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. 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
