Back to Multiple platform build/check report for BioC 3.17
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This page was generated on 2023-04-12 10:55:40 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.1 LTS)x86_644.3.0 alpha (2023-04-03 r84154) 4547
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_64R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" 4333
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:
- 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.

Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details.

raw results

Package 1565/2207HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.25.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2023-04-11 14:00:16 -0400 (Tue, 11 Apr 2023)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: devel
git_last_commit: 2e8fe2b
git_last_commit_date: 2022-11-01 11:14:40 -0400 (Tue, 01 Nov 2022)
nebbiolo1Linux (Ubuntu 22.04.1 LTS) / x86_64  OK    OK    WARNINGS  
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    OK  

Summary

Package: psichomics
Version: 1.25.0
Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings psichomics_1.25.0.tar.gz
StartedAt: 2023-04-12 08:32:22 -0400 (Wed, 12 Apr 2023)
EndedAt: 2023-04-12 08:41:43 -0400 (Wed, 12 Apr 2023)
EllapsedTime: 560.5 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings psichomics_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/psichomics.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.25.0’
* 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: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
* checking installed package size ... NOTE
  installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   2.2Mb
* 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  18.587  0.937  20.914
listSplicingAnnotations 11.170  0.492  12.599
plotProtein              0.982  0.048   5.357
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/psichomics.Rcheck/00check.log’
for details.



Installation output

psichomics.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c progressBar.cpp -o progressBar.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c psiFastCalc.cpp -o psiFastCalc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.17-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c vastToolsParser.cpp -o vastToolsParser.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.17-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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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 
  0.211   0.041   0.238 

psichomics.Rcheck/tests/testthat.Rout


R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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 1.25.0: 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 
 22.681   1.046  30.934 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0010.0000.001
assignValuePerSubject0.0150.0040.019
blendColours0.0000.0000.001
calculateLoadingsContribution0.0010.0080.010
convertGeneIdentifiers18.587 0.93720.914
correlateGEandAS0.0290.0000.030
createGroupByAttribute0.0010.0000.002
createJunctionsTemplate0.0030.0000.002
customRowMeans0.0010.0000.001
diffAnalyses0.2040.0000.204
downloadFiles0.0010.0000.000
ensemblToUniprot0.0360.0041.209
filterGeneExpr0.0090.0000.009
filterGroups0.0020.0000.002
filterPSI0.0110.0080.018
getAttributesTime0.0030.0000.003
getDownloadsFolder000
getFirebrowseDateFormat000
getGeneList0.0020.0040.005
getGtexDataTypes0.0560.0040.305
getGtexTissues000
getNumerics0.0020.0000.003
getSampleFromSubject0.0020.0000.002
getSplicingEventFromGenes0.0060.0000.006
getSplicingEventTypes000
getSubjectFromSample000
getTCGAdataTypes0.0570.0000.345
getValidEvents0.0050.0000.005
groupPerElem0.0010.0000.001
hchart.survfit0.2810.0240.324
isFirebrowseUp0.0050.0000.013
labelBasedOnCutoff0.0000.0000.001
leveneTest0.0070.0000.008
listAllAnnotations2.3630.1082.834
listSplicingAnnotations11.170 0.49212.599
loadAnnotation2.8920.1283.292
loadGtexData0.0000.0000.001
loadLocalFiles000
loadSRAproject0.0010.0000.000
loadTCGAdata0.0140.0000.027
missingDataModal000
normaliseGeneExpression0.0200.0040.024
optimalSurvivalCutoff0.0870.0040.091
parseCategoricalGroups0.0010.0000.000
parseFirebrowseMetadata0.0670.0000.134
parseMatsEvent0.0050.0000.006
parseMatsGeneric0.0180.0040.022
parseMisoAnnotation0.1150.0200.138
parseMisoEvent0.0040.0000.003
parseMisoEventID0.0060.0000.006
parseMisoGeneric0.0310.0000.031
parseMisoId000
parseSplicingEvent0.0040.0000.005
parseSuppaEvent0.0040.0000.004
parseSuppaGeneric0.0200.0000.019
parseTcgaSampleInfo0.0020.0030.004
parseUrlsFromFirebrowseResponse0.0400.0050.092
parseVastToolsEvent0.0020.0040.006
parseVastToolsSE0.0160.0040.020
performICA0.0070.0000.007
performPCA0.0020.0000.002
plot.GEandAScorrelation0.5130.0240.536
plotDistribution0.7200.0440.764
plotGeneExprPerSample0.1080.0040.112
plotGroupIndependence0.1640.0000.163
plotICA0.1080.0000.110
plotLibrarySize0.2260.0040.230
plotPCA0.2310.0280.259
plotPCAvariance0.0500.0040.054
plotProtein0.9820.0485.357
plotRowStats0.6200.0080.628
plotSingleICA0.2710.0160.287
plotSplicingEvent0.0360.0080.045
plotSurvivalCurves0.0790.0040.083
plotSurvivalPvaluesByCutoff0.4450.0280.473
plotTranscripts0.0310.0002.149
prepareAnnotationFromEvents0.2320.0000.233
prepareFirebrowseArchives000
prepareJunctionQuantSTAR0.0000.0000.001
prepareSRAmetadata000
processSurvTerms0.0130.0000.012
psichomics000
quantifySplicing0.0150.0000.016
queryEnsembl0.0480.0000.613
queryEnsemblByGene0.1600.0004.393
queryFirebrowseData0.0660.0000.145
queryPubMed0.0580.0040.601
queryUniprot0.0660.0042.188
readFile0.0020.0000.001
renameDuplicated0.0000.0000.001
renderBoxplot0.1200.0080.127
survdiffTerms0.0090.0000.010
survfit.survTerms0.0360.0000.036
testGroupIndependence0.0040.0000.005
testSurvival0.0300.0040.032
textSuggestions0.0010.0000.001
trimWhitespace0.0000.0010.001