Dear Peter: On Mon, Mar 10, 2014 at 3:07 AM, peter dalgaard <[email protected]> wrote: > (oops, forgot to cc: R-Sig-Mac...) > > On 10 Mar 2014, at 05:53 , 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. >> >> 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. > > I see you're building in the source directory. > > You might try compiling in a separate directory (tar xvfz R-*.tgz; mkdir > BUILD; cp config.site BUILD ; cd BUILD; ../R/configure; ...), that's what all > the developers do. > > I haven't got the foggiest why compiling in the source dir might step on the > recommended packages, but since it is an option that is rarely taken, various > anomalies may happen. > (One guess is that ownership or permissions on the source directory don't > allow the creation of ./Rtmp*, umask settings are another common culprit). > > What's in your config.site, by the way? > > -pd > > -- > Peter Dalgaard, Professor, > Center for Statistics, Copenhagen Business School > Solbjerg Plads 3, 2000 Frederiksberg, Denmark > Phone: (+45)38153501 > Email: [email protected] Priv: [email protected]
Thanks so much for your time. As you saw from the message I just sent, the problem was with the setting of the TEMPDIR environment variable to ".". According to Simon, this needs to have an absolute path. To get things working, I simply unset the variable and then the make finished without error. If I need the value set in the future (I think for latex2html, but I cannot remember now), then I'll try with an absolute path. I'll take your suggestion on separate build directory under advisement going forward. I appreciate this tidbit. Also, I assume your question re config.site is moot, but I'm happy to send it if you are still interested for some reason. ;) Thank you again for your time. Take care. _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
