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This page was generated on 2023-11-30 11:36:58 -0500 (Thu, 30 Nov 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.2 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4685
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4420
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4439
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 1608/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
psichomics 1.28.0  (landing page)
Nuno Saraiva-Agostinho
Snapshot Date: 2023-11-29 14:05:05 -0500 (Wed, 29 Nov 2023)
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: RELEASE_3_18
git_last_commit: 4010198
git_last_commit_date: 2023-10-24 10:53:32 -0500 (Tue, 24 Oct 2023)
nebbiolo2Linux (Ubuntu 22.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

CHECK results for psichomics on palomino4


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: 1.28.0
Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:psichomics.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings psichomics_1.28.0.tar.gz
StartedAt: 2023-11-30 04:56:00 -0500 (Thu, 30 Nov 2023)
EndedAt: 2023-11-30 05:03:40 -0500 (Thu, 30 Nov 2023)
EllapsedTime: 459.6 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: psichomics.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:psichomics.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings psichomics_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/psichomics.Rcheck'
* using R version 4.3.2 (2023-10-31 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'psichomics/DESCRIPTION' ... OK
* this is package 'psichomics' version '1.28.0'
* 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 whether package 'psichomics' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* 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 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 startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
survfit:
  function(formula, ...)
survfit.survTerms:
  function(survTerms, ...)
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/psichomics/libs/x64/psichomics.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
convertGeneIdentifiers  12.44   1.61   14.54
listSplicingAnnotations  9.30   1.36   10.92
* 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'F:/biocbuild/bbs-3.18-bioc/meat/psichomics.Rcheck/00check.log'
for details.



Installation output

psichomics.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL psichomics
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library'
* installing *source* package 'psichomics' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c progressBar.cpp -o progressBar.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c psiFastCalc.cpp -o psiFastCalc.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include'   -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c vastToolsParser.cpp -o vastToolsParser.o
g++ -std=gnu++17 -shared -s -static-libgcc -o psichomics.dll tmp.def RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-psichomics/00new/psichomics/libs/x64
** 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
** 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 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 
   0.25    0.03    0.28 

psichomics.Rcheck/tests/testthat.Rout


R version 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 1.28.0: 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 (4) ═══════════════════════════════════════════════════════════
• Couldn't resolve host name (1): 'testGeneInfo.R:99:5'
• On Bioconductor (2): 'testDiscardLowCoveragePSIs.R:61:5',
  'testGeneInfo.R:50:5'
• On CRAN (1): 'testSRAloading.R:4:5'

[ FAIL 0 | WARN 1 | SKIP 4 | PASS 1418 ]
> 
> proc.time()
   user  system elapsed 
  22.39    1.78   26.96 

Example timings

psichomics.Rcheck/psichomics-Ex.timings

nameusersystemelapsed
addObjectAttrs0.020.000.02
assignValuePerSubject0.000.010.01
blendColours000
calculateLoadingsContribution0.010.000.02
convertGeneIdentifiers12.44 1.6114.54
correlateGEandAS0.010.000.02
createGroupByAttribute000
createJunctionsTemplate0.020.000.01
customRowMeans000
diffAnalyses0.080.000.08
downloadFiles000
ensemblToUniprot0.000.001.28
filterGeneExpr0.010.020.03
filterGroups000
filterPSI0.020.000.02
getAttributesTime000
getDownloadsFolder000
getFirebrowseDateFormat000
getGeneList0.000.020.02
getGtexDataTypes0.030.000.36
getGtexTissues000
getNumerics000
getSampleFromSubject0.000.010.01
getSplicingEventFromGenes000
getSplicingEventTypes000
getSubjectFromSample000
getTCGAdataTypes0.030.020.13
getValidEvents000
groupPerElem000
hchart.survfit0.310.342.70
isFirebrowseUp0.000.000.02
labelBasedOnCutoff000
leveneTest0.010.000.01
listAllAnnotations2.080.342.50
listSplicingAnnotations 9.30 1.3610.92
loadAnnotation2.400.282.71
loadGtexData000
loadLocalFiles000
loadSRAproject000
loadTCGAdata0.020.000.04
missingDataModal000
normaliseGeneExpression0.010.000.02
optimalSurvivalCutoff0.080.000.08
parseCategoricalGroups000
parseFirebrowseMetadata0.080.000.16
parseMatsEvent000
parseMatsGeneric0.030.000.03
parseMisoAnnotation0.120.020.16
parseMisoEvent000
parseMisoEventID0.050.000.04
parseMisoGeneric0.010.000.02
parseMisoId000
parseSplicingEvent000
parseSuppaEvent000
parseSuppaGeneric0.020.000.02
parseTcgaSampleInfo0.010.000.02
parseUrlsFromFirebrowseResponse0.030.000.12
parseVastToolsEvent000
parseVastToolsSE0.030.000.03
performICA0.020.000.02
performPCA000
plot.GEandAScorrelation0.410.030.44
plotDistribution0.670.170.93
plotGeneExprPerSample0.120.100.22
plotGroupIndependence0.170.000.17
plotICA0.110.030.24
plotLibrarySize0.240.120.37
plotPCA0.420.330.78
plotPCAvariance0.130.130.25
plotProtein0.590.141.39
plotRowStats0.50.00.5
plotSingleICA0.230.310.58
plotSplicingEvent0.080.000.08
plotSurvivalCurves0.110.110.24
plotSurvivalPvaluesByCutoff0.410.110.51
plotTranscripts0.030.000.86
prepareAnnotationFromEvents0.230.000.25
prepareFirebrowseArchives000
prepareJunctionQuantSTAR000
prepareSRAmetadata000
processSurvTerms0.020.000.02
psichomics000
quantifySplicing0.030.000.03
queryEnsembl0.030.000.95
queryEnsemblByGene0.200.012.80
queryFirebrowseData0.070.000.22
queryPubMed0.010.000.46
queryUniprot0.100.000.35
readFile000
renameDuplicated000
renderBoxplot0.090.110.20
survdiffTerms000
survfit.survTerms0.030.000.03
testGroupIndependence000
testSurvival0.030.000.03
textSuggestions000
trimWhitespace000