| Back to Build/check report for BioC 3.18: simplified long |
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This page was generated on 2023-05-31 05:44:40 -0000 (Wed, 31 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4219 |
| 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 | ||||
|
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. |
| Package 1553/2197 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.27.0 (landing page) Nuno Saraiva-Agostinho
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | WARNINGS | |||||||||
| Package: psichomics |
| Version: 1.27.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings psichomics_1.27.0.tar.gz |
| StartedAt: 2023-05-30 15:51:53 -0000 (Tue, 30 May 2023) |
| EndedAt: 2023-05-30 16:06:33 -0000 (Tue, 30 May 2023) |
| EllapsedTime: 880.1 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: psichomics.Rcheck |
| Warnings: 1 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.0/bin/R CMD check --install=check:psichomics.install-out.txt --library=/home/biocbuild/R/R-4.3.0/site-library --timings psichomics_1.27.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/psichomics.Rcheck’
* using R version 4.3.0 (2023-04-21)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.27.0’
* 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 11.3.0-1ubuntu1~22.04.1) 11.3.0’
* 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 loading without being on the library search path ... 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 18.681 2.579 30.730
listSplicingAnnotations 14.320 1.054 25.164
loadAnnotation 3.696 0.256 6.001
listAllAnnotations 3.404 0.335 5.778
plotProtein 0.994 0.027 53.291
queryPubMed 0.211 0.004 6.331
queryUniprot 0.052 0.012 45.180
queryFirebrowseData 0.042 0.012 7.685
queryEnsemblByGene 0.034 0.004 22.444
queryEnsembl 0.038 0.000 5.867
plotTranscripts 0.006 0.001 10.006
* 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: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/psichomics.Rcheck/00check.log’
for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.0/site-library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04.1) 11.3.0’ g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c progressBar.cpp -o progressBar.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c psiFastCalc.cpp -o psiFastCalc.o g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.0/site-library/Rcpp/include' -I/usr/local/include -fPIC -g -O2 -c vastToolsParser.cpp -o vastToolsParser.o g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.0/lib -L/usr/local/lib -o psichomics.so RcppExports.o progressBar.o psiFastCalc.o vastToolsParser.o -L/home/biocbuild/R/R-4.3.0/lib -lR installing to /home/biocbuild/R/R-4.3.0/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)
psichomics.Rcheck/tests/spelling.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
0.204 0.033 0.219
psichomics.Rcheck/tests/testthat.Rout
R version 4.3.0 (2023-04-21) -- "Already Tomorrow"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 1.27.0: 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
31.332 2.346 58.007
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0.001 | 0.000 | 0.002 | |
| assignValuePerSubject | 0.020 | 0.003 | 0.025 | |
| blendColours | 0.001 | 0.000 | 0.001 | |
| calculateLoadingsContribution | 0.006 | 0.007 | 0.013 | |
| convertGeneIdentifiers | 18.681 | 2.579 | 30.730 | |
| correlateGEandAS | 0.019 | 0.007 | 0.027 | |
| createGroupByAttribute | 0.001 | 0.000 | 0.001 | |
| createJunctionsTemplate | 0.002 | 0.000 | 0.003 | |
| customRowMeans | 0.001 | 0.000 | 0.002 | |
| diffAnalyses | 0.090 | 0.015 | 0.105 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.029 | 0.000 | 1.019 | |
| filterGeneExpr | 0.009 | 0.000 | 0.009 | |
| filterGroups | 0.002 | 0.000 | 0.002 | |
