Back to Multiple platform build/check report for BioC 3.16:   simplified   long
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This page was generated on 2023-04-12 11:05:14 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
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 nebbiolo2


To the developers/maintainers of the psichomics package:
- Please 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 How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1545/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.24.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_16
git_last_commit: ff95655
git_last_commit_date: 2022-11-01 11:14:40 -0400 (Tue, 01 Nov 2022)
nebbiolo2Linux (Ubuntu 20.04.5 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
lconwaymacOS 12.5.1 Monterey / x86_64  OK    ERROR  skippedskipped

Summary

Package: psichomics
Version: 1.24.0
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings psichomics_1.24.0.tar.gz
StartedAt: 2023-04-10 23:08:17 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:16:26 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 489.3 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings psichomics_1.24.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/psichomics.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.24.0’
* 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
* 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 loading without being on the library search path ... 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  13.881  1.338  16.397
listSplicingAnnotations 12.084  1.031  14.124
* 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 ...
  ‘AS_events_preparation.Rmd’ using ‘UTF-8’... OK
  ‘CLI_tutorial.Rmd’ using ‘UTF-8’... OK
  ‘GUI_tutorial.Rmd’ using ‘UTF-8’... OK
  ‘custom_data.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.16-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c progressBar.cpp -o progressBar.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c psiFastCalc.cpp -o psiFastCalc.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c vastToolsParser.cpp -o vastToolsParser.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.16-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.16-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 
  0.170   0.042   0.196 

psichomics.Rcheck/tests/testthat.Rout


R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 1.24.0: 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 1 | SKIP 4 | PASS 1418 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• Couldn't resolve host name (1)
• On Bioconductor (2)
• On CRAN (1)

[ FAIL 0 | WARN 1 | SKIP 4 | PASS 1418 ]
> 
> proc.time()
   user  system elapsed 
 22.761   1.586  26.750 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0000.001
assignValuePerSubject0.0160.0000.016
blendColours0.0000.0000.001
calculateLoadingsContribution0.0080.0000.009
convertGeneIdentifiers13.881 1.33816.397
correlateGEandAS0.0130.0040.018
createGroupByAttribute0.0010.0000.001
createJunctionsTemplate0.0020.0000.002
customRowMeans0.0010.0000.000
diffAnalyses0.0720.0040.076
downloadFiles000
ensemblToUniprot0.0370.0000.438
filterGeneExpr0.0020.0040.006
filterGroups0.0010.0000.001
filterPSI0.0090.0030.012
getAttributesTime0.0020.0010.002
getDownloadsFolder0.0010.0000.001
getFirebrowseDateFormat000
getGeneList0.0030.0000.003
getGtexDataTypes0.0400.0080.365
getGtexTissues000
getNumerics0.0060.0000.006
getSampleFromSubject0.0010.0000.000
getSplicingEventFromGenes0.0030.0000.003
getSplicingEventTypes0.0010.0000.000
getSubjectFromSample000
getTCGAdataTypes0.0340.0200.105
getValidEvents0.0050.0000.005
groupPerElem0.0000.0010.001
hchart.survfit0.2250.0300.274
isFirebrowseUp0.0050.0000.023
labelBasedOnCutoff0.0000.0000.001
leveneTest0.0070.0000.008
listAllAnnotations2.4400.2363.027
listSplicingAnnotations12.084 1.03114.124
loadAnnotation2.9900.1813.456
loadGtexData000
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.0110.0000.023
missingDataModal000
normaliseGeneExpression0.0250.0040.028
optimalSurvivalCutoff0.0860.0040.090
parseCategoricalGroups0.0010.0000.001
parseFirebrowseMetadata0.0490.0040.093
parseMatsEvent0.0060.0000.005
parseMatsGeneric0.0190.0000.019
parseMisoAnnotation0.1190.0040.127
parseMisoEvent0.0040.0040.008
parseMisoEventID0.0050.0000.005
parseMisoGeneric0.0230.0040.027
parseMisoId000
parseSplicingEvent0.0050.0000.004
parseSuppaEvent0.0000.0030.003
parseSuppaGeneric0.0160.0000.016
parseTcgaSampleInfo0.0010.0020.003
parseUrlsFromFirebrowseResponse0.0300.0050.077
parseVastToolsEvent0.0050.0000.005
parseVastToolsSE0.0130.0040.018
performICA0.0070.0000.007
performPCA0.0020.0000.001
plot.GEandAScorrelation0.3930.0360.428
plotDistribution0.5910.0360.627
plotGeneExprPerSample0.0900.0110.102
plotGroupIndependence0.1500.0010.150
plotICA0.1000.0030.106
plotLibrarySize0.2070.0080.215
plotPCA0.2040.0210.224
plotPCAvariance0.0410.0040.045
plotProtein0.6100.0723.572
plotRowStats0.3650.0360.402
plotSingleICA0.1780.0200.197
plotSplicingEvent0.0440.0000.044
plotSurvivalCurves0.0870.0120.099
plotSurvivalPvaluesByCutoff0.4530.0280.481
plotTranscripts0.0270.0040.891
prepareAnnotationFromEvents0.1460.0000.145
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.0080.0000.008
psichomics000
quantifySplicing0.0090.0000.009
queryEnsembl0.0370.0040.743
queryEnsemblByGene0.1250.0163.315
queryFirebrowseData0.0650.0030.148
queryPubMed0.0610.0080.837
queryUniprot0.0690.0001.138
readFile0.0020.0000.001
renameDuplicated0.0000.0010.001
renderBoxplot0.1310.0140.145
survdiffTerms0.0030.0040.008
survfit.survTerms0.0250.0080.033
testGroupIndependence0.0030.0000.003
testSurvival0.0250.0000.025
textSuggestions0.0010.0000.000
trimWhitespace000