.005	0.187
plotICA	0.103	0.004	0.108
plotLibrarySize	0.153	0.024	0.176
plotPCA	0.232	0.020	0.252
plotPCAvariance	0.044	0.008	0.052
plotProtein	0.570	0.104	1.588
plotRowStats	0.431	0.064	0.494
plotSingleICA	0.182	0.020	0.212
plotSplicingEvent	0.043	0.000	0.043
plotSurvivalCurves	0.073	0.016	0.089
plotSurvivalPvaluesByCutoff	0.391	0.028	0.419
plotTranscripts	0.028	0.004	1.855
prepareAnnotationFromEvents	0.200	0.024	0.223
prepareFirebrowseArchives	0	0	0
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0	0	0
processSurvTerms	0.005	0.004	0.009
psichomics	0	0	0
quantifySplicing	0.012	0.000	0.013
queryEnsembl	0.028	0.012	0.469
queryEnsemblByGene	0.121	0.036	2.996
queryFirebrowseData	0.069	0.012	0.375
queryPubMed	0.140	0.028	0.677
queryUniprot	0.112	0.012	0.870
readFile	0.001	0.001	0.001
renameDuplicated	0.001	0.000	0.001
renderBoxplot	0.071	0.012	0.083
survdiffTerms	0.000	0.007	0.006
survfit.survTerms	0.021	0.004	0.025
testGroupIndependence	0.003	0.000	0.003
testSurvival	0.010	0.008	0.018
textSuggestions	0.001	0.000	0.001
trimWhitespace	0.000	0.000	0.001