Multiple platform build/check report for BioC 3.9 - CHECK report for RGMQL on malbec2

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings RGMQL_1.3.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RGMQL.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 20.1Mb
  sub-directories of 1Mb or more:
    example  19.5Mb
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
aggr-class   9.428  0.457  15.309
take         5.711  0.211   7.089
show_dataset 0.075  0.013  11.236
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/RGMQL.Rcheck/00check.log’
for details.

Installation output

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL RGMQL
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	9.428	0.457	15.309
aggregate	0.039	0.004	0.033
arrange	0.061	0.000	0.041
collect	0.058	0.000	0.046
compile_query	0.260	0.004	1.651
cover-param-class	0.102	0.007	0.064
cover	0.064	0.000	0.048
delete_dataset	0.001	0.000	0.000
distal-class	0.092	0.000	0.219
download_dataset	0	0	0
execute	0.045	0.003	0.030
export_gmql	0.579	0.084	0.944
extend	0.048	0.004	0.040
filter	0.128	0.015	0.101
filter_and_extract	0.535	0.040	1.234
group_by	0.126	0.011	0.074
import_gmql	0.182	0.020	0.099
init_gmql	0.033	0.000	0.199
log_job	0.030	0.000	0.319
login_gmql	0.018	0.000	0.189
map	0.068	0.005	0.061
merge	0.074	0.004	0.052
operator-class	0.183	0.012	0.184
ordering-class	0.047	0.000	0.043
read-function	0.098	0.004	0.369
register_gmql	0.001	0.000	0.000
remote_processing	0.016	0.000	0.008
run_query	0.001	0.000	0.000
sample_metadata	0.040	0.000	0.464
sample_region	0.001	0.000	0.000
save_query	0.060	0.000	0.805
select	0.068	0.004	0.072
semijoin	0.070	0.000	0.052
setdiff	0.056	0.003	0.053
show_dataset	0.075	0.013	11.236
show_jobs_list	0.030	0.000	0.366
show_queries_list	0.030	0.000	0.322
show_samples_list	0.026	0.000	0.331
show_schema	0.028	0.000	0.329
stop_gmql	0.133	0.032	0.383
stop_job	0	0	0
take	5.711	0.211	7.089
union	0.054	0.012	0.047
upload_dataset	0.000	0.000	0.001

CHECK report for RGMQL on malbec2

Summary

Command output

Installation output

Tests output

Example timings