Re: [Rd] Compilation problems
Well, I didn't go there because I don't have a clue
What I usually try in such circumstances is to Google the error message and see
if any ideas crop up. Looks like it is common to several applications that use
Java, so not likely an R issue per se.
I'd look into
- how to provoke the error to occur without make
- what are your resource limits (ulimit -a is your friend)?
- are any environment variables affecting the Java memory use? If not, perhaps
you need to set them to values less than the max allowed. Or twiddle command
line options.
etc.
-pd
On 13 Aug 2014, at 10:46 , André Z. D. A. wrote:
> Thanks a lot for this atention, Peter. But the fonts problem is just a
> warning: "configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF
> vignettes and package manuals will not be rendered optimally". So, no
> worries. I can live with render errors for the manuals. :)
>
> But the error I have with the 'make' is with Java. I don't know why. I even
> restarted the compilation again (the only detail I change is to pass
> "--prefix=/home/me/r/" to configure, to install it on my own folder instead
> of defaults). Then a "make" without arguments and it ends with this:
>
> -
> configuring Java ...
> Java interpreter : /usr/bin/java
> Could not create the Java virtual machine.
> Error occurred during initialization of VM
> Could not reserve enough space for object heap
>
> *** Java interpreter doesn't work properly.
>
> make[1]: [stamp-java] Error 1 (ignored)
> make[1]: Leaving directory `/home/me/r-src-second-try/R-3.1.1'
>
> -
>
>
> But how do anyone explain that onde a second run of 'make' it finished!? And
> on two more times it won't show the error again!
>
> Lets try to run R. Done 'make install'... and then run... it works!
>
> I'm lost. A bug? Something is not working as it should? What? Or is it fine??
>
> Andre'
>
>
>> On 11 Aug 2014, at 16:49 , peter dalgaard wrote:
>>
>>> On 11 Aug 2014, at 15:46 , André Z. D. A. wrote:
>>>
No, Peter, I have the "(2014-07-10, Sock it to Me) R-3.1.1.tar.gz" source.
Thanks for pointing it. So (I hope) it should be ok. Right?
>>>
>>> Not unlikely. (I goofed and thought that it only affected the development
>>> version.)
>>>
>>> Check
>>>
>>> kpsewhich inconsolata.sty
>>>
>>> if it is found, and zi4.sty is not, then it should be fixed by an upcoming
>>> patch release.
>>
>> ... and for a quick fix, edit the configure script. There is a section
>> looking like this
>>
>> if test -n "${KPSEWHICH}"; then
>> ${KPSEWHICH} zi4.sty > /dev/null
>> if test $? -eq 0; then
>> { $as_echo "$as_me:${as_lineno-$LINENO}: result: found zi4.sty" >&5
>> $as_echo "found zi4.sty" >&6; }
>> else
>> ${KPSEWHICH} inconsolata.sty > /dev/null
>> if test $? -ne 0; then
>> { $as_echo "$as_me:${as_lineno-$LINENO}: result: found inconsolata.sty" >&5
>>
>> (Search for "incons" and you'll get there.)
>>
>> Change the -ne in the penultimate line to -eq and rerun configure. This
>> isn't the correct fix because configure is autogenerated from other files,
>> but it should get you going.
>>
>> -pd
>>
>>> -pd
>>>
Peter Dalgaard, Professor wrote:
> If you are playing with the R-devel branch (or rather, trunk), then just
> hold
> your horses for a little while. There seems to be a reversed-logic bug
> that
> bites if you have inconsolata.sty and not zi4.sty.
>>>
>>> --
>>> Peter Dalgaard, Professor,
>>> Center for Statistics, Copenhagen Business School
>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>> Phone: (+45)38153501
>>> Email: pd@cbs.dk Priv: pda...@gmail.com
>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Email: pd@cbs.dk Priv: pda...@gmail.com
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Request to review a patch for rpart
Dear list For my work, it would be helpful if rpart worked seamlessly with an empty model: library(rpart); rpart(formula=y~0, data=data.frame(y=factor(1:10))) Currently, an unrelated error (originating from na.rpart) is thrown. At some point in the near future, I'd like to release a package to CRAN which uses rpart and relies on that functionality. I have prepared a patch (minor modifications at three places, and a test) which I'd like to propose for inclusion in the next CRAN release of rpart. The patch can be reviewed at https://github.com/krlmlr/rpart/tree/empty-model, the files (based on the current CRAN release 4.1-8) can be downloaded from https://github.com/krlmlr/rpart/archive/empty-model.zip. Thanks for your attention. With kindest regards Kirill Müller __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation problems
I would add it would be useful to know what system you are on and how much
overall memory the machine has (not to mention how many other users are on the
box). If you are on a linux variant, you can see installed memory by running:
cat /proc/meminfo. You might also want to look at top to see how many resources
are being used by you and others.
Regarding Java, if you had done a search for 'java xmx', you'd see that you can
control the maximum heap size of the JVM using this option. [1] So, if you
know how much memory you have available on your system, then you can set this
value to something lower and verify that you can start the JVM in isolation. As
for specifics, I wouldn't know, since you didn't provide the JVM version you're
using. Try java -version to give us specifics.
