| Back to Multiple platform build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-09-21 11:36:31 -0400 (Thu, 21 Sep 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4625 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4378 |
| merida1 | macOS 12.6.4 Monterey | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4394 |
| 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 1580/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.26.0 (landing page) Nuno Saraiva-Agostinho
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | WARNINGS |  | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.6.4 Monterey / x86_64 | OK | OK | WARNINGS | NA | |||||||||
|
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. |
| Package: psichomics |
| Version: 1.26.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.26.0.tar.gz |
| StartedAt: 2023-09-21 06:59:24 -0400 (Thu, 21 Sep 2023) |
| EndedAt: 2023-09-21 07:19:56 -0400 (Thu, 21 Sep 2023) |
| EllapsedTime: 1231.4 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: psichomics.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings psichomics_1.26.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/psichomics.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.26.0’
* 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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
convertGeneIdentifiers 25.508 2.787 42.183
listSplicingAnnotations 21.224 2.367 38.281
loadAnnotation 5.385 0.565 8.807
listAllAnnotations 4.324 0.556 7.612
ensemblToUniprot 0.034 0.004 6.538
plotTranscripts 0.035 0.003 7.018
* 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
‘/Users/biocbuild/bbs-3.17-bioc/meat/psichomics.Rcheck/00check.log’
for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c progressBar.cpp -o progressBar.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c psiFastCalc.cpp -o psiFastCalc.o clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vastToolsParser.cpp -o vastToolsParser.o clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/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)
psichomics.Rcheck/tests/spelling.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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
0.358 0.131 0.609
psichomics.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (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 1.26.0: 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
45.632 3.091 76.316
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0.002 | 0.001 | 0.003 | |
| assignValuePerSubject | 0.036 | 0.019 | 0.069 | |
| blendColours | 0.001 | 0.000 | 0.001 | |
| calculateLoadingsContribution | 0.017 | 0.006 | 0.046 | |
| convertGeneIdentifiers | 25.508 | 2.787 | 42.183 | |
| correlateGEandAS | 0.037 | 0.014 | 0.081 | |
| createGroupByAttribute | 0.001 | 0.001 | 0.003 | |
| createJunctionsTemplate | 0.004 | 0.002 | 0.011 | |
| customRowMeans | 0.002 | 0.001 | 0.010 | |
| diffAnalyses | 0.167 | 0.022 | 0.327 | |
| downloadFiles | 0.001 | 0.001 | 0.001 | |
| ensemblToUniprot | 0.034 | 0.004 | 6.538 | |
| filterGeneExpr | 0.012 | 0.003 | 0.016 | |
| filterGroups | 0.003 | 0.001 | 0.003 | |
| filterPSI | 0.028 | 0.008 | 0.037 | |
| getAttributesTime | 0.005 | 0.001 | 0.005 | |
| getDownloadsFolder | 0.000 | 0.000 | 0.001 | |
| getFirebrowseDateFormat | 0.000 | 0.000 | 0.002 | |
| getGeneList | 0.006 | 0.002 | 0.008 | |
| getGtexDataTypes | 0.052 | 0.004 | 0.359 | |
| getGtexTissues | 0.000 | 0.001 | 0.000 | |
| getNumerics | 0.004 | 0.001 | 0.005 | |
