Package: RGMQL

Version: 1.4.1

Command: /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_1.4.1.tar.gz

StartedAt: 2019-10-16 04:30:38 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 04:35:37 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 299.8 seconds

RetCode: 0

Status:  OK

CheckDir: RGMQL.Rcheck

Warnings: 0

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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_1.4.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/RGMQL.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.4.1’
* 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   6.228  0.476  57.913
take         5.811  0.271  12.925
show_dataset 0.056  0.005  11.401
* 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.

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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)

name	user	system	elapsed
aggr-class	6.228	0.476	57.913
aggregate	0.036	0.003	0.024
arrange	0.051	0.004	0.044
collect	0.053	0.004	0.070
compile_query	0.229	0.008	2.294
cover-param-class	0.085	0.016	0.050
cover	0.042	0.017	0.037
delete_dataset	0.000	0.000	0.001
distal-class	0.091	0.008	0.133
download_dataset	0.001	0.000	0.000
execute	0.052	0.003	0.035
export_gmql	0.508	0.028	0.711
extend	0.046	0.000	0.034
filter	0.734	0.011	1.087
filter_and_extract	0.450	0.000	0.687
group_by	0.079	0.004	1.058
import_gmql	0.146	0.000	0.146
init_gmql	0.028	0.000	0.185
log_job	0.030	0.000	0.301
login_gmql	0.018	0.000	0.182
logout_gmql	0.036	0.000	0.396
map	0.053	0.004	0.036
merge	0.081	0.005	0.053
operator-class	0.342	0.007	0.526
ordering-class	0.036	0.000	0.032
read-function	0.118	0.000	0.360
register_gmql	0.001	0.000	0.000
remote_processing	0.005	0.000	0.005
run_query	0.000	0.000	0.001
sample_metadata	0.035	0.004	0.493
sample_region	0	0	0
save_query	0.064	0.000	0.793
select	0.051	0.001	0.030
semijoin	0.046	0.005	0.028
setdiff	0.056	0.000	0.033
show_dataset	0.056	0.005	11.401
show_jobs_list	0.029	0.000	0.310
show_queries_list	0.029	0.000	0.286
show_samples_list	0.029	0.000	0.312
show_schema	0.020	0.000	0.311
stop_gmql	0.141	0.046	1.282
stop_job	0	0	0
take	5.811	0.271	12.925
union	0.046	0.001	0.035
upload_dataset	0.000	0.000	0.001