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

Tue Mar 11 16:04:24 CET 2014

Dear Brian:

On Tue, Mar 11, 2014 at 1:51 AM, Prof Brian Ripley
<ripley at stats.ox.ac.uk> wrote:
> On 11/03/2014 07:40, Berend Hasselman wrote:
>>
>>
>> On 11-03-2014, at 05:32, Bryan Renne <brenne at gmail.com> wrote:
>>
>>> Dear Simon:
>>>
>>> On Mon, Mar 10, 2014 at 11:23 AM, Simon Urbanek
>>> <simon.urbanek at r-project.org> wrote:
>>>>
>>>> Bryan,
>>>>
>>>> based on the gist output I think I have a candidate - please check that
>>>> you're not re-defining TMP or TMPDIR to a relative path - that would break
>>>> pretty much anything. Check with
>>>>
>>>> set | grep 'T*MP'
>>>>
>>>> This must be either undefined or the paths *must* be absolute, i.e.
>>>> start with a slash /
>>>>
>>>> Other replies below, but I think the above may be the main issue.
>>>
>>>
>>> That's it!  I can't believe you noticed that.  Thank you so much for your
>>> help.
>>>
>>> I had executed "export TEMPDIR=." for some other program (I think
>>> latex2html?) that requires some non-null setting and, after clearing
>>> this setting so that TEMPDIR is unset, the installation of recommended
>>> packages completed and the make script finished without errors.  Looks
>>> like an absolute path should be used as you suggest.
>>>
>>
>> Isn't TMPDIR set automatically by OS X?
>> I've never seen it to be null on my machines.
>
>
> Yes, but you can reset it (and sometimes it is necessary because of its
> length or the non-alphanumeric characters Apple used to put in it).
>
> What puzzles me is that TEMPDIR (with an E) is ever used: it is not used by
> R.

Yes, you're right, it was TMPDIR (without an E) that caused the
problem.  The extra E I entered in the variable name in my previous
message was a typo.

And indeed, I had set TMPDIR in my .profile (for bash) because
latex2html would for some reason not work without me setting a value
for this explicitly.  I think I first chose the value of TMPDIR=.
based on this page (under the section title "Documentation"):

https://www.lri.fr/~filliatr/bibtex2html/

Take care.

>
>>
>> Berend
>>
>>> Problem solved.  Thank you so much for your help with this.
>>>
>>>>
>>>> On Mar 10, 2014, at 12:53 AM, 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.
>>>>>
>>>>
>>>> Thanks, it would be sufficient to just rename /usr/local and re-install
>>>> the gfortran from CRAN.
>>>>
>>>> I cannot reproduce the issue with exactly your settings on a clean
>>>> machine, so it must be some custom configuration of yours. I suspect you may
>>>> have set TMP/TMPDIR to . which is invalid - please check.
>>>>
>>>> Thanks,
>>>> Simon
>>>
>>>
>>> Acknowledged.  Will take the point about /usr/local under advisement
>>> going forward.
>>>
>>> Thank you again for your time.
>>>
>>>>
>>>>> 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.
>>>>>
>>>>
>>>
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>>
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>
>
> --
> Brian D. Ripley,                  ripley at stats.ox.ac.uk
> Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
> University of Oxford,             Tel:  +44 1865 272861 (self)
> 1 South Parks Road,                     +44 1865 272866 (PA)
> Oxford OX1 3TG, UK                Fax:  +44 1865 272595