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### Running command:
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###   /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:trena.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings trena_1.21.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/trena.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
    GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 LTS
* using session charset: UTF-8
* checking for file ‘trena/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘trena’ version ‘1.21.0’
* 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 ‘trena’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.1Mb
    extdata   2.6Mb
* 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'trena-package.Rd':
  ‘BayesSpikeSolver’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'EnsembleSolver'
  ‘nOrderings.bayes’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Found ‘inst/doc/makefile’: should be ‘Makefile’ and will be ignored
* checking running R code from vignettes ...
  ‘TReNA_Vignette.Rmd’ using ‘UTF-8’... OK
  ‘caseStudyFour.Rmd’ using ‘UTF-8’... OK
  ‘caseStudyOne.Rmd’ using ‘UTF-8’... OK
  ‘caseStudyThree.Rmd’ using ‘UTF-8’... OK
  ‘caseStudyTwo.Rmd’ using ‘UTF-8’... OK
  ‘overview.Rmd’ using ‘UTF-8’... OK
  ‘simple.Rmd’ using ‘UTF-8’... OK
  ‘tiny.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘TReNA_Vignette.Rmd’ using knitr
--- finished re-building ‘TReNA_Vignette.Rmd’

--- re-building ‘caseStudyFour.Rmd’ using knitr
--- finished re-building ‘caseStudyFour.Rmd’

--- re-building ‘caseStudyOne.Rmd’ using knitr
--- finished re-building ‘caseStudyOne.Rmd’

--- re-building ‘caseStudyThree.Rmd’ using knitr
--- finished re-building ‘caseStudyThree.Rmd’

--- re-building ‘caseStudyTwo.Rmd’ using knitr
--- finished re-building ‘caseStudyTwo.Rmd’

--- re-building ‘overview.Rmd’ using knitr
--- finished re-building ‘overview.Rmd’

--- re-building ‘simple.Rmd’ using knitr
Quitting from lines 32-33 (simple.Rmd) 
Error: processing vignette 'simple.Rmd' failed with diagnostics:
there is no package called 'limma'
--- failed re-building ‘simple.Rmd’

--- re-building ‘tiny.Rmd’ using knitr
--- finished re-building ‘tiny.Rmd’

SUMMARY: processing the following file failed:
  ‘simple.Rmd’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 ERROR, 3 WARNINGs, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.17-bioc/meat/trena.Rcheck/00check.log’
for details.