| getSampleFromSubject | 0.001 | 0.000 | 0.003 | |
| getSplicingEventFromGenes | 0.007 | 0.002 | 0.008 | |
| getSplicingEventTypes | 0.000 | 0.001 | 0.001 | |
| getSubjectFromSample | 0.001 | 0.000 | 0.002 | |
| getTCGAdataTypes | 0.044 | 0.005 | 0.237 | |
| getValidEvents | 0.008 | 0.002 | 0.010 | |
| groupPerElem | 0.002 | 0.001 | 0.002 | |
| hchart.survfit | 0.543 | 0.216 | 1.118 | |
| isFirebrowseUp | 0.008 | 0.001 | 0.039 | |
| labelBasedOnCutoff | 0.001 | 0.001 | 0.002 | |
| leveneTest | 0.014 | 0.001 | 0.016 | |
| listAllAnnotations | 4.324 | 0.556 | 7.612 | |
| listSplicingAnnotations | 21.224 | 2.367 | 38.281 | |
| loadAnnotation | 5.385 | 0.565 | 8.807 | |
| loadGtexData | 0.000 | 0.001 | 0.002 | |
| loadLocalFiles | 0.000 | 0.001 | 0.005 | |
| loadSRAproject | 0.000 | 0.000 | 0.001 | |
| loadTCGAdata | 0.013 | 0.005 | 0.091 | |
| missingDataModal | 0.000 | 0.001 | 0.001 | |
| normaliseGeneExpression | 0.041 | 0.005 | 0.047 | |
| optimalSurvivalCutoff | 0.220 | 0.005 | 0.337 | |
| parseCategoricalGroups | 0.002 | 0.001 | 0.005 | |
| parseFirebrowseMetadata | 0.062 | 0.011 | 0.269 | |
| parseMatsEvent | 0.011 | 0.002 | 0.013 | |
| parseMatsGeneric | 0.045 | 0.006 | 0.053 | |
| parseMisoAnnotation | 0.303 | 0.028 | 0.634 | |
| parseMisoEvent | 0.008 | 0.002 | 0.014 | |
| parseMisoEventID | 0.012 | 0.006 | 0.030 | |
| parseMisoGeneric | 0.072 | 0.010 | 0.126 | |
| parseMisoId | 0.001 | 0.001 | 0.001 | |
| parseSplicingEvent | 0.010 | 0.004 | 0.023 | |
| parseSuppaEvent | 0.008 | 0.003 | 0.017 | |
| parseSuppaGeneric | 0.044 | 0.006 | 0.073 | |
| parseTcgaSampleInfo | 0.008 | 0.003 | 0.021 | |
| parseUrlsFromFirebrowseResponse | 0.040 | 0.002 | 0.230 | |
| parseVastToolsEvent | 0.012 | 0.002 | 0.014 | |
| parseVastToolsSE | 0.041 | 0.003 | 0.044 | |
| performICA | 0.012 | 0.009 | 0.027 | |
| performPCA | 0.003 | 0.001 | 0.004 | |
| plot.GEandAScorrelation | 0.931 | 0.049 | 1.598 | |
| plotDistribution | 1.688 | 0.184 | 3.086 | |
| plotGeneExprPerSample | 0.201 | 0.075 | 0.478 | |
| plotGroupIndependence | 0.345 | 0.008 | 0.589 | |
| plotICA | 0.271 | 0.024 | 0.491 | |
| plotLibrarySize | 0.525 | 0.077 | 1.015 | |
| plotPCA | 0.548 | 0.272 | 1.356 | |
| plotPCAvariance | 0.104 | 0.069 | 0.270 | |
| plotProtein | 1.441 | 0.180 | 3.102 | |
| plotRowStats | 0.929 | 0.038 | 1.556 | |
| plotSingleICA | 0.446 | 0.201 | 1.136 | |
| plotSplicingEvent | 0.112 | 0.004 | 0.194 | |
| plotSurvivalCurves | 0.174 | 0.070 | 0.434 | |
| plotSurvivalPvaluesByCutoff | 1.038 | 0.097 | 1.695 | |
| plotTranscripts | 0.035 | 0.003 | 7.018 | |
| prepareAnnotationFromEvents | 0.375 | 0.014 | 0.451 | |
| prepareFirebrowseArchives | 0.000 | 0.001 | 0.002 | |
| prepareJunctionQuantSTAR | 0.000 | 0.000 | 0.009 | |
| prepareSRAmetadata | 0.001 | 0.000 | 0.007 | |
| processSurvTerms | 0.019 | 0.002 | 0.031 | |
| psichomics | 0.000 | 0.001 | 0.001 | |
| quantifySplicing | 0.025 | 0.013 | 0.066 | |
| queryEnsembl | 0.050 | 0.009 | 0.502 | |
| queryEnsemblByGene | 0.184 | 0.046 | 2.605 | |
| queryFirebrowseData | 0.061 | 0.004 | 0.334 | |
| queryPubMed | 0.066 | 0.022 | 0.646 | |
| queryUniprot | 0.082 | 0.002 | 0.362 | |
| readFile | 0.002 | 0.001 | 0.003 | |
| renameDuplicated | 0.001 | 0.001 | 0.002 | |
| renderBoxplot | 0.171 | 0.065 | 0.301 | |
| survdiffTerms | 0.012 | 0.002 | 0.022 | |
| survfit.survTerms | 0.038 | 0.003 | 0.072 | |
| testGroupIndependence | 0.005 | 0.001 | 0.006 | |
| testSurvival | 0.034 | 0.002 | 0.065 | |
| textSuggestions | 0.001 | 0.000 | 0.006 | |
| trimWhitespace | 0.001 | 0.001 | 0.002 | |