Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDEFGHIJKLMNO[P]QRSTUVWXYZ

This page was generated on 2024-11-20 12:08 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1613/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.32.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_20
git_last_commit: e9a5f73
git_last_commit_date: 2024-10-29 10:15:03 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for psichomics on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: psichomics
Version: 1.32.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings psichomics_1.32.0.tar.gz
StartedAt: 2024-11-20 11:15:34 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 11:26:18 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 644.2 seconds
RetCode: 0
Status:   OK  
CheckDir: psichomics.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings psichomics_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.32.0’
* 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++ (conda-forge gcc 14.2.0-1) 14.2.0’
* 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  18.376  1.126  28.764
listSplicingAnnotations 13.762  0.735  21.262
loadAnnotation           3.510  0.155   5.608
* 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
  ‘/home/biocbuild/bbs-3.20-bioc/meat/psichomics.Rcheck/00check.log’
for details.


Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  0.288   0.024   0.211 

psichomics.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 1.32.0: start the visual interface by running psichomics()
Full documentation and tutorials at https://nuno-agostinho.github.io/psichomics
> 
> test_check("psichomics")
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 





























Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving rMATS annotation...

Parsing rMATS annotation...

Retrieving MISO annotation...

Parsing MISO annotation...
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 
  |                                        |   0% 
  |========                                |  20% 
  |================                        |  40% 
  |========================                |  60% 
  |================================        |  80% 
  |========================================| 100% 

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 
 30.963   2.483  41.705 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs000
assignValuePerSubject0.0220.0000.024
blendColours0.0010.0000.001
calculateLoadingsContribution0.0030.0080.011
convertGeneIdentifiers18.376 1.12628.764
correlateGEandAS0.0220.0010.023
createGroupByAttribute0.0010.0000.002
createJunctionsTemplate0.0020.0000.002
customRowMeans0.0010.0000.001
diffAnalyses0.0930.0120.106
downloadFiles000
ensemblToUniprot0.0260.0041.498
filterGeneExpr0.0010.0070.009
filterGroups0.0010.0000.002
filterPSI0.0140.0040.018
getAttributesTime0.0040.0000.004
getDownloadsFolder0.0000.0000.001
getFirebrowseDateFormat0.0010.0000.001
getGeneList0.0050.0000.005
getGtexDataTypes0.0010.0000.001
getGtexTissues000
getNumerics0.0020.0000.002
getSampleFromSubject0.0000.0000.001
getSplicingEventFromGenes0.0020.0030.005
getSplicingEventTypes000
getSubjectFromSample0.0000.0000.001
getTCGAdataTypes0.0330.0031.528
getValidEvents0.0010.0030.004
groupPerElem0.0010.0000.000
hchart.survfit0.2960.0360.334
isFirebrowseUp0.0060.0000.253
labelBasedOnCutoff0.0000.0000.001
leveneTest0.0070.0020.010
listAllAnnotations2.9400.1834.954
listSplicingAnnotations13.762 0.73521.262
loadAnnotation3.5100.1555.608
loadGtexData000
loadLocalFiles0.0010.0000.000
loadSRAproject0.0000.0000.001
loadTCGAdata0.0090.0040.518
missingDataModal0.0000.0000.001
normaliseGeneExpression0.0270.0040.032
optimalSurvivalCutoff0.1460.0040.150
parseCategoricalGroups0.0010.0010.001
parseFirebrowseMetadata0.0560.0031.329
parseMatsEvent0.0060.0000.006
parseMatsGeneric0.0270.0000.027
parseMisoAnnotation0.1700.0120.205
parseMisoEvent0.0050.0000.005
parseMisoEventID0.0030.0040.007
parseMisoGeneric0.0400.0000.039
parseMisoId000
parseSplicingEvent0.0060.0000.005
parseSuppaEvent0.0020.0040.005
parseSuppaGeneric0.0200.0040.024
parseTcgaSampleInfo0.0050.0000.005
parseUrlsFromFirebrowseResponse0.0370.0000.827
parseVastToolsEvent0.0070.0000.007
parseVastToolsSE0.0250.0000.025
performICA0.0080.0000.008
performPCA0.0000.0020.002
plot.GEandAScorrelation0.6940.0330.728
plotDistribution0.9480.0280.977
plotGeneExprPerSample0.1090.0080.118
plotGroupIndependence0.2530.0040.257
plotICA0.1560.0080.169
plotLibrarySize0.2470.0080.255
plotPCA0.3020.0280.330
plotPCAvariance0.0610.0040.065
plotProtein0.8280.0162.304
plotRowStats0.6320.0080.642
plotSingleICA0.2570.0160.274
plotSplicingEvent0.060.000.06
plotSurvivalCurves0.1010.0080.108
plotSurvivalPvaluesByCutoff0.5580.0080.568
plotTranscripts0.0250.0001.492
prepareAnnotationFromEvents0.2550.0040.259
prepareFirebrowseArchives0.0010.0000.000
prepareJunctionQuantSTAR000
prepareSRAmetadata0.0000.0000.001
processSurvTerms0.0100.0030.013
psichomics000
quantifySplicing0.0110.0040.015
queryEnsembl0.0390.0000.960
queryEnsemblByGene0.1230.0004.073
queryFirebrowseData0.0470.0041.572
queryPubMed0.0400.0002.107
queryUniprot0.0470.0000.921
readFile0.0010.0000.001
renameDuplicated0.0010.0000.001
renderBoxplot0.0930.0080.101
survdiffTerms0.0030.0040.007
survfit.survTerms0.0290.0000.028
testGroupIndependence0.0030.0000.003
testSurvival0.0270.0000.027
textSuggestions0.0010.0000.001
trimWhitespace000