Multiple platform build/check report for BioC 3.9 - CHECK report for RGMQL on merida2

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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_1.3.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RGMQL.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* 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 ‘1.3.0’
* 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    7.197  0.829  46.735
take          6.914  0.631   2.469
show_dataset  1.877  0.089  11.934
compile_query 0.397  0.019   6.322
* 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-3.9-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’ ...
** 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
* DONE (RGMQL)

Tests output

Example timings

name	user	system	elapsed
aggr-class	7.197	0.829	46.735
aggregate	0.067	0.005	0.035
arrange	0.056	0.005	0.043
collect	0.052	0.004	0.041
compile_query	0.397	0.019	6.322
cover-param-class	0.107	0.012	0.077
cover	0.076	0.009	0.060
delete_dataset	0.000	0.000	0.001
distal-class	0.102	0.010	0.093
download_dataset	0.000	0.000	0.001
execute	0.055	0.007	0.038
export_gmql	0.602	0.068	0.675
extend	0.061	0.008	0.053
filter	0.164	0.018	0.129
filter_and_extract	0.590	0.082	0.684
group_by	0.087	0.006	0.077
import_gmql	0.156	0.001	0.158
init_gmql	0.032	0.001	0.212
log_job	0.022	0.002	0.316
login_gmql	0.013	0.000	0.180
map	0.081	0.006	0.062
merge	0.083	0.005	0.054
operator-class	0.203	0.020	0.141
ordering-class	0.101	0.004	0.046
read-function	0.170	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	0.022	0.002	0.477
sample_region	0.000	0.000	0.001
save_query	0.051	0.002	0.854
select	0.082	0.006	0.070
semijoin	0.091	0.007	0.059
setdiff	0.077	0.004	0.063
show_dataset	1.877	0.089	11.934
show_jobs_list	0.021	0.001	0.331
show_queries_list	0.019	0.001	0.324
show_samples_list	0.024	0.001	0.330
show_schema	0.024	0.001	0.326
stop_gmql	0.200	0.060	0.111
stop_job	0	0	0
take	6.914	0.631	2.469
union	0.061	0.004	0.046
upload_dataset	0.000	0.000	0.001

CHECK report for RGMQL on merida2

Summary

Command output

Installation output

Tests output

Example timings