Multiple platform build/check report for BioC 3.11 - CHECK report for cellbaseR on machv2

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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_1.12.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/cellbaseR.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.12.0’
* 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 6.540  1.542  10.315
getTf-CellBaseR-method       0.062  0.002   7.188
* 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	6.540	1.542	10.315
CellBaseParam	0.002	0.000	0.002
CellBaseR	0.053	0.006	0.383
createGeneModel	0.591	0.073	1.230
getCaddScores	0.062	0.003	0.513
getCellBase-CellBaseR-method	0.057	0.004	0.531
getCellBaseResourceHelp	0.289	0.008	0.821
getChromosomeInfo-CellBaseR-method	0.057	0.003	0.534
getClinical-CellBaseR-method	1.103	0.075	1.979
getClinicalByRegion	2.080	0.046	3.667
getConservationByRegion	0.104	0.005	0.783
getGene-CellBaseR-method	0.164	0.004	0.799
getGeneInfo	0.063	0.003	0.620
getMeta-CellBaseR-method	0.066	0.004	0.520
getProtein-CellBaseR-method	0.125	0.002	0.718
getProteinInfo	0.178	0.003	0.842
getRegion-CellBaseR-method	0.166	0.003	0.931
getRegulatoryByRegion	0.202	0.004	1.091
getSnp-CellBaseR-method	0.082	0.002	0.542
getSnpByGene	0.090	0.002	0.581
getTf-CellBaseR-method	0.062	0.002	7.188
getTfbsByRegion	0.087	0.003	0.622
getTranscript-CellBaseR-method	0.067	0.002	0.564
getTranscriptByGene	0.067	0.002	0.543
getVariant-CellBaseR-method	0.178	0.004	0.847
getVariantAnnotation	0.196	0.003	0.816
getXref-CellBaseR-method	0.059	0.001	0.568

CHECK report for cellbaseR on machv2

Summary

Command output

Installation output

Tests output

Example timings