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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:BgeeCall.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings BgeeCall_1.18.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/BgeeCall.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BgeeCall/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘BgeeCall’ version ‘1.18.1’
* 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 ‘BgeeCall’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   8.7Mb
* 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 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
approachesMerging : <anonymous>: no visible global function definition
  for ‘p.adjust’
generate_calls_workflow: no visible binding for global variable
  ‘myUserMetadata’
generate_qValue: no visible global function definition for ‘approxfun’
generate_qValue: no visible global function definition for ‘integrate’
generate_qValue : calculate_qValue: no visible global function
  definition for ‘integrate’
generate_theoretical_pValue: no visible binding for global variable
  ‘abundance’
generate_theoretical_pValue: no visible binding for global variable
  ‘type’
generate_theoretical_pValue: no visible global function definition for
  ‘pnorm’
merging_libraries: no visible binding for global variable ‘read.delim’
should_ignore_tx_version: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  abundance approxfun complete.cases integrate myUserMetadata p.adjust
  pnorm read.delim type
Consider adding
  importFrom("stats", "approxfun", "complete.cases", "integrate",
             "p.adjust", "pnorm")
  importFrom("utils", "read.delim")
to your NAMESPACE file.
* 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
generate_presence_absence          3.976  0.320   9.073
merge_transcriptome_and_intergenic 0.635  0.077   5.846
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘bgeecall-manual.Rmd’ using ‘UTF-8’... OK
 OK
* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
  ...
--- re-building ‘bgeecall-manual.Rmd’ using rmarkdown
trying URL 'https://www.bgee.org/ftp/intergenic/1.0/ref_intergenic/6239_intergenic.fa.gz'
Content type 'application/x-gzip' length 4054193 bytes (3.9 MB)
==================================================
downloaded 3.9 MB


Quitting from lines  at lines 124-127 [unnamed-chunk-7] (bgeecall-manual.Rmd)
Error: processing vignette 'bgeecall-manual.Rmd' failed with diagnostics:
can not generate presence/absence calls. 
Abundance file is missing : /home/biocbuild/bbs-3.18-bioc/R/site-library/BgeeCall/extdata/intergenic_1.0/all_results/SRX099901_subset/abundance.tsv.
--- failed re-building ‘bgeecall-manual.Rmd’

SUMMARY: processing the following file failed:
  ‘bgeecall-manual.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/BgeeCall.Rcheck/00check.log’
for details.