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

[Bryan Renne]

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, and so I did
not say that up front, though perhaps I could have been more clear on
this point rather than relegating it to a mention in passing to
"CRAN-provided source."  My apologies.

To clarify:  I have this problem both with CRAN-provided source that I
try to compile directly by hand (with "configure" and "make") and with
the homebrew-driven automatic compilation procedure.  In either case,
the error seems to be the same and to occur in the same place:  R
compiles but once it comes time to install the recommended libraries,
the R binary has some problem reading (or untarring/decompressing?)
the .tgz of various libraries, such as MASS, and this leads the "make"
script to abort.  I provide the links to the homebrew output because
what is seen there in the "configure" and "make" output is essentially
the same as what I see when I try to compile from CRAN-provided source
by hand (and I don't want to cut-and-paste everything here since it is
already available there via the links to the gists below).

Right now I am trying to get the CRAN-provided source to complete its
"make" script before I try and go back to homebrew.  So right now this
really is about R 3.0.2 (or 3.0.3) on OS X 10.9.2.  (Though perhaps
some of the other non-R tools provided by homebrew may be relevant
here.)

>>  Everything seems to work up to the installation of
>> recommended R packages.  At that point, the make fails.  In particular,
>> after running "R CMD INSTALL MASS.tgz" (directly or the essentially
>> equivalent but multi-optioned version that is run via the Makefile), I end
>> up with the following fatal error:
>>
>> Warning in read.dcf(fd <- file.path(pkg, "DESCRIPTION")) :
>>>  cannot open compressed file
>>> './RtmpeHPfcG/R.INSTALLb9055b3c3f45/MASS/DESCRIPTION', probable reason 'No
>>> such file or directory'
>>> Error: error reading file
>>> './RtmpeHPfcG/R.INSTALLb9055b3c3f45/MASS/DESCRIPTION'
>>
>>
>> For more detailed output of "configure" and "make" please see the output
>> from these failed homebrew installations (which are essentially identical
>> with what I get when I try to install from CRAN-provided source):
>>
>> for R 3.0.2:  https://gist.github.com/bprenne/8626679
>>
>> for R 3.0.3:  https://gist.github.com/bprenne/9405569
>>
>> Someone on the homebrew team recommended I contact people via an R list (
>> https://github.com/Homebrew/homebrew-science/issues/640), so here I am.
>>
>> 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?

I tried using the debug command you suggested.  I'm not sure if I am
doing this right (as I am completely new to R, so new I cannot even
get the install to fully complete!), but here is what I did and what I
saw:

$ ../../../bin/R

R version 3.0.2 (2013-09-25) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.1.0 (64-bit)
[[...warranty and initial instructions deleted...]]

> debug(tools:::.install_packages)
> install.packages("MASS.tgz", repos=NULL)

Warning in read.dcf(fd <- file.path(pkg, "DESCRIPTION")) :
  cannot open compressed file
'./Rtmp8WNcfs/R.INSTALLbf2333341aff/MASS/DESCRIPTION', probable reason
'No such file or directory'
Error: error reading file './Rtmp8WNcfs/R.INSTALLbf2333341aff/MASS/DESCRIPTION'
Warning message:
In install.packages("MASS.tgz", repos = NULL) :
  installation of package 'MASS.tgz' had non-zero exit status

This seems to just be a repeat of the error message provided if I use
the command-line version "R INSTALL CMD MASS.tgz".  Doesn't it seem
like something strange is going on with the untar/decompress internals
here?

Other ideas as to how I might proceed?

I hope all is well.