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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:anota2seq.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings anota2seq_1.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/anota2seq.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 ‘anota2seq/DESCRIPTION’ ... OK
* this is package ‘anota2seq’ version ‘1.28.0’
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘anota2seq’ can be installed ... OK
* checking installed package size ... OK
* 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 ... 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                               user system elapsed
anota2seqGetQualityControl   30.434  0.259  30.693
anota2seqGetResidOutlierTest 29.421  0.105  29.527
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
  ...
--- re-building ‘anota2seq.Rnw’ using knitr
Error: processing vignette 'anota2seq.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'anota2seq.tex' failed.
LaTeX errors:
! Package pdftex.def Error: File `figure/badSim.pdf' not found: using draft set
ting.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Emergency stop.
 ...                                              
                                                  
l.301 \includegraphics[]{figure/badSim.pdf}
                                           
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘anota2seq.Rnw’

SUMMARY: processing the following file failed:
  ‘anota2seq.Rnw’

Error: Vignette re-building failed.
Execution halted

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

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/anota2seq.Rcheck/00check.log’
for details.