Multiple platform build/check report for BioC 3.12 - CHECK report for cellbaseR on merida1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cellbaseR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cellbaseR_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/cellbaseR.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 ‘cellbaseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellbaseR’ version ‘1.14.0’
* 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 ‘cellbaseR’ 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
AnnotateVcf-CellBaseR-method 13.483  3.764  16.927
* 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: OK

Installation output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cellbaseR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘cellbaseR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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 (cellbaseR)

Tests output

Example timings

name	user	system	elapsed
AnnotateVcf-CellBaseR-method	13.483	3.764	16.927
CellBaseParam	0.002	0.001	0.002
CellBaseR	0.043	0.005	0.346
createGeneModel	0.914	0.562	0.844
getCaddScores	0.057	0.006	0.552
getCellBase-CellBaseR-method	0.058	0.015	0.564
getCellBaseResourceHelp	0.260	0.033	0.870
getChromosomeInfo-CellBaseR-method	0.062	0.006	0.557
getClinical-CellBaseR-method	0.913	0.053	1.804
getClinicalByRegion	1.769	0.058	3.092
getConservationByRegion	0.084	0.003	0.743
getGene-CellBaseR-method	0.518	0.012	1.160
getGeneInfo	0.069	0.002	0.568
getMeta-CellBaseR-method	0.070	0.003	0.559
getProtein-CellBaseR-method	0.142	0.002	0.734
getProteinInfo	0.131	0.002	0.813
getRegion-CellBaseR-method	0.126	0.005	0.844
getRegulatoryByRegion	0.164	0.003	1.023
getSnp-CellBaseR-method	0.074	0.002	0.567
getSnpByGene	0.083	0.003	0.590
getTf-CellBaseR-method	0.060	0.002	2.853
getTfbsByRegion	0.082	0.002	0.611
getTranscript-CellBaseR-method	0.063	0.001	0.559
getTranscriptByGene	0.056	0.002	0.551
getVariant-CellBaseR-method	0.173	0.004	0.831
getVariantAnnotation	0.144	0.002	0.795
getXref-CellBaseR-method	0.050	0.002	0.540

CHECK report for cellbaseR on merida1

Summary

Command output

Installation output

Tests output

Example timings