[Rd] Compilation problems
Hello, I'm trying to compile and install R for my user in a machine without admin privileges. I have done this before, so this is fine. But I have 2 problems with R compilation right now. After ./configure --prefix=/home/me/dir/ I get this: R is now configured for x86_64-unknown-linux-gnu Source directory: . Installation directory:/home/balacobaco/bbin C compiler:gcc -std=gnu99 -g -O2 Fortran 77 compiler: gfortran -g -O2 C++ compiler: g++ -g -O2 C++ 11 compiler: g++ -std=c++11 -g -O2 Fortran 90/95 compiler:gfortran -g -O2 Obj-C compiler: Interfaces supported: X11, tcltk External libraries:readline, ICU Additional capabilities: PNG, JPEG, TIFF, NLS, cairo Options enabled: shared BLAS, R profiling Recommended packages: yes configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes and package manuals will not be rendered optimally Problem 1) How do I get rid of this warning about "inconsolata.sty" and "zi4.sty". Can I have this file locally for my installation or compilation? Where do I download it? Where do I put them? Problem 2) The compilation fails with the following message: (...) 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/dir' What happened? What's wrong with my server's java? What caused this error, so I can try to fix or skip it, if possible. Thank you, Andre' __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation problems
> Worst case is that you'll have to install TeX in your local user directory. I'll try to find it again. The search I tried didn't look as easy, very few results, none helpful. And if I could install *just the fonts* on my local dir, instead of the full TeX, it would be perfect. But I don't know how to do it. Is it possible? > Second, your JVM is requesting more memory than is available on the > box. How much memory do you have available? Make sure you have a > sufficient amount that is free. Worst case you can set the Xmx variable > to reduce max memory allowed to the JVM, but your app performance > will be pathetic. The Xmx variable from what? From R's code? Or is it java config? The server is pretty big. 12GiB RaM and 500GiB of disk free. Process' limits may exist (I guess), but I don't know how to find about them. Andre' "Brian Lee Yung Rowe" wrote: > Hi your first problem is a common issue. Make sure you TeX installation has > the inconsolata.sty file installed. There are numerous pages on the web to > address this. Worst case is that you'll have to install TeX in your local > user directory. > > Second, your JVM is requesting more memory than is available on the box. How > much memory do you have available? Make sure you have a sufficient amount > that is free. Worst case you can set the Xmx variable to reduce max memory > allowed to the JVM, but your app performance will be pathetic. > > Good luck, > Brian > > • > Brian Lee Yung RoweFounder, Zato Novo > Professor, M.S. Data Analytics, CUNY > > On Aug 9, 2014, at 7:41 AM, "André Z. D. A." wrote: > >> Hello, >> >> I'm trying to compile and install R for my user in a machine without admin >> privileges. I have done this before, so this is fine. But I have 2 problems >> with R compilation right now. >> >> After ./configure --prefix=/home/me/dir/ I get this: >> >> >> >> R is now configured for x86_64-unknown-linux-gnu >> >> Source directory: . >> Installation directory: /home/balacobaco/bbin >> >> C compiler: gcc -std=gnu99 -g -O2 >> Fortran 77 compiler: gfortran -g -O2 >> >> C++ compiler: g++ -g -O2 >> C++ 11 compiler: g++ -std=c++11 -g -O2 >> Fortran 90/95 compiler: gfortran -g -O2 >> Obj-C compiler: >> >> Interfaces supported: X11, tcltk >> External libraries: readline, ICU >> Additional capabilities: PNG, JPEG, TIFF, NLS, cairo >> Options enabled: shared BLAS, R profiling >> >> Recommended packages: yes >> >> configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes >> and package manuals will not be rendered optimally >> >> >> >> Problem 1) How do I get rid of this warning about "inconsolata.sty" and >> "zi4.sty". Can I have this file locally for my installation or compilation? >> Where do I download it? Where do I put them? >> >> Problem 2) The compilation fails with the following message: >> >> >> (...) >> 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/dir' >> >> >> >> What happened? What's wrong with my server's java? What caused this error, >> so I can try to fix or skip it, if possible. >> >> Thank you, >> >> Andre' >> >> __ >> 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
Re: [Rd] Compilation problems
On 09 Aug 2014, at 16:50 , André Z. D. A. wrote: >> Worst case is that you'll have to install TeX in your local user directory. > > I'll try to find it again. The search I tried didn't look as easy, very few > results, none helpful. And if I could install *just the fonts* on my local > dir, instead of the full TeX, it would be perfect. But I don't know how to do > it. Is it possi 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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation problems
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? 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. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation problems
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. -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 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation problems
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
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
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
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] 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
Re: [Rd] Compilation problems
It is not a virtual machine. But every process has it's memory limited. And Java will insanely (try to) reserve 1/4 of memory for its heap on every run, by default. Ugly language, that would be at least 3GB on this server. So the fix is -Xms and -Xmx passed using _JAVA_OPTIONS variable. Now it happily runs saying: "Picked up _JAVA_OPTIONS: -Xmx64m -Xms6m" > 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