Brian
[1]
http://docs.oracle.com/cd/E13150_01/jrockit_jvm/jrockit/jrdocs/refman/optionX.html
�
Brian Lee Yung Rowe
Founder, Zato Novo
Professor, M.S. Data Analytics, CUNY
On Aug 13, 2014, at 5:15 AM, peter dalgaard wrote:
> Well, I didn't go there because I don't have a clue
>
> What I usually try in such circumstances is to Google the error message and
> see if any ideas crop up. Looks like it is common to several applications
> that use Java, so not likely an R issue per se.
>
> I'd look into
>
> - how to provoke the error to occur without make
> - what are your resource limits (ulimit -a is your friend)?
> - are any environment variables affecting the Java memory use? If not,
> perhaps you need to set them to values less than the max allowed. Or twiddle
> command line options.
>
> etc.
>
> -pd
>
> On 13 Aug 2014, at 10:46 , Andr� Z. D. A. wrote:
>
>> Thanks a lot for this atention, Peter. But the fonts problem is just a
>> warning: "configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF
>> vignettes and package manuals will not be rendered optimally". So, no
>> worries. I can live with render errors for the manuals. :)
>>
>> But the error I have with the 'make' is with Java. I don't know why. I even
>> restarted the compilation again (the only detail I change is to pass
>> "--prefix=/home/me/r/" to configure, to install it on my own folder instead
>> of defaults). Then a "make" without arguments and it ends with this:
>>
>> -
>> configuring Java ...
>> Java interpreter : /usr/bin/java
>> Could not create the Java virtual machine.
>> Error occurred during initialization of VM
>> Could not reserve enough space for object heap
>>
>> *** Java interpreter doesn't work properly.
>>
>> make[1]: [stamp-java] Error 1 (ignored)
>> make[1]: Leaving directory `/home/me/r-src-second-try/R-3.1.1'
>>
>> -
>>
>>
>> But how do anyone explain that onde a second run of 'make' it finished!? And
>> on two more times it won't show the error again!
>>
>> Lets try to run R. Done 'make install'... and then run... it works!
>>
>> I'm lost. A bug? Something is not working as it should? What? Or is it fine??
>>
>> Andre'
>>
>>
>>> On 11 Aug 2014, at 16:49 , peter dalgaard wrote:
>>>
On 11 Aug 2014, at 15:46 , Andr� Z. D. A. wrote:
> No, Peter, I have the "(2014-07-10, Sock it to Me) R-3.1.1.tar.gz"
> source. Thanks for pointing it. So (I hope) it should be ok. Right?
Not unlikely. (I goofed and thought that it only affected the development
version.)
Check
kpsewhich inconsolata.sty
if it is found, and zi4.sty is not, then it should be fixed by an upcoming
patch release.
>>>
>>> ... and for a quick fix, edit the configure script. There is a section
>>> looking like this
>>>
>>> if test -n "${KPSEWHICH}"; then
>>> ${KPSEWHICH} zi4.sty > /dev/null
>>> if test $? -eq 0; then
>>> { $as_echo "$as_me:${as_lineno-$LINENO}: result: found zi4.sty" >&5
>>> $as_echo "found zi4.sty" >&6; }
>>> else
>>> ${KPSEWHICH} inconsolata.sty > /dev/null
>>> if test $? -ne 0; then
>>> { $as_echo "$as_me:${as_lineno-$LINENO}: result: found inconsolata.sty" >&5
>>>
>>> (Search for "incons" and you'll get there.)
>>>
>>> Change the -ne in the penultimate line to -eq and rerun configure. This
>>> isn't the correct fix because configure is autogenerated from other files,
>>> but it should get you going.
>>>
>>> -pd
>>>
-pd
> Peter Dalgaard, Professor wrote:
>
>> If you are playing with the R-devel branch (or rather, trunk), then just
>> hold
>> your horses for a little while. There seems to be a reversed-logic bug
>> that
>> bites if you have inconsolata.sty and not zi4.sty.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk Priv: pda...@gmail.com
>>>
>>> --
>>> Peter Dalgaard, Professor,
>>> Center for Statistics, Cope
Re: [Rd] could not find function "anyNA" when building tools package in R 3.1.1
I figured out what I did wrong. The end of my $LDFLAGS contained "-Wl,-rpath,/path/to/an/old/R/installation/lib64/R/lib" (which predated anyNA) and I was also using --enable-R-shlib, so possibly related to PR#15790 (I say possibly, because I was not using "make install-libR"). __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation problems
On Sat, Aug 9, 2014 at 10:56 AM, André Z. D. A. wrote: > Could not create the Java virtual machine. > Error occurred during initialization of VM > Could not reserve enough space for object heap I have seen this error before when running java inside a vm container (openvz, lxc) where the kernel does not give java permission to query the amount of available memory, and hence java assumes it must be 0. In these cases you need to manually set the MaxHeapSize by passing a parameter to java, see: http://stackoverflow.com/questions/4401396/could-not-reserve-enough-space-for-object-heap. I am not sure where in the compilation that java gets invoked, and if there is a way to pass parameters. Perhaps you can use the _JAVA_OPTIONS environment variable. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
