| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:47 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the psichomics package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1454/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.18.6 (landing page) Nuno Saraiva-Agostinho
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: psichomics |
| Version: 1.18.6 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psichomics_1.18.6.tar.gz |
| StartedAt: 2021-10-14 22:38:22 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 22:46:58 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 515.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: psichomics.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:psichomics.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings psichomics_1.18.6.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/psichomics.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘psichomics/DESCRIPTION’ ... OK
* this is package ‘psichomics’ version ‘1.18.6’
* 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:
.git_fetch_output.txt
.git_merge_output.txt
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
* 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 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 ... 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 27.528 1.37 31.242
* 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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/psichomics.Rcheck/00check.log’
for details.
psichomics.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL psichomics ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘psichomics’ ... ** using staged installation ** libs clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c progressBar.cpp -o progressBar.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c psiFastCalc.cpp -o psiFastCalc.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c vastToolsParser.cpp -o vastToolsParser.o clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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
0.309 0.069 0.354
psichomics.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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 1.18.6: 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
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (2)
• On CRAN (1)
[ FAIL 0 | WARN 0 | SKIP 3 | PASS 1396 ]
>
> proc.time()
user system elapsed
29.145 1.314 36.578
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0.002 | 0.001 | 0.002 | |
| assignValuePerSubject | 0.026 | 0.009 | 0.037 | |
| blendColours | 0.002 | 0.000 | 0.001 | |
| calculateLoadingsContribution | 0.017 | 0.005 | 0.023 | |
| convertGeneIdentifiers | 27.528 | 1.370 | 31.242 | |
| correlateGEandAS | 0.021 | 0.006 | 0.026 | |
| createGroupByAttribute | 0.002 | 0.001 | 0.003 | |
| createJunctionsTemplate | 0.004 | 0.001 | 0.005 | |
| customRowMeans | 0.000 | 0.000 | 0.001 | |
| diffAnalyses | 0.135 | 0.010 | 0.146 | |
| downloadFiles | 0.000 | 0.001 | 0.001 | |
| ensemblToUniprot | 0.316 | 0.014 | 0.880 | |
| filterGeneExpr | 0.011 | 0.002 | 0.013 | |
| filterGroups | 0.002 | 0.000 | 0.003 | |
| filterPSI | 0.021 | 0.005 | 0.026 | |
| getAttributesTime | 0.003 | 0.001 | 0.003 | |
| getDownloadsFolder | 0.001 | 0.001 | 0.001 | |
| getFirebrowseDateFormat | 0.000 | 0.001 | 0.001 | |
| getGeneList | 0.004 | 0.001 | 0.005 | |
| getGtexDataTypes | 0.089 | 0.005 | 0.441 | |
| getGtexTissues | 0.000 | 0.000 | 0.001 | |
| getNumerics | 0.005 | 0.000 | 0.006 | |
