similar to: .Internal(quit(...)): system call failed: Cannot allocate memory

The call to system() probably is an internal call used to delete the session's tempdir(). This sort of failure means that a potentially large amount of disk space is not being recovered when R is done. Perhaps R_CleanTempDir() could call R_unlink() instead of having a subprocess call 'rm -rf ...'. Then it could also issue a specific warning if it was impossible to delete all of

On 11/24/20 11:27 AM, Jan Gorecki wrote: > Thanks Bill for checking that. > It was my impression that warnings are raised from some internal > system calls made when quitting R. At that point I don't have much > control over checking the return status of those. > Your suggestion looks good to me. > > Tomas, do you think this could help? could this be implemented? I think

On Tue, 24 Nov 2020, Jan Gorecki wrote: > As for other calls to system. I avoid calling system. In the past I > had some (to get memory stats from OS), but they were failing with > exactly the same issue. So yes, if I would add call to system before > calling quit, I believe it would fail with the same error. > At the same time I think (although I am not sure) that new allocations

Thanks Bill for checking that. It was my impression that warnings are raised from some internal system calls made when quitting R. At that point I don't have much control over checking the return status of those. Your suggestion looks good to me. Tomas, do you think this could help? could this be implemented? On Mon, Nov 23, 2020 at 7:10 PM Bill Dunlap <williamwdunlap at gmail.com>

As for other calls to system. I avoid calling system. In the past I had some (to get memory stats from OS), but they were failing with exactly the same issue. So yes, if I would add call to system before calling quit, I believe it would fail with the same error. At the same time I think (although I am not sure) that new allocations made in R are working fine. So R seems to reserve some memory and

On 11/21/20 6:51 PM, Jan Gorecki wrote: > Dear R-developers, > > Some of the more fat scripts (50+ GB mem used by R) that I am running, > when they finish they do quit with q("no", status=0) > Quite often it happens that there is an extra stderr output produced > at the very end which looks like this: > > Warning message: > In .Internal(quit(save, status,

On 2/16/23 15:09, Ivan Krylov wrote: > Hello, > > This is probably a very minor point, but R_CleanTempDir may still have > a shell injection in it. I couldn't find a way to shoot the user in the > foot in a significant way (by, say, accidentally removing ~), thanks to > R disallowing spaces in the path, but if Sys_TempDir somehow acquires a > value of

On Fri, Aug 31, 2018 at 2:51 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: [...] > kill(sig=0) is specified by POSIX but indeed as you say there is a race > condition due to PID-reuse. In principle, detecting that a worker > process is still alive cannot be done correctly outside base R. I am not sure why you think so. > At user-level I would probably consider some

Dear R developers, I spotted that R_isNA and R_IsNaN could be improved when applied on a vector where we could take out small part of their logic, run it once, and then reuse inside the loop. I setup tiny plain-C experiment. Taking R_IsNA, R_IsNaN from R's arithmetic.c, and building R_vIsNA and R_vIsNaN accordingly. For double input of size 1e9 (having some NA and NaN) I observed following

On Fri, Aug 31, 2018 at 3:35 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: > > On 08/31/2018 03:13 PM, G?bor Cs?rdi wrote: > > On Fri, Aug 31, 2018 at 2:51 PM Tomas Kalibera <tomas.kalibera at gmail.com> wrote: > > [...] > >> kill(sig=0) is specified by POSIX but indeed as you say there is a race > >> condition due to PID-reuse. In

Full_Name: Byron Ellis Version: R 1.9.0 (and 2.0.0) OS: Linux (Redhat Fedora Core) Submission from: (NULL) (140.247.241.197) It appears that `R CMD build` cannot handle spaces in the path when building packages for distribution. For instance: [ellis@net-78815 ~/Bayesian Networks]$ R CMD build bnsl * checking for file 'bnsl/DESCRIPTION' ... OK * preparing 'bnsl': * cleaning src *

Many thanks to Peter and Brian for their help; it was indeed a permissions problem; thanks also to Josh Paulson of the RStudio team for pointing me to instructions for making the necessary changes. But at the risk of seeming not only ungrateful and pedantic, but also off-topic, can I point out that all this strictly only answers part of my question, which was "why **all of a sudden** I

On 6/30/20 1:06 PM, Jan Gorecki wrote: > It is quite known that R documentation on R C api could be improved... Please see "5.11 Evaluating R expressions from C" from "Writing R Extensions" Best Tomas > Still R-package-devel mailing list should be preferred for this kind > of questions. > Not sure if that is the best way, but works. > > call_to_sum <-

On 10/30/23 17:18, Yihui Xie wrote: > Hi, > > It may have been so for 20+ years but I just discovered today that system() > would always try to use the short path of a command on Windows: > https://github.com/wch/r-source/blob/635a67/src/gnuwin32/run.c#L141 If > that's true, I wonder if it could provide an option to disable this > behavior, because we recently ran into a

Hello, This is probably a very minor point, but R_CleanTempDir may still have a shell injection in it. I couldn't find a way to shoot the user in the foot in a significant way (by, say, accidentally removing ~), thanks to R disallowing spaces in the path, but if Sys_TempDir somehow acquires a value of "/tmp/';echo;'", R_CleanTempDir() will remove /tmp instead of its

Yes, the performance overhead of fixing this at R level would be too large and it would complicate the code significantly. The result of binary operations involving NA and NaN is hardware dependent (the propagation of NaN payload) - on some hardware, it actually works the way we would like - NA is returned - but on some hardware you get NaN or sometimes NA and sometimes NaN. Also there are C

(On Unix/Linux) Is it possible to set the --no-save command line option as an option in the .Rprofile file. I have looked in the sources and do not see any obvious (user initiated) ways of changing the command line defaults, but I am hoping I have missed something. I *know* I can write my own shell script wrapper that calls R with whatever arguments I want (and I do that). However there

Hi, I'd like to test whether a (localhost) PSOCK cluster node is still running or not by its PID, e.g. it may have crashed / core dumped. I'm ok with getting false-positive results due to *another* process with the same PID has since started. I can the PID of each cluster nodes by querying them for their Sys.getpid(), e.g. pids <- parallel::clusterEvalQ(cl, Sys.getpid()) Is there

On 10/31/23 10:05, Duncan Murdoch wrote: > On 31/10/2023 4:32 a.m., Tomas Kalibera wrote: >> >> On 10/30/23 19:07, Yihui Xie wrote: >>> Sure. I'm not sure if it's possible to make it easier to reproduce, >>> but for now the example would require installing TinyTeX (via >>> tinytex::install_tinytex(), which can be later uninstalled cleanly via

Sure. I'm not sure if it's possible to make it easier to reproduce, but for now the example would require installing TinyTeX (via tinytex::install_tinytex(), which can be later uninstalled cleanly via tinytex::uninstall_tinytex() after you finish the investigation). Then run: system2('fmtutil-sys', '--all') # or tinytex:::fmtutil() if fmtutil-sys.exe is not on PATH