[Rd] system/system2 and open file descriptors
It seems that the system() and system2() functions don't close file
descriptors between the fork() and exec() (on Unix platforms, of course).
This means that the child processes inherit open files and socket
connections.
Running this (from a terminal) will result in the child process writing to
a file that was opened by R:
R
f <- file('foo.txt', 'w')
system('echo "abc" >&3')
You can also see the open files if you run the following:
f <- file('foo.txt', 'w')
system2('sleep', '100', wait=F)
And then in another terminal:
lsof -c R -c sleep
it will show that both the R and sleep processes have the file open:
...
R 324 root3w REG 0,480 4259 /foo.txt
...
sleep 327 root3w REG 0,480 4259 /foo.txt
This behavior can cause problems if R spawns a child process that outlives
the R process, but keeps open some resources.
Would it be possible to add an option to close file descriptors for child
processes? It would be nice if that were the default, but I suspect that
making that change would break a lot of existing code.
To take an example from the Python world, subprocess.Popen() has an option,
close_fds, which closes all file descriptors except 0, 1, and 2.
https://docs.python.org/2/library/subprocess.html#popen-constructor
-Winston
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Crash after (wrongly) applying product operator on object from LIMMA package
Hi,
this is a problem that occurs in the presence of two libraries (limma,
xlsx) and leads to a crash of R. The problematic code is the wrong
application of sweep or the product ("*") function on an LIMMA MAList
object. To my knowledge, limma does not define a "*" method for MAList
objects.
If only LIMMA is loaded but not package xlsx, the code does not crash
but rather produces an error ("Error: C stack usage 7970512 is too
close to the limit"). Loading only package rJava instead of xlsx does
also not produce the crash but the error message instead. Note that xlsx
functions are not explicitly used.
It could be reproduced on two different Linux machines running R-3.2.5,
R-3.3.0 and R-3.3.2.
Code to reproduce the problem:
-
library(limma)
library(xlsx)
# a MAList
ma = new("MAList", list(A=matrix(rnorm(300), 30,10),
M=matrix(rnorm(300), 30,10)))
# This should actually be sweep(ma$M, ...) for functional code, but I
omitted the $M...
#sweep(ma, 2, c(1:10), "*")
# sweep will crash when doing the final operation of applying the
function over the input matrix, which in this case is function "*"
f = match.fun("*")
# This is not exactly the same as in sweep but it also tries to multiply
the MAList object with a matrix of same size and leads to the crash
f(ma, ma$M)
# ma * ma$M has the same effect
-
My output:
R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(limma)
> library(xlsx)
Loading required package: rJava
Loading required package: xlsxjars
>
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8LC_MONETARY=en_US.UTF-8
LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=en_US.UTF-8
LC_ADDRESS=en_US.UTF-8
[10] LC_TELEPHONE=en_US.UTF-8 LC_MEASUREMENT=en_US.UTF-8
LC_IDENTIFICATION=en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xlsx_0.5.7 xlsxjars_0.6.1 rJava_0.9-8limma_3.30.7
loaded via a namespace (and not attached):
[1] tools_3.3.0
>
> ma = new("MAList", list(A=matrix(rnorm(300), 30,10),
M=matrix(rnorm(300), 30,10)))
> #sweep(ma, 2, c(1:10), "*")
>
> f = match.fun("*")
> f
function (e1, e2) .Primitive("*")
> f(ma, ma$M)
> crash to command line with segfault.
Best regards,
Hilmar
--
Dr. Hilmar Berger, MD
Max Planck Institute for Infection Biology
Charitéplatz 1
D-10117 Berlin
GERMANY
Phone: + 49 30 28460 430
Fax:+ 49 30 28460 401
E-Mail: ber...@mpiib-berlin.mpg.de
Web : www.mpiib-berlin.mpg.de
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.4 has broken C++11 support
Whoops, sorry. The links are supposed to be: [This commit]: https://github.com/wch/r-source/commit/45899dba734cbd80a77432af9a3a7829a9ad48da [the documentation]: https://github.com/wch/r-source/blob/45899dba734cbd80a77432af9a3a7829a9ad48da/config.site#L264 - Ursprüngliche Mail - Von: "Angerer, Philipp" An: "r-devel" Gesendet: Dienstag, 18. April 2017 15:11:52 Betreff: R 3.4 has broken C++11 support Hi, [This commit] (I’m using the mirror to have a working link) broke C++11 compilation. Before (and still now, according to the comments in the configure script), it’s sufficient to just have “SystemRequirements: C++11” in the DESCRIPTION file. But now “R CMD install” fails with “C++11 standard requested but CXX11 is not defined”, which is, according to [the documentation], a lie. I can’t even circumvent this, as setting “CXX11=$(CXX)” in the src/Makevars file fails with “CXX definition recursive”, and hardcoding “CXX11=g++” is a bad idea. Did I do sth. wrong or is the C++11 support in R just broken atm.? Best, Philipp PS: After addressing all points in the submission of my popular package “IRkernel”, I didn’t get any feedback, and the file just vanished from the incoming directory in CRAN. I asked about it multiple times but got no answer. What can I do now? Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 3.4 has broken C++11 support
