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

[Bryan Renne]

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.