[R] Compiling R with zlib in non-standard location

[Marc Schwartz]

Hi David,

It has been a while since I have worked on RH based systems, but looking at Martyn's reply, which includes:

CFLAGS="-g -O2 -I/path/to/my/headers" \
LDFLAGS="-L/path/to/my/libs" \
./configure

and references to the R Installation and Administration manual sections B3.3 and B7, if you used the lines verbatim as above, you will likely need to explicitly 'export' the two flag variables. Thus try:

export CFLAGS="-g -O2 -I/path/to/my/headers" \
export LDFLAGS="-L/path/to/my/libs" \
./configure


Using 'export' will ensure that the environment variables are also passed down to child processes started within the current shell session, which may be where it is failing.

See if that works. If not, subscribe to and post a new thread to R-SIG-Fedora, as there will be a focused audience there.

Regards,

Marc


> On May 23, 2017, at 12:02 PM, David Chin <david.chin.work at gmail.com> wrote:
> 
> Hi Marc,
> 
> Pre-compiled RPMs for R are up to 3x slower than "self-compiled" R using
> Intel MKL.  Yes, I do know about Microsoft R Open, but it wants to
> overwrite the default /usr/bin/R and I have AMD machines in my cluster,
> which cannot run MRO. So, I want to do my own compilation and install R in
> a non-standard location so that it can be used by loading a modulefile.  I
> also have users who have varying requirements for versions of R (for
> whatever reason), so I need to provide different versions.
> 
> I also tried the suggested solution
> https://stat.ethz.ch/pipermail/r-devel/2017-April/074162.html  -- but it
> did not work for me. The configure script still picked up zlib.h from
> /usr/include and deduced that it was an older version and would quit with
> error.
> 
> Apologies if this is a duplicate. I sent my first response with the wrong
> email address.
> 
> 
> On Tue, May 23, 2017 at 12:50 PM, Marc Schwartz <marc_schwartz at me.com>
> wrote:
> 
>> 
>>> On May 23, 2017, at 11:07 AM, David Chin <david.chin.work at gmail.com>
>> wrote:
>>> 
>>> Hi all,
>>> 
>>> I am trying to compile R 3.4.0 on a RHEL 6.5 system. R requires a newer
>>> version of zlib than is standard on RHEL 6.5. I do have a newer version
>>> that satisfies R's requirement, but the configure script gives no way of
>>> specifying a non-standard location of zlib.
>>> 
>>> Is there a way around this? Or should I try to make a feature request?
>>> 
>>> Thanks in advance,
>>>   Dave
>> 
>> 
>> Hi,
>> 
>> This was recently asked here:
>> 
>>  https://stat.ethz.ch/pipermail/r-devel/2017-April/074157.html
>> 
>> Martyn provided a resolution in the follow up post, including a pointer to
>> the EPEL, where there are pre-compiled RPMs for R.
>> 
>> For future reference, there is a dedicated e-mail list for queries
>> pertaining to R on RH/Fedora based distributions:
>> 
>>  https://stat.ethz.ch/mailman/listinfo/r-sig-fedora
>> 
>> Regards,
>> 
>> Marc Schwartz
>> 
>>