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[Bioc-devel] Running vignettes one at a time works but build_vignettes causes buffer overflow

2 messages · Shraddha Pai, Martin Morgan

Original
Shraddha Pai
# 
Hello BioC community,
Still haven't figured out why I get a buffer_overflow_detected error when I
build vignettes for our package netDx.

I find that running "devtools::build_vignetttes()" causes a "*** buffer
overflow detected ***" error after the first vignette has been built and
the second is just named.
But running the vignettes one at a time leads to them all running smoothing.

Any thoughts as to what could be causing the problem would be appreciated.

Thanks,Shraddha

--
Shraddha Pai, PhD
http://shraddhapai.com ; @spaiglass on Twitter
Post-doctoral Fellow, http://baderlab.org
The Donnelly Centre for Cellular and Biomolecular Research
University of Toronto
Martin Morgan
# 
It would really help (maybe this has been mentioned before, but I'm not very good at remembering things) to indicate what package this is!

When R installs a package, it (probably this is not the right thing to do) builds all vignettes in the same session. Maybe devtools does this too? You could work toward debugging by creating the source code of each vignette using tools::Stangle() or knitr::purl(), then starting a new, clean, R session and source()ing the first, second... vignettes. Basically the goal is to simplify the problem so that it can be reproduced in a single R session, and perhaps even further...

Buffer overflow is a C-level problem, e.g., copying too many characters into a buffer. If I were trying to debug this I'd brush up on my gdb / lldb skills and try to reproduce this with something like

  $ R -d gdb
  gdb> run
  > source("vig1.R")
  > source("vig2.R")
  ...
 
If this triggers the error, you'd find yourself at the gdb prompt, and you could use `up` to navigate the stack until the location of the buffer overflow (in your code) is found...

If you provide more information, especially an easily reproducible example, I can try to provide more specific advice.

Martin

?On 11/23/20, 11:39 AM, "Bioc-devel on behalf of Shraddha Pai" <bioc-devel-bounces at r-project.org on behalf of shraddha.pai at utoronto.ca> wrote:

    Hello BioC community,
    Still haven't figured out why I get a buffer_overflow_detected error when I
    build vignettes for our package netDx.

    I find that running "devtools::build_vignetttes()" causes a "*** buffer
    overflow detected ***" error after the first vignette has been built and
    the second is just named.
    But running the vignettes one at a time leads to them all running smoothing.

    Any thoughts as to what could be causing the problem would be appreciated.

    Thanks,Shraddha

    --
    Shraddha Pai, PhD
    http://shraddhapai.com ; @spaiglass on Twitter
    Post-doctoral Fellow, http://baderlab.org
    The Donnelly Centre for Cellular and Biomolecular Research
    University of Toronto


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