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

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4755
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4489
lconway	macOS 12.7.1 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4520
kjohnson3	macOS 13.6.5 Ventura	arm64	4.4.0 (2024-04-24) -- "Puppy Cup"	4466
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 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: 1.30.0

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_1.30.0.tar.gz

StartedAt: 2024-06-05 22:26:01 -0400 (Wed, 05 Jun 2024)

EndedAt: 2024-06-05 22:35:02 -0400 (Wed, 05 Jun 2024)

EllapsedTime: 541.2 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_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* 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: ‘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 ... 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  18.614  1.263  27.014
listSplicingAnnotations 14.439  1.134  16.088
queryPubMed              0.036  0.007   6.804
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.19-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/4.4-x86_64/Resources/library’
* installing *source* package ‘psichomics’ ...
** 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/4.4-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/4.4-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/4.4-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/4.4-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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-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 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 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)
NULL
> 
> proc.time()
   user  system elapsed 
  0.230   0.086   0.309

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-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 1.30.0: 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 
 26.959   1.962  30.913

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0.001	0.001	0.001
assignValuePerSubject	0.019	0.010	0.029
blendColours	0.001	0.000	0.001
calculateLoadingsContribution	0.011	0.003	0.013
convertGeneIdentifiers	18.614	1.263	27.014
correlateGEandAS	0.020	0.005	0.025
createGroupByAttribute	0.001	0.000	0.001
createJunctionsTemplate	0.001	0.000	0.002
customRowMeans	0.001	0.000	0.001
diffAnalyses	0.090	0.009	0.098
downloadFiles	0.000	0.000	0.001
ensemblToUniprot	0.024	0.002	2.535
filterGeneExpr	0.008	0.002	0.010
filterGroups	0.001	0.000	0.002
filterPSI	0.016	0.005	0.021
getAttributesTime	0.004	0.001	0.004
getDownloadsFolder	0.001	0.001	0.001
getFirebrowseDateFormat	0.001	0.001	0.001
getGeneList	0.004	0.001	0.005
getGtexDataTypes	0.000	0.000	0.002
getGtexTissues	0.000	0.001	0.001
getNumerics	0.002	0.000	0.002
getSampleFromSubject	0.001	0.000	0.002
getSplicingEventFromGenes	0.004	0.001	0.005
getSplicingEventTypes	0	0	0
getSubjectFromSample	0	0	0
getTCGAdataTypes	0.031	0.003	0.344
getValidEvents	0.003	0.000	0.004
groupPerElem	0.000	0.000	0.001
hchart.survfit	0.272	0.145	0.433
isFirebrowseUp	0.007	0.000	0.018
labelBasedOnCutoff	0.001	0.000	0.001
leveneTest	0.008	0.000	0.009
listAllAnnotations	3.037	0.253	3.449
listSplicingAnnotations	14.439	1.134	16.088
loadAnnotation	3.532	0.261	3.905
loadGtexData	0.000	0.001	0.001
loadLocalFiles	0	0	0
loadSRAproject	0.000	0.000	0.001
loadTCGAdata	0.010	0.002	0.035
missingDataModal	0	0	0
normaliseGeneExpression	0.028	0.003	0.031
optimalSurvivalCutoff	0.124	0.002	0.127
parseCategoricalGroups	0.001	0.001	0.001
parseFirebrowseMetadata	0.036	0.005	0.120
parseMatsEvent	0.006	0.002	0.007
parseMatsGeneric	0.018	0.003	0.021
parseMisoAnnotation	0.146	0.019	0.169
parseMisoEvent	0.003	0.000	0.004
parseMisoEventID	0.005	0.003	0.008
parseMisoGeneric	0.030	0.004	0.034
parseMisoId	0.001	0.000	0.001
parseSplicingEvent	0.004	0.001	0.006
parseSuppaEvent	0.003	0.000	0.003
parseSuppaGeneric	0.022	0.002	0.025
parseTcgaSampleInfo	0.004	0.002	0.007
parseUrlsFromFirebrowseResponse	0.029	0.001	0.136
parseVastToolsEvent	0.006	0.000	0.006
parseVastToolsSE	0.021	0.001	0.023
performICA	0.007	0.003	0.010
performPCA	0.002	0.000	0.002
plot.GEandAScorrelation	0.637	0.017	0.656
plotDistribution	0.894	0.105	1.003
plotGeneExprPerSample	0.105	0.047	0.153
plotGroupIndependence	0.239	0.003	0.242
plotICA	0.147	0.013	0.163
plotLibrarySize	0.236	0.047	0.285
plotPCA	0.324	0.182	0.508
plotPCAvariance	0.061	0.047	0.109
plotProtein	0.709	0.102	1.764
plotRowStats	0.609	0.009	0.621
plotSingleICA	0.222	0.135	0.363
plotSplicingEvent	0.046	0.001	0.047
plotSurvivalCurves	0.093	0.045	0.139
plotSurvivalPvaluesByCutoff	0.530	0.051	0.589
plotTranscripts	0.018	0.001	1.777
prepareAnnotationFromEvents	0.242	0.008	0.251
prepareFirebrowseArchives	0.001	0.000	0.000
prepareJunctionQuantSTAR	0.000	0.000	0.001
prepareSRAmetadata	0.000	0.001	0.000
processSurvTerms	0.012	0.001	0.013
psichomics	0.001	0.001	0.000
quantifySplicing	0.014	0.004	0.018
queryEnsembl	0.034	0.003	1.295
queryEnsemblByGene	0.118	0.017	3.979
queryFirebrowseData	0.043	0.002	0.213
queryPubMed	0.036	0.007	6.804
queryUniprot	0.051	0.002	0.543
readFile	0.002	0.001	0.002
renameDuplicated	0.001	0.000	0.001
renderBoxplot	0.093	0.047	0.141
survdiffTerms	0.008	0.001	0.009
survfit.survTerms	0.034	0.001	0.035
testGroupIndependence	0.002	0.001	0.002
testSurvival	0.032	0.001	0.034
textSuggestions	0.000	0.001	0.001
trimWhitespace	0.000	0.001	0.000