same result with BiocManager::version() 3.13 From: Shraddha Pai <shraddha....@utoronto.ca> Date: Tuesday, November 24, 2020 at 8:13 AM To: Martin Morgan <mtmorgan.b...@gmail.com> Cc: Bioc-devel <bioc-devel@r-project.org> Subject: Re: [Bioc-devel] Running vignettes one at a time works but build_vignettes causes buffer overflow
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.b...@gmail.com<mailto:mtmorgan.b...@gmail.com>> wrote: Please respond on the list. After creating a new clone of your package git clone g...@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....@utoronto.ca<mailto:shraddha....@utoronto.ca>> Date: Monday, November 23, 2020 at 12:14 PM To: Martin Morgan <mtmorgan.b...@gmail.com<mailto:mtmorgan.b...@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.b...@gmail.com<mailto:mtmorgan.b...@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-boun...@r-project.org<mailto:bioc-devel-boun...@r-project.org> on behalf of shraddha....@utoronto.ca<mailto:shraddha....@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org<mailto:Bioc-devel@r-project.org> mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
