[R-SIG-Mac] R 3.0.2/3.0.3 source install problems on OS X 10.9.2

[peter dalgaard]

(oops, forgot to cc: R-Sig-Mac...)

On 10 Mar 2014, at 05:53 , Bryan Renne <brenne at gmail.com> wrote:

> Hi Simon.  Thank you for your reply.
> 
> On Sun, Mar 9, 2014 at 6:41 PM, Simon Urbanek
> <simon.urbanek at r-project.org> wrote:
>> Bryan,
>> 
>> On Mar 9, 2014, at 3:59 PM, Bryan Renne <brenne at gmail.com> wrote:
>> 
>>> Thank you for your reply, Peter.
>>> 
>>> On Sun, Mar 9, 2014 at 3:31 AM, peter dalgaard <pdalgd at gmail.com> wrote:
>>>> 
>>>> On 09 Mar 2014, at 00:21 , Bryan Renne <brenne at gmail.com> wrote:
>>>> 
>>>>> Hi there.  I am having compilation problems with R 3.0.2 (and R 3.0.3) on
>>>>> OS X 10.9.2.
>>>> 
>>>> On homebrew.... (Would have been useful to say up front.)
>>> 
>>> Actually, no.  This is *not* a homebrew specific problem,
>> 
>> It *is* as you even point yourself further down. It doesn't occur on a clean OS X system.
> 
> OK, so to rule out any possible homebrew issues, I used the homebrew
> uninstall script to delete homebrew and all homebrew-installed stuff
> (https://gist.github.com/mxcl/1173223).  This script wipes the system
> clean of homebrew.
> 
> I then installed gfortran 4.8.2 binaries using the provided pkg file
> for OS X Mavericks (http://gcc.gnu.org/wiki/GFortranBinaries#MacOS).
> 
> I then downloaded R-3.0.3.tar.gz from the main page
> (http://cran.r-project.org/).  I untarred, configured (with options
> "--with-aqua --enable-R-framework --with-lapack") and ran make.  I
> received the same error as before.  Here is the tail end of the "make"
> output:
> 
> begin installing recommended package MASS
> Warning in read.dcf(fd <- file.path(pkg, "DESCRIPTION")) :
> cannot open compressed file
> './RtmpwOScIp/R.INSTALL588267e46267/MASS/DESCRIPTION', probable reason
> 'No such file or directory'
> Error: error reading file './RtmpwOScIp/R.INSTALL588267e46267/MASS/DESCRIPTION'
> make[2]: *** [MASS.ts] Error 1
> make[1]: *** [recommended-packages] Error 2
> make: *** [stamp-recommended] Error 2
> 
> Please see the following gist for full details of the system
> configuration and output of "configure" and "make":
> 
> https://gist.github.com/bprenne/9459571
> 
> In particular, you'll notice in the section for make the error I
> quoted above.  Also, at the very bottom of the gist, I have provided
> what I think shows that the error is happening with the "R CMD INSTALL
> MASS.tgz" step in the installation of recommended packages (somewhere
> deep within the Makefile steps).
> 
>>>>> [[...snip...]
>>>>> I also tried setting R_INSTALL_TAR to the system tar or to a
>>>>> homebrew-installed gnutar.  Neither helped.
>>>>> 
>>>>> Any suggestions on how I might proceed?
>>>> 
>>>> Hmm, difficult to tell. If push comes to shove, you could try getting more info out of the INSTALL process (inject a debug(tools:::.install_packages), I suppose, but it is a bit beyond me currently). But first, I'd check what Makeconf sets the TAR variable to.
>>> 
>>> Thank you for these suggestions.  Makeconf contains this line:
>>> 
>>> TAR = /usr/local/bin/gtar
>>> 
>>> This is the homebrew-installed gnutar.  However, is the R binary
>>> (which has properly compiled and is the source of the error in library
>>> installation) reading Makeconf to determine how to untar the library
>>> .tgz?
>>> 
>> 
>> No, it is set in etc/Renviron which is in turn populated via configure by the value you see in Makeconf.
>> 
>> Try setting
>> 
>> TAR=/usr/bin/tar
>> 
>> since system tar normally works. But that may be only the tip of the iceberg, we can't tell what else you installed that breaks otherwise working system. If in doubt, share the list with us so we can try to replicate it.
>> 
>> Cheers,
>> Simon
> 
> Thanks for this suggestion with setting the TAR variable.  As you can
> see from the gist (https://gist.github.com/bprenne/9459571), this is
> now the default value because homebrew has been wiped from the system.
> However, even with this value, the problem still obtains.
> 
> I've tried to provide everything I can think will be useful in the gist.
> 
> Is there something more I can provide or some way I can get more
> fine-grained debugging information to help in diagnosis?
> 
> I appreciate your time and any thoughts you might have that you think
> would help.

I see you're building in the source directory.

You might try compiling in a separate directory (tar xvfz R-*.tgz; mkdir BUILD; cp config.site BUILD ; cd BUILD; ../R/configure; ...), that's what all the developers do. 

I haven't got the foggiest why compiling in the source dir might step on the recommended packages, but since it is an option that is rarely taken, various anomalies may happen.
(One guess is that ownership or permissions on the source directory don't allow the creation of ./Rtmp*, umask settings are another common culprit).

What's in your config.site, by the way?

-pd

-- 
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