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, 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? 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. _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
