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Have read the latest code, but I still don't understand why mc_exit needs to write zero on exit. If a child closes its pipe, parent will know that on next select. Best, Yijiang Tomas Kalibera <tomas.kalibera at gmail.com> ?2019?5?20??? ??10:52??? > > This issue has already been addressed in 76462 (R-devel) and also ported > to R-patched. In fact rmChild() is used in mccollect(wait=FALSE). > > Best > Tomas > > On 5/19/19 11:39 AM, Sun Yijiang...

...I hope we can discuss a solution on it. In fact, I don't see why we need to write to the pipe on child exit and how it has anything to do with "Fedora security settings" as suggested in the comments. Removing it, IMHO, would be a good and clean way to solve this problem. Regards, Yijiang

...ng to do with library(methods)? If library(h5) works, it should just work, not depend on an environment variable. Rscript is not consistent with R, that's my confusion. Steve 2017-12-26 20:46 GMT+08:00 Dirk Eddelbuettel <edd at debian.org>: > > On 26 December 2017 at 15:24, Sun Yijiang wrote: > | After looking into C source code, I found that Rscript by default fills > | environment variable R_DEFAULT_PACKAGES with > | "datasets,utils,grDevices,graphics,stats", and it somehow fails some > | package like h5. > | > | The problem here is, not setting R_DE...

This issue has already been addressed in 76462 (R-devel) and also ported to R-patched. In fact rmChild() is used in mccollect(wait=FALSE). Best Tomas On 5/19/19 11:39 AM, Sun Yijiang wrote: > I've been hacking with parallel package for some time and built a > parallel processing framework with it. However, although very rarely, > I did notice "ignoring SIGPIPE signal" error every now and then. > After a deep dig into the source code, I think I found s...

Consider this script (with h5 installed): $ cat test.R library(h5) name <- tempfile() f <- h5file(name) file.remove(name) $ Rscript test.R Error in initialize(value, ...) : cannot use object of class "character" in new(): class "H5File" does not extend that class Calls: h5file -> new -> initialize -> initialize Execution halted $ /usr/lib64/R/bin/R --slave

...find memory corruption. Please feel free to ask more when you have more > information/updates. If this ends up being a bug in R, please report > (and with a reproducible example, if it is not obvious from the source > code). > > Best > Tomas > > > On 8/2/19 10:23 AM, Sun Yijiang wrote: > > The R script I run daily for hours looks like this: > > > > while (!finish) { > > Sys.sleep(0.1) > > time = as.integer(format(Sys.time(), "%H%M")) # always crash here > > if (new.data.timestamp() <= time) > >...

On 26/12/2017 9:40 AM, Dirk Eddelbuettel wrote: > > On 26 December 2017 at 22:14, Sun Yijiang wrote: > | Thanks for the solution. Now I know the work-arounds, but still don't > | quite get it. Why does R_DEFAULT_PACKAGES has anything to do with > | library(methods)? > > Because it governs which packages are loaded by default. And while R also > loads 'methods...

The R script I run daily for hours looks like this: while (!finish) { Sys.sleep(0.1) time = as.integer(format(Sys.time(), "%H%M")) # always crash here if (new.data.timestamp() <= time) next # ... do some jobs for about 2 minutes ... gc() } Basically it waits for new data, which comes in every 10 minutes, and do some jobs, then gc(), then loop again. It

On 26 December 2017 at 22:14, Sun Yijiang wrote: | Thanks for the solution. Now I know the work-arounds, but still don't | quite get it. Why does R_DEFAULT_PACKAGES has anything to do with | library(methods)? Because it governs which packages are loaded by default. And while R also loads 'methods', Rscript does not. Source o...

On 26 December 2017 at 15:24, Sun Yijiang wrote: | After looking into C source code, I found that Rscript by default fills | environment variable R_DEFAULT_PACKAGES with | "datasets,utils,grDevices,graphics,stats", and it somehow fails some | package like h5. | | The problem here is, not setting R_DEFAULT_PACKAGES is equivalent...

Thanks for the details. I?m new to R, and I?m not blaming anything here, just that I?m still not clear what good it makes to keep this inconsistency between R and Rscript. To me (and probably to many others from Perl/Python etc.), this is shockingly weird. I can live with that, and I also want to know why. Steve Dirk Eddelbuettel <edd at debian.org>?2017?12?27? ??21:15??? > > Duncan,

...I hope we can discuss a solution on it. In fact, I don't see why we need to write to the pipe on child exit and how it has anything to do with "Fedora security settings" as suggested in the comments. Removing it, IMHO, would be a good and clean way to solve this problem. Regards, Yijiang

..., e.g. sometimes a watchpoint helps to find memory corruption. Please feel free to ask more when you have more information/updates. If this ends up being a bug in R, please report (and with a reproducible example, if it is not obvious from the source code). Best Tomas On 8/2/19 10:23 AM, Sun Yijiang wrote: > The R script I run daily for hours looks like this: > > while (!finish) { > Sys.sleep(0.1) > time = as.integer(format(Sys.time(), "%H%M")) # always crash here > if (new.data.timestamp() <= time) > next > # ... do some jobs f...