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symbioticMe / proBatch

Tools for Batch Effects Diagnostics and Correction
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Error when building vignettes for version 1.3.0 #13

Open eneskemalergin opened 3 years ago

eneskemalergin commented 3 years ago

There is an error when installing the package as suggested in the README file with build_vignettes=TRUE. 

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

   Error: Vignette re-building failed.
   Execution halted
Error: Failed to install 'proBatch' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
E> Error: processing vignette 'proBatch.Rmd' failed with diagnostics:
E> ERROR; return code from pthread_create() is 22
E> 
E> --- failed re-building ‘proBatch.Rmd’
E> 
E> SUMMARY: processing the following file failed:
E>   ‘proBatch.Rmd’
E> 
E> Error: Vignette re-building failed.
E> Execution halted

Without building the vignettes, package installs without any other problems.

lzy604 commented 11 months ago

Dear developer,

Thanks for developing this tool. I think I got the similar error.

--- re-building ‘proBatch.Rmd’ using rmarkdown

Quitting from lines 933-934 [citation] (proBatch.Rmd) Error: processing vignette 'proBatch.Rmd' failed with diagnostics: A bibentry of bibtype 'Article' has to specify the fields: journal, year --- failed re-building ‘proBatch.Rmd’

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

Error: Vignette re-building failed. Execution halted Error: Failed to install 'proBatch' from GitHub: ! System command 'R' failed

aliibarry commented 9 months ago

Can confirm, I was able to repeat this error. Build is still successful with build_vignettes=FALSE.

── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file 'path\Local\Temp\RtmpOsLZTt\remotes6930438b1736\symbioticMe-proBatch-84322c0/DESCRIPTION' (472ms)
─  preparing 'proBatch': (1.7s)
✔  checking DESCRIPTION meta-information ... 
─  installing the package to build vignettes (511ms)
E  creating vignettes (1m 6.3s)
   --- re-building 'proBatch.Rmd' using rmarkdown

   Quitting from lines 579-582 [plot_PVCA] (proBatch.Rmd)
   Error: processing vignette 'proBatch.Rmd' failed with diagnostics:
   function 'cholmod_factor_ldetA' not provided by package 'Matrix'
   --- failed re-building 'proBatch.Rmd'

   SUMMARY: processing the following file failed:
     'proBatch.Rmd'

   Error: Vignette re-building failed.
   Execution halted