Nuno Saraiva-Agostinho
| Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021) |
| URL: https://git.bioconductor.org/packages/psichomics |
| Branch: RELEASE_3_12 |
| Last Commit: 7b7d873 |
| Last Changed Date: 2020-10-27 11:18:41 -0400 (Tue, 27 Oct 2020) |
| Back to Multiple platform build/check report for BioC 3.12 |
|
This page was generated on 2021-05-06 12:36:13 -0400 (Thu, 06 May 2021).
|
To the developers/maintainers of the psichomics package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1408/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| psichomics 1.16.0 (landing page) Nuno Saraiva-Agostinho
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: psichomics |
| Version: 1.16.0 |
| 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_1.16.0.tar.gz |
| StartedAt: 2021-05-06 04:59:46 -0400 (Thu, 06 May 2021) |
| EndedAt: 2021-05-06 05:07:59 -0400 (Thu, 06 May 2021) |
| EllapsedTime: 493.3 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_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/psichomics.Rcheck’ * using R version 4.0.5 (2021-03-31) * 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 ‘1.16.0’ * 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 ... OK * 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 * 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 NOTE See ‘/Users/biocbuild/bbs-3.12-bioc/meat/psichomics.Rcheck/00check.log’ for details.
psichomics.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL psichomics
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘psichomics’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
In file included from RcppExports.cpp:4:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I/usr/local/include -fPIC -Wall -g -O2 -c psiFastCalc.cpp -o psiFastCalc.o
In file included from psiFastCalc.cpp:1:
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp.h:57:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include/Rcpp/DataFrame.h:136:18: warning: unused variable 'data' [-Wunused-variable]
SEXP data = Parent::get__();
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -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 psiFastCalc.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/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 4.0.5 (2021-03-31) -- "Shake and Throw"
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
0.274 0.066 0.316
psichomics.Rcheck/tests/testthat.Rout
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
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 1.16.0: 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
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)
• On CRAN (1)
[ FAIL 0 | WARN 0 | SKIP 2 | PASS 1396 ]
>
> proc.time()
user system elapsed
28.161 1.255 37.794
psichomics.Rcheck/psichomics-Ex.timings
| name | user | system | elapsed | |
| addObjectAttrs | 0.000 | 0.001 | 0.001 | |
| assignValuePerSubject | 0.022 | 0.008 | 0.030 | |
| blendColours | 0.001 | 0.001 | 0.001 | |
| calculateLoadingsContribution | 0.010 | 0.002 | 0.013 | |
| convertGeneIdentifiers | 0.460 | 0.022 | 0.483 | |
| correlateGEandAS | 0.025 | 0.005 | 0.030 | |
| createGroupByAttribute | 0.002 | 0.000 | 0.001 | |
| createJunctionsTemplate | 0.003 | 0.001 | 0.005 | |
| customRowMeans | 0.001 | 0.001 | 0.002 | |
| diffAnalyses | 0.134 | 0.010 | 0.144 | |
| downloadFiles | 0 | 0 | 0 | |
| ensemblToUniprot | 0.305 | 0.017 | 0.685 | |
| filterGeneExpr | 0.009 | 0.001 | 0.011 | |
| filterGroups | 0.001 | 0.001 | 0.001 | |
| filterPSI | 0.018 | 0.004 | 0.022 | |
| getAttributesTime | 0.004 | 0.000 | 0.005 | |
| getDownloadsFolder | 0.000 | 0.000 | 0.001 | |
| getFirebrowseDateFormat | 0.001 | 0.000 | 0.001 | |
