From rowe at muxspace.com  Wed Aug 13 14:10:15 2014
From: rowe at muxspace.com (Brian Lee Yung Rowe)
Date: Wed, 13 Aug 2014 08:10:15 -0400
Subject: [Rd] Compilation problems
In-Reply-To: <85765E3D-DEE8-414A-94F3-1F8553226B4C@gmail.com>
References: <2376271407919565@web30m.yandex.ru>
	<85765E3D-DEE8-414A-94F3-1F8553226B4C@gmail.com>
Message-ID: <7E170D2A-887B-4DAD-ABAC-AF26D3453A41@muxspace.com>

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 <pdalgd at gmail.com> 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. <andrezda10 at yandex.com> 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 <pdalgd at gmail.com> wrote:
>>> 
>>>> On 11 Aug 2014, at 15:46 , Andr? Z. D. A. <andrezda10 at yandex.com> 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.mes at cbs.dk Priv: PDalgd at gmail.com
>>> 
>>> --
>>> Peter Dalgaard, Professor,
>>> Center for Statistics, Copenhagen Business School
>>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>>> Phone: (+45)38153501
>>> Email: pd.mes at cbs.dk Priv: PDalgd at gmail.com
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Email: pd.mes at cbs.dk  Priv: PDalgd at gmail.com
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel


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[Rd] Compilation problems
Brian Lee Yung Rowe