Package: RGMQL

Version: 1.6.0

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings RGMQL_1.6.0.tar.gz

StartedAt: 2020-04-13 05:17:52 -0400 (Mon, 13 Apr 2020)

EndedAt: 2020-04-13 05:21:44 -0400 (Mon, 13 Apr 2020)

EllapsedTime: 232.6 seconds

RetCode: 0

Status:  OK

CheckDir: RGMQL.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings RGMQL_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/RGMQL.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.6.0’
* 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 20.1Mb
  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   7.680  0.264   5.486
take         5.216  0.140   2.387
show_dataset 0.084  0.004   6.986
* 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-3.10-bioc/meat/RGMQL.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL RGMQL
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* installing to library ‘/home/biocbuild/bbs-3.10-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	7.680	0.264	5.486
aggregate	0.036	0.000	0.034
arrange	0.060	0.000	0.046
collect	0.048	0.000	0.037
compile_query	0.248	0.004	1.627
cover-param-class	0.104	0.004	0.069
cover	0.064	0.004	0.052
delete_dataset	0.000	0.000	0.001
distal-class	0.084	0.008	0.096
download_dataset	0.000	0.000	0.001
execute	0.048	0.000	0.031
export_gmql	0.820	0.036	0.854
extend	0.056	0.000	0.040
filter	0.140	0.000	0.107
filter_and_extract	0.640	0.024	0.667
group_by	0.076	0.004	0.072
import_gmql	0.180	0.016	0.196
init_gmql	0.036	0.000	0.197
log_job	0.024	0.004	0.318
login_gmql	0.016	0.000	0.178
logout_gmql	0.032	0.000	0.399
map	0.048	0.004	0.038
merge	0.088	0.000	0.047
operator-class	0.256	0.012	0.106
ordering-class	0.084	0.000	0.037
read-function	0.080	0.016	0.357
register_gmql	0.000	0.000	0.001
remote_processing	0.008	0.004	0.010
run_query	0	0	0
sample_metadata	0.024	0.008	0.451
sample_region	0	0	0
save_query	0.056	0.008	0.757
select	0.080	0.004	0.071
semijoin	0.064	0.004	0.053
setdiff	0.064	0.000	0.055
show_dataset	0.084	0.004	6.986
show_jobs_list	0.028	0.004	0.300
show_queries_list	0.024	0.004	0.298
show_samples_list	0.032	0.000	0.299
show_schema	0.032	0.000	0.293
stop_gmql	0.148	0.016	0.191
stop_job	0	0	0
take	5.216	0.140	2.387
union	0.112	0.004	0.034
upload_dataset	0	0	0