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This page was generated on 2022-08-12 13:20:44 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for RGMQL on nebbiolo1


To the developers/maintainers of the RGMQL package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RGMQL.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1635/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RGMQL 1.16.0  (landing page)
Simone Pallotta
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/RGMQL
git_branch: RELEASE_3_15
git_last_commit: 4f9e75c
git_last_commit_date: 2022-04-26 11:46:12 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    ERROR    OK  
merida1macOS 10.14.6 Mojave / x86_64... NOT SUPPORTED ...

Summary

Package: RGMQL
Version: 1.16.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RGMQL_1.16.0.tar.gz
StartedAt: 2022-08-11 21:47:25 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 21:51:05 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 219.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: RGMQL.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings RGMQL_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/RGMQL.Rcheck’
* using R version 4.2.1 (2022-06-23)
* 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 ‘1.16.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... WARNING
Found the following files with non-portable file names:
  Example of workflows/use_case_1 - GITHUB.Rmd
  Example of workflows/use_case_1 - GITHUB.html
  Example of workflows/use_case_3 - GITHUB.Rmd
  Example of workflows/use_case_3 - GITHUB.html
  Example of workflows
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘RGMQL’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 48.9Mb
  sub-directories of 1Mb or more:
    example  48.3Mb
* 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 ... OK
* 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
take         6.530  0.381   1.527
aggr-class   5.843  0.507   2.246
show_dataset 0.088  0.025   5.870
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/RGMQL.Rcheck/00check.log’
for details.



Installation output

RGMQL.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL RGMQL
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-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-class5.8430.5072.246
aggregate0.0370.0030.021
arrange0.0450.0070.025
collect0.0430.0000.023
compile_query0.8360.1162.978
cover-param-class0.0730.0020.037
cover0.0530.0020.028
delete_dataset000
distal-class0.0640.0070.045
download_dataset000
execute0.0320.0000.018
export_gmql0.3690.0240.389
extend0.0370.0010.028
filter0.0890.0270.070
filter_and_extract2.3470.1372.476
group_by0.0600.0120.053
import_gmql0.1340.0080.140
init_gmql0.0160.0000.174
log_job0.0350.0000.364
login_gmql0.0170.0010.175
logout_gmql0.0290.0030.445
map0.0510.0030.034
merge0.0660.0040.036
operator-class0.1670.0120.073
ordering-class0.0600.0010.027
read-function0.0900.0040.395
register_gmql0.0000.0000.001
remote_processing0.0030.0030.006
run_query000
sample_metadata0.0260.0120.515
sample_region0.0000.0000.001
save_query0.0430.0361.647
select0.0430.0090.034
semijoin0.0690.0000.033
setdiff0.0570.0010.037
show_all_metadata0.0530.0350.684
show_dataset0.0880.0255.870
show_jobs_list0.0270.0040.358
show_queries_list0.0300.0000.353
show_samples_list0.0340.0000.360
show_schema0.0270.0000.355
stop_gmql0.0890.0360.053
stop_job0.0000.0010.001
take6.5300.3811.527
union0.1380.0080.042
upload_dataset0.0050.0040.000