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This page was generated on 2024-05-04 11:37:00 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 1627/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.30.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_19
git_last_commit: 67f272c
git_last_commit_date: 2024-04-30 10:54:27 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  NO, package depends on 'recount' which is not available
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  NO, package depends on 'recount' which is not available
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for psichomics on nebbiolo1


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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings psichomics_1.30.0.tar.gz
StartedAt: 2024-05-04 02:34:01 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 02:43:04 -0400 (Sat, 04 May 2024)
EllapsedTime: 542.6 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings psichomics_1.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* 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 loading without being on the library search path ... 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  15.528  1.930  18.388
listSplicingAnnotations 11.067  1.259  13.256
queryEnsemblByGene       0.163  0.032   6.695
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.19-bioc/meat/psichomics.Rcheck/00check.log’
for details.


Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
  0.163   0.025   0.179 

psichomics.Rcheck/tests/testthat.Rout


R version 4.4.0 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 
 22.540   1.921  26.381 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.0000.0000.001
assignValuePerSubject0.0190.0040.024
blendColours0.0000.0000.001
calculateLoadingsContribution0.0080.0040.012
convertGeneIdentifiers15.528 1.93018.388
correlateGEandAS0.0190.0000.019
createGroupByAttribute0.0010.0000.001
createJunctionsTemplate0.0000.0020.003
customRowMeans0.0000.0010.001
diffAnalyses0.0710.0040.075
downloadFiles000
ensemblToUniprot0.0200.0040.461
filterGeneExpr0.0070.0010.007
filterGroups0.0020.0000.002
filterPSI0.0140.0000.015
getAttributesTime0.0020.0000.003
getDownloadsFolder0.0000.0000.001
getFirebrowseDateFormat0.0000.0000.001
getGeneList0.0020.0010.004
getGtexDataTypes0.0010.0010.001
getGtexTissues000
getNumerics0.0000.0020.002
getSampleFromSubject0.0000.0020.001
getSplicingEventFromGenes0.0040.0000.003
getSplicingEventTypes0.0000.0010.000
getSubjectFromSample0.0000.0010.000
getTCGAdataTypes0.0230.0100.082
getValidEvents0.0040.0000.003
groupPerElem0.0010.0000.001
hchart.survfit0.2200.0350.271
isFirebrowseUp0.0050.0010.012
labelBasedOnCutoff0.0000.0000.001
leveneTest0.0030.0040.007
listAllAnnotations2.5150.4003.120
listSplicingAnnotations11.067 1.25913.256
loadAnnotation2.7590.3443.290
loadGtexData0.0010.0000.000
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.0080.0040.025
missingDataModal0.0010.0000.001
normaliseGeneExpression0.0200.0040.024
optimalSurvivalCutoff0.0840.0000.084
parseCategoricalGroups0.0010.0010.001
parseFirebrowseMetadata0.0490.0030.100
parseMatsEvent0.0050.0000.005
parseMatsGeneric0.0160.0040.020
parseMisoAnnotation0.1110.0080.122
parseMisoEvent0.0030.0000.003
parseMisoEventID0.0060.0000.006
parseMisoGeneric0.0200.0080.028
parseMisoId000
parseSplicingEvent0.0010.0030.005
parseSuppaEvent0.0000.0040.003
parseSuppaGeneric0.0170.0010.017
parseTcgaSampleInfo0.0040.0000.005
parseUrlsFromFirebrowseResponse0.0250.0040.093
parseVastToolsEvent0.0050.0000.006
parseVastToolsSE0.0130.0040.017
performICA0.0040.0040.009
performPCA0.0010.0000.002
plot.GEandAScorrelation0.5610.0160.576
plotDistribution0.5570.0240.581
plotGeneExprPerSample0.0770.0080.085
plotGroupIndependence0.140.000.14
plotICA0.1120.0090.122
plotLibrarySize0.2080.0230.232
plotPCA0.2290.0400.269
plotPCAvariance0.0490.0080.057
plotProtein0.5780.0431.654
plotRowStats0.4120.0120.424
plotSingleICA0.1520.0280.180
plotSplicingEvent0.0380.0000.038
plotSurvivalCurves0.0690.0080.076
plotSurvivalPvaluesByCutoff0.3590.0080.368
plotTranscripts0.0160.0032.660
prepareAnnotationFromEvents0.1570.0160.172
prepareFirebrowseArchives0.0010.0000.000
prepareJunctionQuantSTAR0.0000.0000.001
prepareSRAmetadata000
processSurvTerms0.0060.0030.009
psichomics000
quantifySplicing0.0020.0110.013
queryEnsembl0.0300.0053.173
queryEnsemblByGene0.1630.0326.695
queryFirebrowseData0.0530.0000.164
queryPubMed0.1150.0120.840
queryUniprot0.0700.0030.446
readFile0.0020.0000.003
renameDuplicated0.0020.0000.002
renderBoxplot0.1100.0200.129
survdiffTerms0.0020.0080.009
survfit.survTerms0.0240.0080.033
testGroupIndependence0.0030.0000.003
testSurvival0.0200.0030.023
textSuggestions0.0010.0000.001
trimWhitespace0.0010.0000.000