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This page was generated on 2024-04-12 11:37:57 -0400 (Fri, 12 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4675
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4413
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4436
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 1608/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.28.1  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2024-04-10 14:05:05 -0400 (Wed, 10 Apr 2024)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_18
git_last_commit: 444a86a
git_last_commit_date: 2024-02-04 17:55:30 -0400 (Sun, 04 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for psichomics on merida1


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: 1.28.1
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_1.28.1.tar.gz
StartedAt: 2024-04-11 07:14:32 -0400 (Thu, 11 Apr 2024)
EndedAt: 2024-04-11 07:29:54 -0400 (Thu, 11 Apr 2024)
EllapsedTime: 921.1 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### 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_1.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/psichomics.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* 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 ‘1.28.1’
* 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 R 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 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 ... OK
* 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  24.404  1.988  32.931
listSplicingAnnotations 21.433  1.920  25.208
loadAnnotation           5.236  0.411   5.770
listAllAnnotations       4.368  0.450   5.131
queryPubMed              0.051  0.016   5.676
* 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 
  0.352   0.118   0.446 

psichomics.Rcheck/tests/testthat.Rout

R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

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 1.28.1: 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 
 43.710   2.890  49.765 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0000.0010.002
assignValuePerSubject0.0360.0240.146
blendColours0.0020.0000.002
calculateLoadingsContribution0.0160.0060.097
convertGeneIdentifiers24.404 1.98832.931
correlateGEandAS0.0370.0100.048
createGroupByAttribute0.0020.0010.003
createJunctionsTemplate0.0040.0020.005
customRowMeans0.0010.0010.003
diffAnalyses0.1600.0170.191
downloadFiles0.0000.0010.001
ensemblToUniprot0.0320.0020.989
filterGeneExpr0.0130.0030.017
filterGroups0.0020.0010.003
filterPSI0.0280.0100.038
getAttributesTime0.0040.0010.004
getDownloadsFolder0.0000.0000.001
getFirebrowseDateFormat0.0010.0000.001
getGeneList0.0050.0020.008
getGtexDataTypes0.0010.0010.002
getGtexTissues000
getNumerics0.0040.0010.005
getSampleFromSubject0.0020.0010.003
getSplicingEventFromGenes0.0060.0020.008
getSplicingEventTypes0.0010.0010.001
getSubjectFromSample0.0010.0000.001
getTCGAdataTypes0.0450.0050.242
getValidEvents0.0070.0020.009
groupPerElem0.0010.0000.002
hchart.survfit0.4570.1970.667
isFirebrowseUp0.0100.0010.041
labelBasedOnCutoff0.0010.0010.001
leveneTest0.0150.0010.025
listAllAnnotations4.3680.4505.131
listSplicingAnnotations21.433 1.92025.208
loadAnnotation5.2360.4115.770
loadGtexData0.0000.0010.002
loadLocalFiles0.0000.0010.001
loadSRAproject0.0000.0000.001
loadTCGAdata0.0130.0040.089
missingDataModal0.0000.0010.001
normaliseGeneExpression0.0380.0040.043
optimalSurvivalCutoff0.2000.0030.203
parseCategoricalGroups0.0020.0000.003
parseFirebrowseMetadata0.0590.0100.254
parseMatsEvent0.0070.0020.010
parseMatsGeneric0.0420.0060.048
parseMisoAnnotation0.2650.0220.293
parseMisoEvent0.0080.0010.009
parseMisoEventID0.0110.0050.016
parseMisoGeneric0.0660.0090.075
parseMisoId0.0000.0000.001
parseSplicingEvent0.0100.0050.014
parseSuppaEvent0.0080.0010.009
parseSuppaGeneric0.0420.0060.048
parseTcgaSampleInfo0.0060.0020.009
parseUrlsFromFirebrowseResponse0.0400.0020.182
parseVastToolsEvent0.0120.0010.014
parseVastToolsSE0.0390.0040.044
performICA0.0120.0090.020
performPCA0.0020.0010.003
plot.GEandAScorrelation1.0560.0241.082
plotDistribution1.5490.1801.814
plotGeneExprPerSample0.1690.0700.239
plotGroupIndependence0.3030.0030.306
plotICA0.2370.0200.261
plotLibrarySize0.4250.0640.573
plotPCA0.4990.2450.830
plotPCAvariance0.0930.0620.156
plotProtein1.3150.1332.067
plotRowStats0.8950.0150.910
plotSingleICA0.4070.1870.639
plotSplicingEvent0.1140.0020.122
plotSurvivalCurves0.1680.0680.288
plotSurvivalPvaluesByCutoff0.9680.0801.115
plotTranscripts0.0330.0021.735
prepareAnnotationFromEvents0.4200.0120.441
prepareFirebrowseArchives0.0010.0000.001
prepareJunctionQuantSTAR0.0000.0010.001
prepareSRAmetadata0.0000.0010.001
processSurvTerms0.0200.0010.035
psichomics0.0000.0010.000
quantifySplicing0.0260.0100.042
queryEnsembl0.0520.0070.578
queryEnsemblByGene0.1880.0324.638
queryFirebrowseData0.0600.0030.326
queryPubMed0.0510.0165.676
queryUniprot0.0950.0030.362
readFile0.0020.0010.004
renameDuplicated0.0010.0000.002
renderBoxplot0.1510.0680.228
survdiffTerms0.0120.0020.015
survfit.survTerms0.0370.0030.044
testGroupIndependence0.0050.0010.006
testSurvival0.0330.0020.039
textSuggestions0.0010.0010.002
trimWhitespace0.0010.0010.002