| getGeneList | 0.004 | 0.000 | 0.005 | |
| getGtexDataTypes | 0.030 | 0.003 | 0.400 | |
| getGtexTissues | 0 | 0 | 0 | |
| getNumerics | 0.004 | 0.000 | 0.005 | |
| getSampleFromSubject | 0.002 | 0.001 | 0.003 | |
| getSplicingEventFromGenes | 0.005 | 0.001 | 0.007 | |
| getSplicingEventTypes | 0.000 | 0.000 | 0.001 | |
| getSubjectFromSample | 0.001 | 0.000 | 0.001 | |
| getTCGAdataTypes | 0.051 | 0.006 | 0.196 | |
| getValidEvents | 0.004 | 0.001 | 0.005 | |
| groupPerElem | 0.001 | 0.001 | 0.001 | |
| hchart.survfit | 0.329 | 0.136 | 0.486 | |
| isFirebrowseUp | 0.006 | 0.001 | 0.039 | |
| labelBasedOnCutoff | 0.001 | 0.000 | 0.002 | |
| leveneTest | 0.012 | 0.001 | 0.013 | |
| listAllAnnotations | 0.001 | 0.000 | 0.002 | |
| listSplicingAnnotations | 0.004 | 0.000 | 0.004 | |
| loadAnnotation | 0.001 | 0.000 | 0.001 | |
| loadGtexData | 0.001 | 0.000 | 0.000 | |
| loadLocalFiles | 0 | 0 | 0 | |
| loadTCGAdata | 0.010 | 0.002 | 0.045 | |
| missingDataModal | 0.001 | 0.001 | 0.001 | |
| normaliseGeneExpression | 0.033 | 0.004 | 0.037 | |
| optimalSurvivalCutoff | 0.151 | 0.003 | 0.155 | |
| parseCategoricalGroups | 0.001 | 0.001 | 0.001 | |
| parseFirebrowseMetadata | 0.051 | 0.004 | 0.222 | |
| parseMatsEvent | 0.007 | 0.001 | 0.009 | |
| parseMatsGeneric | 0.031 | 0.003 | 0.034 | |
| parseMisoAnnotation | 0.234 | 0.021 | 0.261 | |
| parseMisoEvent | 0.006 | 0.000 | 0.006 | |
| parseMisoEventID | 0.007 | 0.001 | 0.009 | |
| parseMisoGeneric | 0.054 | 0.004 | 0.058 | |
| parseMisoId | 0.000 | 0.000 | 0.001 | |
| parseSplicingEvent | 0.008 | 0.002 | 0.009 | |
| parseSuppaEvent | 0.008 | 0.001 | 0.008 | |
| parseSuppaGeneric | 0.033 | 0.017 | 0.118 | |
| parseTcgaSampleInfo | 0.005 | 0.001 | 0.006 | |
| parseUrlsFromFirebrowseResponse | 0.036 | 0.007 | 0.186 | |
| parseVastToolsEvent | 0.012 | 0.002 | 0.013 | |
| parseVastToolsSE | 0.030 | 0.003 | 0.033 | |
| performICA | 0.009 | 0.007 | 0.015 | |
| performPCA | 0.001 | 0.000 | 0.003 | |
| plot.GEandAScorrelation | 0.434 | 0.013 | 0.448 | |
| plotDistribution | 0.848 | 0.107 | 0.960 | |
| plotGeneExprPerSample | 0.129 | 0.047 | 0.179 | |
| plotGroupIndependence | 0.145 | 0.002 | 0.147 | |
| plotICA | 0.170 | 0.015 | 0.188 | |
| plotLibrarySize | 0.277 | 0.041 | 0.322 | |
| plotPCA | 0.461 | 0.175 | 0.654 | |
| plotPCAvariance | 0.075 | 0.041 | 0.120 | |
| plotProtein | 0.783 | 0.101 | 1.656 | |
| plotRowStats | 1.303 | 0.015 | 1.320 | |
| plotSingleICA | 0.284 | 0.139 | 0.434 | |
| plotSplicingEvent | 1.005 | 0.009 | 1.016 | |
| plotSurvivalCurves | 0.118 | 0.047 | 0.168 | |
| plotSurvivalPvaluesByCutoff | 0.736 | 0.051 | 0.792 | |
| plotTranscripts | 0.026 | 0.001 | 2.032 | |
| prepareAnnotationFromEvents | 0.270 | 0.008 | 0.278 | |
| prepareFirebrowseArchives | 0.000 | 0.000 | 0.001 | |
| prepareJunctionQuantSTAR | 0.001 | 0.000 | 0.001 | |
| prepareSRAmetadata | 0.000 | 0.000 | 0.001 | |
| processSurvTerms | 0.014 | 0.001 | 0.014 | |
| psichomics | 0 | 0 | 0 | |
| quantifySplicing | 0.016 | 0.004 | 0.020 | |
| queryEnsembl | 0.042 | 0.003 | 0.946 | |
| queryEnsemblByGene | 0.197 | 0.022 | 3.253 | |
| queryFirebrowseData | 0.048 | 0.002 | 0.266 | |
| queryPubMed | 0.077 | 0.014 | 0.526 | |
| queryUniprot | 0.154 | 0.005 | 0.711 | |
| readFile | 0.001 | 0.001 | 0.002 | |
| renameDuplicated | 0.001 | 0.000 | 0.001 | |
| renderBoxplot | 0.132 | 0.053 | 0.188 | |
| survdiffTerms | 0.008 | 0.001 | 0.008 | |
| survfit.survTerms | 0.023 | 0.001 | 0.025 | |
| testGroupIndependence | 0.004 | 0.000 | 0.004 | |
| testSurvival | 0.019 | 0.000 | 0.020 | |
| textSuggestions | 0.001 | 0.000 | 0.001 | |
| trimWhitespace | 0.000 | 0.000 | 0.001 | |