Dear Brian: On Tue, Mar 11, 2014 at 1:51 AM, Prof Brian Ripley <[email protected]> wrote: > On 11/03/2014 07:40, Berend Hasselman wrote: >> >> >> 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. > > > 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 <[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 >> > > > -- > Brian D. Ripley, [email protected] > 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 _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
