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

[Shraddha Pai]

Hi Martin,
The issue is on the bioc-devel version, not the release version (3.12).
Shraddha

On Tue, Nov 24, 2020 at 4:06 AM Martin Morgan <mtmorgan.bioc using gmail.com>
wrote:

> Please respond on the list. After creating a new clone of your package
>
>
>
>   git clone git using git.bioconductor.org:packages/netDx
>
>
>
> and validating my installation
>
>
>
>   BiocManager::version() # 3.12
>
>   BiocManager::valid()    # TRUE
>
>
>
> I do not see a problem
>
>
>
> > devtools::build_vignettes()
>
> Building netDx vignettes
>
> …
>
> Building vignette index
>
> >
>
>
>
> so can’t really help further…?
>
>
>
> *From: *Shraddha Pai <shraddha.pai using utoronto.ca>
> *Date: *Monday, November 23, 2020 at 12:14 PM
> *To: *Martin Morgan <mtmorgan.bioc using gmail.com>
> *Subject: *Re: [Bioc-devel] Running vignettes one at a time works but
> build_vignettes causes buffer overflow
>
>
>
> Hi Martin,
>
> Thanks for responding. Sorry, left out the package name(!).
>
> This is netDx, v 1.3.1, currently the version in bioc-devel.
>
>
>
> I have tried opening a single session, and then running
>
> > rmarkdown::render("vignette1.rmd")
>
> > rmarkdown::render("vignette2.rmd")
>
> > rmarkdown::render("vignette3.rmd")
>
>
>
> This works.  But if I call
>
> > devtools::build_vignettes()
>
> I get the buffer overflow error.
>
>
>
> I expect that if I use gdb and then run one vignette at a time, I may not
> get an error message.
>
> But let me try running gdb and then calling devtools::build_vignettes(),
> see if that turns up something.
>
>
>
> If it helps, this only started after I switched using rJava to make java
> calls, instead of using system2(). I have tried looking to see if I need to
> empty some kind of buffer at the end of all java operations for a given
> vignette (maybe they build up over time?) but a quick Google search hasn't
> turned up anything.
>
>
>
> Aside from the gdb tool, I basically don't know how to debug the problem.
> Any other thoughts would be great.
>
>
>
> Thanks,Shraddha
>
>
>
>
>
> On Mon, Nov 23, 2020 at 11:59 AM Martin Morgan <mtmorgan.bioc using gmail.com>
> wrote:
>
> 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 using r-project.org on behalf of shraddha.pai using 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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