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

[Simon Urbanek]

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.


> 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?
> 

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


> 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.
> 
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