Package: RGMQL

Version: 1.0.2

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings RGMQL_1.0.2.tar.gz

StartedAt: 2018-10-16 03:15:15 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 03:18:17 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 181.4 seconds

RetCode: 0

Status:  OK

CheckDir: RGMQL.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings RGMQL_1.0.2.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/RGMQL.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.0.2’
* 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 20.1Mb
  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   8.192  0.424   4.362
take         5.588  0.252   2.274
show_dataset 0.080  0.004   8.341
* 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-3.7-bioc/meat/RGMQL.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL RGMQL
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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)

name	user	system	elapsed
aggr-class	8.192	0.424	4.362
aggregate	0.040	0.008	0.034
arrange	0.040	0.004	0.036
collect	0.048	0.008	0.029
compile_query	0.580	0.012	2.499
cover-param-class	0.084	0.012	0.051
cover	0.052	0.008	0.041
delete_dataset	0.004	0.000	0.001
distal-class	0.076	0.012	0.072
download_dataset	0.004	0.000	0.001
execute	0.052	0.004	0.035
export_gmql	0.432	0.020	0.452
extend	0.040	0.004	0.029
filter	0.116	0.000	0.071
filter_and_extract	0.888	0.016	0.929
group_by	0.056	0.000	0.042
import_gmql	0.076	0.016	0.090
log_job	0.024	0.004	0.379
login_gmql	0.012	0.004	0.220
logout_gmql	0.036	0.004	0.461
map	0.064	0.012	0.051
merge	0.088	0.000	0.054
operator-class	0.232	0.020	0.121
ordering-class	0.104	0.004	0.051
read-function	0.160	0.012	0.411
register_gmql	0.000	0.000	0.002
remote_processing	0.012	0.000	0.007
run_query	0.000	0.000	0.001
sample_metadata	0.032	0.000	0.672
sample_region	0.004	0.000	0.001
save_query	0.064	0.008	0.959
select	0.080	0.000	0.038
semijoin	0.044	0.016	0.037
setdiff	0.048	0.000	0.041
show_dataset	0.080	0.004	8.341
show_jobs_list	0.024	0.008	0.442
show_queries_list	0.032	0.000	0.395
show_samples_list	0.032	0.000	0.368
show_schema	0.032	0.000	0.367
stop_gmql	0.152	0.016	0.092
stop_job	0.000	0.000	0.001
take	5.588	0.252	2.274
union	0.048	0.004	0.037
upload_dataset	0.004	0.000	0.001