A user with the email address flying-sh...@web.de has submitted a bug report on this topic. https://bugs.r-project.org/bugzilla/show_bug.cgi?id=17260 Assuming that you are the same person, I will address the issue here first. If you get the message “C++11 standard requested but CXX11 is not defined” then this means that there is no available C++11 compiler on your computer. The presence or absence of a working C++11 compiler is determined at configure time when R is built. The tests used by R's configure script to determine C++11 support are more stringent in R 3.4.0 than in previous versions. However, if you are using gcc you should be protected against this change. For versions of gcc prior to 4.8 (which have only partial C++11 support) the same tests as in R 3.3.x are used. This maintains the current behaviour on long-term service Linux distributions that are stuck with old gcc versions. It would be help if you could share more information about your platform - i.e. the output of sessionInfo() - and specify the compiler version you are using. Martyn On Tue, 2017-04-18 at 15:11 +0200, Angerer, Philipp via R-devel wrote: > > Hi, > > This commit (I’m using the mirror to have a working link) broke C++11 > compilation. > > Before (and still now, according to the comments in the configure > script), it’s sufficient to just have “SystemRequirements: C++11” in > the DESCRIPTION file. > > > But now “R CMD install” fails with “C++11 standard requested but > CXX11 is not defined”, which is, according to the documentation , a > lie. > > I can’t even circumvent this, as setting “CXX11=$(CXX)” in the > src/Makevars file fails with “CXX definition recursive”, and > hardcoding “CXX11=g++” is a bad idea. > > Did I do sth. wrong or is the C++11 support in R just broken atm.? > > > Best, Philipp > > PS: After addressing all points in the submission of my popular > package “IRkernel”, I didn’t get any feedback, and the file just > vanished from the incoming directory in CRAN. I asked about it > multiple times but got no answer. What can I do now? > > > > > Helmholtz Zentrum Muenchen > > Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) > > Ingolstaedter Landstr. 1 > > 85764 Neuherberg > > www.helmholtz-muenchen.de > > Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe > > Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. > Alfons Enhsen > > Registergericht: Amtsgericht Muenchen HRB 6466 > > USt-IdNr: DE 129521671 > > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R 3.4 has broken C++11 support
Hi, This commit (I’m using the mirror to have a working link) broke C++11 compilation. Before (and still now, according to the comments in the configure script), it’s sufficient to just have “SystemRequirements: C++11” in the DESCRIPTION file. But now “R CMD install” fails with “C++11 standard requested but CXX11 is not defined”, which is, according to the documentation , a lie. I can’t even circumvent this, as setting “CXX11=$(CXX)” in the src/Makevars file fails with “CXX definition recursive”, and hardcoding “CXX11=g++” is a bad idea. Did I do sth. wrong or is the C++11 support in R just broken atm.? Best, Philipp PS: After addressing all points in the submission of my popular package “IRkernel”, I didn’t get any feedback, and the file just vanished from the incoming directory in CRAN. I asked about it multiple times but got no answer. What can I do now? Helmholtz Zentrum Muenchen Deutsches Forschungszentrum fuer Gesundheit und Umwelt (GmbH) Ingolstaedter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir'in Baerbel Brumme-Bothe Geschaeftsfuehrer: Prof. Dr. Guenther Wess, Heinrich Bassler, Dr. Alfons Enhsen Registergericht: Amtsgericht Muenchen HRB 6466 USt-IdNr: DE 129521671 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Q: Windows/readline: missing history search
Your error is in your subject line: getline rather than readline is used on Windows. (readline was not written for Windows and depends on a 'curses' library not available for Windows terminals let alone RGui. A considerable amount of time was spent trying to use it, unsuccessfully.) On 13/04/2017 07:23, Ulrich Windl wrote: Hello! Ever since I used R on Windows (RGui) I am missing the ability to search the command history (Cntrl+R (reverse-search-history) in BASH, for example). Is there a particular reason for having this function disabled? Another feature would be word-wise delete (kill-word, backward-kill-word). Probably being able to use the Alt-key as Meta key for readline (instead of activating menu entries) would be helpful. At least of the console window has the input focus. That's the Windows way. And users of e.g. Emacs on macOS know how this can cause awkward conflicts. Another nice feature would be PuTTY-like copying of selected text: It's sufficient to mark text in the console to have it put into the clipboard. In Rgui I need an explicit copy. That's the Windows way: PuTTY is using an older Unix/X11 standard (not so much used on Unix nowadays). Finally I'd like if Rgui would remember the state of the MDI main window (maximized or not, maybe position and size also): Currently it always starts maximized. AFAIR that is part of the configuration you can save. Regards, Ulrich -- Brian D. Ripley, rip...@stats.ox.ac.uk Emeritus Professor of Applied Statistics, University of Oxford __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Antw: Re: "table(droplevels(aq)$Month)" in manual page of droplevels
>>> Martin Maechler schrieb am 13.04.2017 um 16:16 >>> in Nachricht <22767.34875.318482.421...@stat.math.ethz.ch>: [...] > Ulrich, please note that in the end this was all because you're > still learning to understand R (e.g., data frames !) better. Hi! I understood that I did not understand the example due to my lack of R knowledge. That is the point you made. However I read a book on R, the introduction on R, and several tutorials on R, and I still never saw the use pattern presented in the example. Thus I think my proposal to present more comprehensible examples is a valid one. Alternatively the introduction to R could be extended to a level that allows the user to understand the example presented. Honestly there are many example I don't understand (plus descriptions that I hope to understand from the examples). While I understand that R developers prefer to be left alone, not hearing about such issues, I think even R developers could benefit from hearing of beginner's problems. Anyway R developers are free to forward messages to R-help if they think more appropriate for R-help. > > As such this was completely inappropriate for R-devel and should > have gotten to the R help list R-help. Regards, Ulrich > > With regards, > Martin Maechler, ETH Zurich [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