| getSampleFromSubject | 0.002 | 0.000 | 0.002 | |
| getSplicingEventFromGenes | 0.004 | 0.001 | 0.004 | |
| getSplicingEventTypes | 0.000 | 0.001 | 0.001 | |
| getSubjectFromSample | 0.001 | 0.001 | 0.001 | |
| getTCGAdataTypes | 0.099 | 0.008 | 0.318 | |
| getValidEvents | 0.006 | 0.002 | 0.009 | |
| groupPerElem | 0.001 | 0.001 | 0.001 | |
| hchart.survfit | 0.405 | 0.138 | 0.555 | |
| isFirebrowseUp | 0.008 | 0.001 | 0.049 | |
| labelBasedOnCutoff | 0.001 | 0.001 | 0.001 | |
| leveneTest | 0.012 | 0.000 | 0.012 | |
| listAllAnnotations | 0.001 | 0.000 | 0.001 | |
| listSplicingAnnotations | 0.002 | 0.001 | 0.003 | |
| loadAnnotation | 0.001 | 0.000 | 0.001 | |
| loadGtexData | 0.000 | 0.000 | 0.001 | |
| loadLocalFiles | 0 | 0 | 0 | |
| loadSRAproject | 0 | 0 | 0 | |
| loadTCGAdata | 0.009 | 0.001 | 0.054 | |
| missingDataModal | 0.000 | 0.000 | 0.001 | |
| normaliseGeneExpression | 0.037 | 0.002 | 0.039 | |
| optimalSurvivalCutoff | 0.175 | 0.001 | 0.176 | |
| parseCategoricalGroups | 0.002 | 0.000 | 0.001 | |
| parseFirebrowseMetadata | 0.057 | 0.005 | 0.315 | |
| parseMatsEvent | 0.010 | 0.001 | 0.011 | |
| parseMatsGeneric | 0.041 | 0.004 | 0.044 | |
| parseMisoAnnotation | 0.179 | 0.012 | 0.195 | |
| parseMisoEvent | 0.008 | 0.000 | 0.009 | |
| parseMisoEventID | 0.006 | 0.002 | 0.008 | |
| parseMisoGeneric | 0.049 | 0.004 | 0.053 | |
| parseMisoId | 0.000 | 0.000 | 0.001 | |
| parseSplicingEvent | 0.009 | 0.002 | 0.011 | |
| parseSuppaEvent | 0.007 | 0.001 | 0.008 | |
| parseSuppaGeneric | 0.032 | 0.002 | 0.033 | |
| parseTcgaSampleInfo | 0.004 | 0.001 | 0.005 | |
| parseUrlsFromFirebrowseResponse | 0.035 | 0.001 | 0.187 | |
| parseVastToolsEvent | 0.012 | 0.001 | 0.012 | |
| parseVastToolsSE | 0.029 | 0.002 | 0.031 | |
| performICA | 0.011 | 0.005 | 0.017 | |
| performPCA | 0.002 | 0.001 | 0.003 | |
| plot.GEandAScorrelation | 0.529 | 0.012 | 0.542 | |
| plotDistribution | 1.144 | 0.086 | 1.238 | |
| plotGeneExprPerSample | 0.131 | 0.043 | 0.181 | |
| plotGroupIndependence | 0.189 | 0.003 | 0.192 | |
| plotICA | 0.209 | 0.016 | 0.227 | |
| plotLibrarySize | 0.250 | 0.040 | 0.291 | |
| plotPCA | 0.390 | 0.163 | 0.570 | |
| plotPCAvariance | 0.076 | 0.044 | 0.238 | |
| plotProtein | 1.066 | 0.103 | 3.077 | |
| plotRowStats | 0.473 | 0.009 | 0.482 | |
| plotSingleICA | 0.321 | 0.126 | 0.459 | |
| plotSplicingEvent | 0.091 | 0.001 | 0.092 | |
| plotSurvivalCurves | 0.147 | 0.048 | 0.244 | |
| plotSurvivalPvaluesByCutoff | 0.653 | 0.048 | 0.705 | |
| plotTranscripts | 0.028 | 0.001 | 0.982 | |
| prepareAnnotationFromEvents | 0.197 | 0.006 | 0.203 | |
| prepareFirebrowseArchives | 0.000 | 0.000 | 0.001 | |
| prepareJunctionQuantSTAR | 0 | 0 | 0 | |
| prepareSRAmetadata | 0.000 | 0.001 | 0.001 | |
| processSurvTerms | 0.012 | 0.001 | 0.013 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.019 | 0.009 | 0.029 | |
| queryEnsembl | 0.047 | 0.006 | 0.601 | |
| queryEnsemblByGene | 0.177 | 0.032 | 2.838 | |
| queryFirebrowseData | 0.056 | 0.002 | 0.353 | |
| queryPubMed | 0.099 | 0.015 | 0.612 | |
| queryUniprot | 0.083 | 0.005 | 1.501 | |
| readFile | 0.001 | 0.000 | 0.001 | |
| renameDuplicated | 0.001 | 0.000 | 0.001 | |
| renderBoxplot | 0.107 | 0.035 | 0.142 | |
| survdiffTerms | 0.007 | 0.002 | 0.009 | |
| survfit.survTerms | 0.032 | 0.001 | 0.034 | |
| testGroupIndependence | 0.005 | 0.000 | 0.006 | |
| testSurvival | 0.026 | 0.001 | 0.028 | |
| textSuggestions | 0.001 | 0.000 | 0.001 | |
| trimWhitespace | 0.001 | 0.001 | 0.001 | |