##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:RGMQL.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings RGMQL_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RGMQL.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘RGMQL/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RGMQL’ version ‘1.25.0’
* 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 file with a non-portable file name:
  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 90.0Mb
  sub-directories of 1Mb or more:
    example  89.3Mb
* 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 code 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... ERROR
Running examples in ‘RGMQL-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sample_metadata
> ### Title: Show metadata list from dataset sample
> ### Aliases: sample_metadata
> 
> ### ** Examples
> 
> ## Login to GMQL REST services suite as guest
> 
> remote_url = "http://www.gmql.eu/gmql-rest/"
> login_gmql(remote_url)
[1] "your Token is 221db9de-49e1-4c2d-b98a-c18842f53f2d"
> 
> ## This statement retrieves metadata of sample 'S_00000' from public 
> ## dataset 'Example_Dataset_1'
> 
> sample_metadata(remote_url, "public.Example_Dataset_1", "S_00000")
Error in sample_metadata(remote_url, "public.Example_Dataset_1", "S_00000") : 
  {"error":"Sample not found: Example_Dataset_1-S_00000"}
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/RGMQL.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL RGMQL
###
##############################################################################
##############################################################################


* installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-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)