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This page was generated on 2024-03-28 11:39:49 -0400 (Thu, 28 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4708
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" 4446
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" 4471
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" 4426
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 1607/2270HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.29.1  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: devel
git_last_commit: 04d06e0
git_last_commit_date: 2024-02-04 17:57:40 -0400 (Sun, 04 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  

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: 1.29.1
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_1.29.1.tar.gz
StartedAt: 2024-03-27 23:19:29 -0400 (Wed, 27 Mar 2024)
EndedAt: 2024-03-27 23:28:58 -0400 (Wed, 27 Mar 2024)
EllapsedTime: 569.2 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_1.29.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2024-03-18 r86148)
* 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 ‘1.29.1’
* 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 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  18.213  1.358  20.586
listSplicingAnnotations 14.887  1.319  16.824
* 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++11 -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++11 -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++11 -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++11 -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++11 -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 Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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 
  0.246   0.095   0.354 

psichomics.Rcheck/tests/testthat.Rout


R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences"
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 1.29.1: 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 
 30.379   2.479  35.266 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0010.001
assignValuePerSubject0.0170.0090.027
blendColours0.0010.0000.001
calculateLoadingsContribution0.0090.0030.011
convertGeneIdentifiers18.213 1.35820.586
correlateGEandAS0.0190.0060.025
createGroupByAttribute0.0020.0000.002
createJunctionsTemplate0.0020.0000.001
customRowMeans0.0010.0000.001
diffAnalyses0.0780.0090.088
downloadFiles000
ensemblToUniprot0.0200.0020.800
filterGeneExpr0.0070.0020.008
filterGroups0.0020.0000.002
filterPSI0.0130.0030.016
getAttributesTime0.0030.0010.004
getDownloadsFolder0.0000.0010.001
getFirebrowseDateFormat0.0010.0000.000
getGeneList0.0050.0010.007
getGtexDataTypes0.0010.0000.001
getGtexTissues0.0010.0000.000
getNumerics0.0020.0000.002
getSampleFromSubject0.0010.0010.001
getSplicingEventFromGenes0.0030.0010.005
getSplicingEventTypes000
getSubjectFromSample0.0010.0000.000
getTCGAdataTypes0.0320.0043.365
getValidEvents0.0030.0010.004
groupPerElem0.0010.0010.001
hchart.survfit0.2910.1630.478
isFirebrowseUp0.0070.0000.014
labelBasedOnCutoff0.0010.0000.001
leveneTest0.010.000.01
listAllAnnotations3.2980.3523.910
listSplicingAnnotations14.887 1.31916.824
loadAnnotation3.8340.3524.388
loadGtexData0.0000.0010.000
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.0110.0020.027
missingDataModal0.0000.0000.001
normaliseGeneExpression0.0300.0030.034
optimalSurvivalCutoff0.1350.0020.139
parseCategoricalGroups0.0010.0000.002
parseFirebrowseMetadata0.0470.0060.102
parseMatsEvent0.0050.0010.007
parseMatsGeneric0.0270.0040.031
parseMisoAnnotation0.1600.0230.188
parseMisoEvent0.0040.0010.006
parseMisoEventID0.0070.0030.010
parseMisoGeneric0.0340.0050.040
parseMisoId000
parseSplicingEvent0.0060.0020.008
parseSuppaEvent0.0040.0010.004
parseSuppaGeneric0.0210.0030.024
parseTcgaSampleInfo0.0040.0020.007
parseUrlsFromFirebrowseResponse0.0260.0020.090
parseVastToolsEvent0.0070.0010.008
parseVastToolsSE0.0230.0030.026
performICA0.0080.0050.014
performPCA0.0020.0010.003
plot.GEandAScorrelation0.6600.0280.698
plotDistribution0.8280.1130.957
plotGeneExprPerSample0.1140.0500.166
plotGroupIndependence0.2090.0050.217
plotICA0.1900.0180.213
plotLibrarySize0.2140.0520.273
plotPCA0.2920.1940.493
plotPCAvariance0.0630.0470.111
plotProtein0.6840.1061.551
plotRowStats0.5240.0130.543
plotSingleICA0.2770.1360.422
plotSplicingEvent0.0550.0020.057
plotSurvivalCurves0.0930.0530.152
plotSurvivalPvaluesByCutoff0.4980.0610.567
plotTranscripts0.0200.0011.395
prepareAnnotationFromEvents0.1870.0110.199
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata0.0000.0000.001
processSurvTerms0.0090.0010.010
psichomics0.0000.0000.001
quantifySplicing0.0110.0030.014
queryEnsembl0.0290.0030.551
queryEnsemblByGene0.1170.0163.491
queryFirebrowseData0.0460.0020.151
queryPubMed0.0350.0062.890
queryUniprot0.0630.0020.443
readFile0.0020.0010.002
renameDuplicated0.0010.0000.001
renderBoxplot0.1570.0510.210
survdiffTerms0.0080.0010.009
survfit.survTerms0.0310.0020.034
testGroupIndependence0.0040.0000.004
testSurvival0.0280.0020.032
textSuggestions0.0010.0010.002
trimWhitespace0.0000.0010.001