Multiple platform build/check report for BioC 3.19 - CHECK results for psichomics on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4760
palomino3	Windows Server 2022 Datacenter	x64	4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"	4494
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 (2024-04-24) -- "Puppy Cup"	4508
kjohnson1	macOS 13.6.6 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 kjohnson1

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: 2024-06-25 05:29:20 -0400 (Tue, 25 Jun 2024)

EndedAt: 2024-06-25 05:38:13 -0400 (Tue, 25 Jun 2024)

EllapsedTime: 533.1 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: aarch64-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 Ventura 13.6.6
* 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 15.0.0 (clang-1500.0.40.1)’
* 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  21.051  1.069  26.209
listSplicingAnnotations 17.122  1.062  20.443
loadAnnotation           4.429  0.271   5.607
* 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-arm64/Resources/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c progressBar.cpp -o progressBar.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c psiFastCalc.cpp -o psiFastCalc.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c vastToolsParser.cpp -o vastToolsParser.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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: aarch64-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 
  0.210   0.051   0.246

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: aarch64-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 
 26.359   1.452  30.331

Example timings

psichomics.Rcheck/psichomics-Ex.timings

name	user	system	elapsed
addObjectAttrs	0.000	0.001	0.001
assignValuePerSubject	0.020	0.008	0.028
blendColours	0.001	0.001	0.001
calculateLoadingsContribution	0.011	0.002	0.013
convertGeneIdentifiers	21.051	1.069	26.209
correlateGEandAS	0.018	0.004	0.022
createGroupByAttribute	0.001	0.000	0.002
createJunctionsTemplate	0.001	0.001	0.002
customRowMeans	0.000	0.001	0.000
diffAnalyses	0.078	0.007	0.085
downloadFiles	0	0	0
ensemblToUniprot	0.022	0.003	0.333
filterGeneExpr	0.007	0.001	0.008
filterGroups	0.001	0.000	0.002
filterPSI	0.012	0.004	0.017
getAttributesTime	0.002	0.000	0.002
getDownloadsFolder	0	0	0
getFirebrowseDateFormat	0	0	0
getGeneList	0.005	0.001	0.006
getGtexDataTypes	0.000	0.000	0.001
getGtexTissues	0	0	0
getNumerics	0.002	0.000	0.002
getSampleFromSubject	0.001	0.000	0.001
getSplicingEventFromGenes	0.004	0.001	0.004
getSplicingEventTypes	0.000	0.001	0.000
getSubjectFromSample	0.000	0.000	0.001
getTCGAdataTypes	0.030	0.004	0.577
getValidEvents	0.003	0.000	0.004
groupPerElem	0.000	0.000	0.001
hchart.survfit	0.243	0.104	0.360
isFirebrowseUp	0.006	0.001	0.090
labelBasedOnCutoff	0.000	0.000	0.001
leveneTest	0.009	0.001	0.009
listAllAnnotations	3.480	0.285	4.270
listSplicingAnnotations	17.122	1.062	20.443
loadAnnotation	4.429	0.271	5.607
loadGtexData	0	0	0
loadLocalFiles	0	0	0
loadSRAproject	0	0	0
loadTCGAdata	0.009	0.002	0.179
missingDataModal	0.000	0.001	0.000
normaliseGeneExpression	0.035	0.002	0.036
optimalSurvivalCutoff	0.091	0.002	0.095
parseCategoricalGroups	0.001	0.000	0.001
parseFirebrowseMetadata	0.039	0.005	0.488
parseMatsEvent	0.004	0.001	0.005
parseMatsGeneric	0.015	0.002	0.018
parseMisoAnnotation	0.120	0.014	0.139
parseMisoEvent	0.004	0.001	0.004
parseMisoEventID	0.006	0.002	0.007
parseMisoGeneric	0.024	0.003	0.028
parseMisoId	0.000	0.000	0.001
parseSplicingEvent	0.005	0.002	0.006
parseSuppaEvent	0.003	0.001	0.004
parseSuppaGeneric	0.014	0.002	0.016
parseTcgaSampleInfo	0.004	0.002	0.006
parseUrlsFromFirebrowseResponse	0.027	0.002	0.333
parseVastToolsEvent	0.005	0.000	0.005
parseVastToolsSE	0.015	0.001	0.015
performICA	0.006	0.003	0.008
performPCA	0.001	0.001	0.002
plot.GEandAScorrelation	0.530	0.015	0.546
plotDistribution	0.673	0.063	0.737
plotGeneExprPerSample	0.084	0.028	0.112
plotGroupIndependence	0.198	0.004	0.202
plotICA	0.107	0.012	0.121
plotLibrarySize	0.180	0.029	0.209
plotPCA	0.226	0.108	0.335
plotPCAvariance	0.043	0.025	0.069
plotProtein	0.571	0.058	0.738
plotRowStats	0.476	0.009	0.485
plotSingleICA	0.175	0.083	0.258
plotSplicingEvent	0.043	0.001	0.044
plotSurvivalCurves	0.079	0.028	0.107
plotSurvivalPvaluesByCutoff	0.378	0.032	0.411
plotTranscripts	0.017	0.002	0.647
prepareAnnotationFromEvents	0.202	0.007	0.208
prepareFirebrowseArchives	0.001	0.000	0.000
prepareJunctionQuantSTAR	0	0	0
prepareSRAmetadata	0.001	0.000	0.000
processSurvTerms	0.009	0.001	0.009
psichomics	0.001	0.000	0.000
quantifySplicing	0.012	0.003	0.016
queryEnsembl	0.028	0.003	0.545
queryEnsemblByGene	0.106	0.018	2.188
queryFirebrowseData	0.039	0.002	0.649
queryPubMed	0.032	0.005	0.897
queryUniprot	0.074	0.001	0.117
readFile	0.002	0.000	0.002
renameDuplicated	0.001	0.001	0.001
renderBoxplot	0.064	0.027	0.091
survdiffTerms	0.007	0.001	0.007
survfit.survTerms	0.024	0.002	0.025
testGroupIndependence	0.003	0.000	0.004
testSurvival	0.022	0.001	0.023
textSuggestions	0.001	0.001	0.004
trimWhitespace	0.001	0.001	0.000