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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings BgeeCall_1.25.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BgeeCall.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘BgeeCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeCall’ version ‘1.25.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘BgeeCall’ can be installed ... OK
* checking installed package size ... INFO
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   8.6Mb
* 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 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
galaxy_calls: no visible binding for global variable ‘output_file’
generate_calls_workflow: no visible binding for global variable
  ‘myUserMetadata’
generate_fasta_intergenic_regions: no visible binding for global
  variable ‘classification’
generate_theoretical_pValue: no visible binding for global variable
  ‘abundance’
get_run_accessions_by_experiment: no visible binding for global
  variable ‘sra_con’
retrieve_gtf_files: no visible global function definition for ‘cols’
Undefined global functions or variables:
  abundance classification cols myUserMetadata output_file sra_con
* 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 ‘BgeeCall-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: merge_transcriptome_and_intergenic
> ### Title: Merge transcriptome file provided by the user with the Bgee
> ###   intergenic fasta file.
> ### Aliases: merge_transcriptome_and_intergenic
> 
> ### ** Examples
> 
> {
+ bgee <- new('BgeeMetadata', intergenic_release = '0.1')
+ user <- new ('UserMetadata', species_id = '6239')
+ kallisto <- new('KallistoMetadata')
+ user <- setTranscriptomeFromFile(user, system.file("extdata", 
+ "transcriptome.fa", package = "BgeeCall"), 'WBcel235')
+ merge_transcriptome_and_intergenic(kallisto, bgee, user)
+ }
Querying Bgee to get intergenic release information...
Start generation of the file containing both transcriptomic
                and intergenic regions.

trying URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4420457 bytes (4.2 MB)
======
downloaded 575 KB

Warning in download.file(url = intergenic_url, destfile = intergenic_file) :
  downloaded length 589536 != reported length 4420457
Warning in download.file(url = intergenic_url, destfile = intergenic_file) :
  URL 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz': status was 'Failed writing received data to disk/application'
Error in download.file(url = intergenic_url, destfile = intergenic_file) : 
  download from 'https://www.bgee.org/ftp/intergenic/0.1/ref_intergenic/6239_intergenic.fa.gz' failed
Calls: merge_transcriptome_and_intergenic ... retrieve_intergenic_path -> download_fasta_intergenic -> download.file
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
                                  user system elapsed
generate_presence_absence        4.090  0.511  51.206
download_kallisto                0.103  0.119  25.799
list_bgee_ref_intergenic_species 0.105  0.007  10.339
* checking for unstated dependencies in ‘tests’ ... WARNING
Fatal error: cannot create 'R_TempDir'
* checking tests ...Fatal error: cannot create 'R_TempDir'
 ERROR
* checking for unstated dependencies in vignettes ... NOTE
Fatal error: cannot create 'R_TempDir'
* checking package vignettes ...Warning in dir.create(tdir) :
  cannot create dir '/home/biocbuild/tmp/RtmpAl3EN8/file18acb875d4030f', reason 'No space left on device'
 OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/BgeeCall.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL BgeeCall
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘BgeeCall’ ...
** this is package ‘BgeeCall’ version ‘1.25.1’
** 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 (BgeeCall)