Multiple platform build/check report for BioC 3.7 - 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_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/RGMQL.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.2’
* 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   8.921  0.873   4.247
take         7.189  0.720   2.550
show_dataset 0.076  0.013   7.957
* 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-3.7-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/3.5/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	8.921	0.873	4.247
aggregate	0.138	0.008	0.042
arrange	0.151	0.007	0.046
collect	0.129	0.005	0.037
compile_query	1.747	0.042	1.904
cover-param-class	0.100	0.013	0.076
cover	0.083	0.011	0.062
delete_dataset	0.002	0.000	0.002
distal-class	0.107	0.014	0.102
download_dataset	0.002	0.001	0.001
execute	0.056	0.007	0.040
export_gmql	0.620	0.026	0.650
extend	0.047	0.003	0.033
filter	0.149	0.012	0.101
filter_and_extract	0.991	0.023	1.026
group_by	0.080	0.006	0.070
import_gmql	0.110	0.001	0.111
log_job	0.023	0.001	0.343
login_gmql	0.013	0.000	0.214
logout_gmql	0.027	0.001	0.445
map	0.081	0.006	0.059
merge	0.086	0.005	0.061
operator-class	0.202	0.023	0.140
ordering-class	0.133	0.006	0.063
read-function	0.136	0.008	0.390
register_gmql	0.003	0.000	0.002
remote_processing	0.024	0.001	0.010
run_query	0.003	0.000	0.002
sample_metadata	0.021	0.003	0.638
sample_region	0.002	0.000	0.003
save_query	0.045	0.005	0.878
select	0.088	0.008	0.062
semijoin	0.076	0.009	0.064
setdiff	0.072	0.007	0.070
show_dataset	0.076	0.013	7.957
show_jobs_list	0.021	0.001	0.357
show_queries_list	0.022	0.001	0.485
show_samples_list	0.023	0.002	0.391
show_schema	0.023	0.003	0.371
stop_gmql	0.187	0.064	0.104
stop_job	0.002	0.001	0.002
take	7.189	0.720	2.550
union	0.105	0.023	0.049
upload_dataset	0.008	0.000	0.002

CHECK report for RGMQL on merida2

Summary

Command output

Installation output

Tests output

Example timings