Multiple platform build/check report for BioC 3.13 - CHECK results 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_1.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/cellbaseR.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 ‘cellbaseR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellbaseR’ version ‘1.16.0’
* 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 ... 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 ‘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 6.399  1.558   8.662
* 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-3.13-bioc/meat/cellbaseR.Rcheck/00check.log’
for details.

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/4.1/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	6.399	1.558	8.662
CellBaseParam	0.002	0.001	0.003
CellBaseR	0.040	0.005	0.377
createGeneModel	0.167	0.017	0.879
getCaddScores	0.059	0.005	0.616
getCellBase-CellBaseR-method	0.060	0.006	0.692
getCellBaseResourceHelp	0.274	0.031	0.965
getChromosomeInfo-CellBaseR-method	0.056	0.005	0.645
getClinical-CellBaseR-method	0.892	0.069	1.905
getClinicalByRegion	1.605	0.041	3.030
getConservationByRegion	0.087	0.003	0.917
getGene-CellBaseR-method	0.144	0.004	0.841
getGeneInfo	0.076	0.002	0.694
getMeta-CellBaseR-method	0.073	0.003	0.666
getProtein-CellBaseR-method	0.131	0.003	0.792
getProteinInfo	0.140	0.002	0.841
getRegion-CellBaseR-method	0.134	0.004	1.003
getRegulatoryByRegion	0.170	0.004	1.149
getSnp-CellBaseR-method	0.078	0.002	0.672
getSnpByGene	0.075	0.002	0.636
getTf-CellBaseR-method	0.050	0.002	2.834
getTfbsByRegion	0.079	0.002	0.704
getTranscript-CellBaseR-method	0.068	0.002	0.652
getTranscriptByGene	0.064	0.002	0.619
getVariant-CellBaseR-method	0.166	0.004	0.905
getVariantAnnotation	0.146	0.004	0.915
getXref-CellBaseR-method	0.058	0.001	0.667

CHECK results for cellbaseR on machv2

Summary

Command output

Installation output

Tests output

Example timings