On 11-03-2014, at 05:32, Bryan Renne <[email protected]> wrote: > Dear Simon: > > On Mon, Mar 10, 2014 at 11:23 AM, Simon Urbanek > <[email protected]> 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. Berend > Problem solved. Thank you so much for your help with this. > >> >> On Mar 10, 2014, at 12:53 AM, Bryan Renne <[email protected]> wrote: >> >>> Hi Simon. Thank you for your reply. >>> >>> On Sun, Mar 9, 2014 at 6:41 PM, Simon Urbanek >>> <[email protected]> wrote: >>>> Bryan, >>>> >>>> On Mar 9, 2014, at 3:59 PM, Bryan Renne <[email protected]> wrote: >>>> >>>>> Thank you for your reply, Peter. >>>>> >>>>> On Sun, Mar 9, 2014 at 3:31 AM, peter dalgaard <[email protected]> wrote: >>>>>> >>>>>> On 09 Mar 2014, at 00:21 , Bryan Renne <[email protected]> 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. >>> >> > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