| filterPSI | 0.018 | 0.000 | 0.018 | |
| getAttributesTime | 0.000 | 0.004 | 0.004 | |
| getDownloadsFolder | 0.000 | 0.000 | 0.001 | |
| getFirebrowseDateFormat | 0.000 | 0.000 | 0.001 | |
| getGeneList | 0.004 | 0.000 | 0.005 | |
| getGtexDataTypes | 0.205 | 0.019 | 2.564 | |
| getGtexTissues | 0 | 0 | 0 | |
| getNumerics | 0.003 | 0.001 | 0.003 | |
| getSampleFromSubject | 0.002 | 0.000 | 0.002 | |
| getSplicingEventFromGenes | 0.001 | 0.004 | 0.005 | |
| getSplicingEventTypes | 0 | 0 | 0 | |
| getSubjectFromSample | 0.000 | 0.001 | 0.000 | |
| getTCGAdataTypes | 0.043 | 0.013 | 3.709 | |
| getValidEvents | 0.005 | 0.000 | 0.004 | |
| groupPerElem | 0.001 | 0.000 | 0.001 | |
| hchart.survfit | 0.305 | 0.128 | 0.479 | |
| isFirebrowseUp | 0.008 | 0.000 | 0.249 | |
| labelBasedOnCutoff | 0.000 | 0.000 | 0.001 | |
| leveneTest | 0.015 | 0.000 | 0.015 | |
| listAllAnnotations | 3.404 | 0.335 | 5.778 | |
| listSplicingAnnotations | 14.320 | 1.054 | 25.164 | |
| loadAnnotation | 3.696 | 0.256 | 6.001 | |
| loadGtexData | 0 | 0 | 0 | |
| loadLocalFiles | 0.001 | 0.000 | 0.001 | |
| loadSRAproject | 0 | 0 | 0 | |
| loadTCGAdata | 0.012 | 0.000 | 0.507 | |
| missingDataModal | 0 | 0 | 0 | |
| normaliseGeneExpression | 0.065 | 0.008 | 0.073 | |
| optimalSurvivalCutoff | 0.128 | 0.004 | 0.132 | |
| parseCategoricalGroups | 0.001 | 0.000 | 0.001 | |
| parseFirebrowseMetadata | 0.053 | 0.004 | 1.289 | |
| parseMatsEvent | 0.006 | 0.000 | 0.007 | |
| parseMatsGeneric | 0.027 | 0.000 | 0.027 | |
| parseMisoAnnotation | 0.170 | 0.012 | 0.195 | |
| parseMisoEvent | 0.005 | 0.000 | 0.005 | |
| parseMisoEventID | 0.008 | 0.000 | 0.008 | |
| parseMisoGeneric | 0.042 | 0.000 | 0.042 | |
| parseMisoId | 0.001 | 0.000 | 0.000 | |
| parseSplicingEvent | 0.002 | 0.004 | 0.005 | |
| parseSuppaEvent | 0.005 | 0.000 | 0.005 | |
| parseSuppaGeneric | 0.026 | 0.000 | 0.025 | |
| parseTcgaSampleInfo | 0.005 | 0.000 | 0.005 | |
| parseUrlsFromFirebrowseResponse | 0.042 | 0.000 | 0.798 | |
| parseVastToolsEvent | 0.008 | 0.000 | 0.008 | |
| parseVastToolsSE | 0.026 | 0.000 | 0.026 | |
| performICA | 0.006 | 0.004 | 0.009 | |
| performPCA | 0.002 | 0.000 | 0.002 | |
| plot.GEandAScorrelation | 0.564 | 0.040 | 0.605 | |
| plotDistribution | 0.920 | 0.028 | 0.948 | |
| plotGeneExprPerSample | 0.122 | 0.012 | 0.134 | |
| plotGroupIndependence | 0.244 | 0.016 | 0.260 | |
| plotICA | 0.160 | 0.000 | 0.165 | |
| plotLibrarySize | 0.247 | 0.008 | 0.255 | |
| plotPCA | 0.298 | 0.036 | 0.334 | |
| plotPCAvariance | 0.055 | 0.012 | 0.067 | |
| plotProtein | 0.994 | 0.027 | 53.291 | |
| plotRowStats | 0.560 | 0.019 | 0.580 | |
| plotSingleICA | 0.250 | 0.023 | 0.274 | |
| plotSplicingEvent | 0.059 | 0.001 | 0.059 | |
| plotSurvivalCurves | 0.108 | 0.007 | 0.116 | |
| plotSurvivalPvaluesByCutoff | 0.530 | 0.043 | 0.574 | |
| plotTranscripts | 0.006 | 0.001 | 10.006 | |
| prepareAnnotationFromEvents | 0.270 | 0.016 | 0.286 | |
| prepareFirebrowseArchives | 0 | 0 | 0 | |
| prepareJunctionQuantSTAR | 0.000 | 0.000 | 0.001 | |
| prepareSRAmetadata | 0 | 0 | 0 | |
| processSurvTerms | 0.011 | 0.000 | 0.011 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.011 | 0.003 | 0.014 | |
| queryEnsembl | 0.038 | 0.000 | 5.867 | |
| queryEnsemblByGene | 0.034 | 0.004 | 22.444 | |
| queryFirebrowseData | 0.042 | 0.012 | 7.685 | |
| queryPubMed | 0.211 | 0.004 | 6.331 | |
| queryUniprot | 0.052 | 0.012 | 45.180 | |
| readFile | 0.001 | 0.000 | 0.001 | |
| renameDuplicated | 0 | 0 | 0 | |
| renderBoxplot | 0.111 | 0.008 | 0.118 | |
| survdiffTerms | 0.004 | 0.004 | 0.008 | |
| survfit.survTerms | 0.027 | 0.000 | 0.028 | |
| testGroupIndependence | 0.004 | 0.000 | 0.004 | |
| testSurvival | 0.022 | 0.004 | 0.026 | |
| textSuggestions | 0.000 | 0.000 | 0.001 | |
| trimWhitespace | 0 | 0 | 0 | |