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CHECK report for RGMQL on malbec2

This page was generated on 2020-10-17 11:55:34 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE RGMQL PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1475/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RGMQL 1.8.0
Simone Pallotta
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/RGMQL
Branch: RELEASE_3_11
Last Commit: 734d3e1
Last Changed Date: 2020-04-27 15:12:55 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: RGMQL
Version: 1.8.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RGMQL_1.8.0.tar.gz
StartedAt: 2020-10-17 04:45:52 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:49:45 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 233.6 seconds
RetCode: 0
Status:  OK 
CheckDir: RGMQL.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RGMQL_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RGMQL.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.8.0’
* 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 (user + system) or elapsed time > 5s
              user system elapsed
aggr-class   8.577  0.458   5.912
take         5.775  0.201   2.901
show_dataset 0.045  0.004   6.080
* 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-3.11-bioc/meat/RGMQL.Rcheck/00check.log’
for details.



Installation output

RGMQL.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RGMQL
###
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* installing to library ‘/home/biocbuild/bbs-3.11-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

RGMQL.Rcheck/RGMQL-Ex.timings

nameusersystemelapsed
aggr-class8.5770.4585.912
aggregate0.0490.0000.034
arrange0.0470.0040.040
collect0.0450.0040.040
compile_query0.3440.0233.115
cover-param-class0.0890.0150.063
cover0.0580.0080.050
delete_dataset0.0010.0000.000
distal-class0.0960.0030.101
download_dataset0.0010.0000.001
execute0.0520.0000.034
export_gmql0.8150.0480.870
extend0.0560.0040.042
filter0.1550.0040.114
filter_and_extract0.7320.0360.768
group_by0.0780.0040.070
import_gmql0.1950.0200.214
init_gmql0.0390.0000.340
log_job0.0280.0080.801
login_gmql0.0240.0000.556
logout_gmql0.0460.0000.662
map0.0650.0110.058
merge0.0850.0010.060
operator-class0.2750.0140.124
ordering-class0.1330.0080.051
read-function0.1920.0070.834
register_gmql0.0000.0010.000
remote_processing0.0040.0060.010
run_query0.0010.0000.000
sample_metadata0.0380.0000.745
sample_region000
save_query0.1060.0001.279
select0.0620.0130.054
semijoin0.0660.0120.054
setdiff0.0770.0040.058
show_dataset0.0450.0046.080
show_jobs_list0.0490.0040.726
show_queries_list0.0360.0000.376
show_samples_list0.0330.0000.350
show_schema0.0330.0000.523
stop_gmql0.1560.0120.195
stop_job000
take5.7750.2012.901
union0.0570.0000.045
upload_dataset000