Multiple platform build/check report for BioC 3.10 - CHECK report for RGMQL 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:RGMQL.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RGMQL_1.6.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/RGMQL.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RGMQL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RGMQL’ version ‘1.6.0’
* 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 ‘RGMQL’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 20.0Mb
  sub-directories of 1Mb or more:
    example  19.4Mb
* 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 ... NOTE
File ‘RGMQL/R/onLoad.R’:
  .onLoad calls:
    packageStartupMessage("Check if GMQL credentials are expired... \n")

See section ‘Good practice’ in '?.onAttach'.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
aggr-class   9.209  0.838  14.744
take         6.981  0.677   2.577
show_dataset 0.033  0.007   6.990
* 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-3.10-bioc/meat/RGMQL.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 RGMQL
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘RGMQL’ ...
** 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 (RGMQL)

Tests output

Example timings

name	user	system	elapsed
aggr-class	9.209	0.838	14.744
aggregate	0.130	0.008	0.040
arrange	0.136	0.013	0.043
collect	0.125	0.007	0.042
compile_query	1.388	0.033	2.103
cover-param-class	0.109	0.014	0.167
cover	0.084	0.010	0.065
delete_dataset	0.000	0.000	0.001
distal-class	0.101	0.011	0.147
download_dataset	0	0	0
execute	0.054	0.007	0.040
export_gmql	0.695	0.040	0.810
extend	0.059	0.004	0.045
filter	0.153	0.013	0.105
filter_and_extract	0.626	0.046	0.707
group_by	0.083	0.013	0.083
import_gmql	0.183	0.029	0.213
init_gmql	0.033	0.005	0.201
log_job	0.020	0.001	0.319
login_gmql	0.012	0.001	0.179
logout_gmql	0.024	0.001	0.392
map	0.078	0.008	0.060
merge	0.077	0.006	0.049
operator-class	0.224	0.024	0.149
ordering-class	0.114	0.006	0.048
read-function	0.166	0.008	0.380
register_gmql	0.000	0.000	0.001
remote_processing	0.010	0.001	0.010
run_query	0	0	0
sample_metadata	0.023	0.003	0.516
sample_region	0.001	0.001	0.001
save_query	0.039	0.004	0.872
select	0.075	0.006	0.063
semijoin	0.074	0.006	0.059
setdiff	0.068	0.003	0.065
show_dataset	0.033	0.007	6.990
show_jobs_list	0.015	0.001	0.314
show_queries_list	0.017	0.001	0.319
show_samples_list	0.020	0.001	0.324
show_schema	0.042	0.004	0.328
stop_gmql	0.198	0.058	0.100
stop_job	0.000	0.001	0.000
take	6.981	0.677	2.577
union	0.069	0.004	0.049
upload_dataset	0	0	0

CHECK report for RGMQL on merida1

Summary

Command output

Installation output

Tests output

Example timings