<div dir="ltr">As promised:<br><br><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div>otool <- Sys.which("otool")</div><div>if (otool == "") {</div><div> stop("This utility requires 'otool' to run")</div>
<div>}</div><div><br></div><div>allPackages <- list.files(.libPaths(), full.names = TRUE)</div><div>stdLibsUsed <- lapply(allPackages, function(path) {</div><div> pkgName <- basename(path)</div><div> libPath <- file.path(path, "libs", paste0(pkgName, ".so"))</div>
<div> if (!file.exists(libPath)) {</div><div> return(character())</div><div> }</div><div> otoolOutput <- system2("otool", args = c("-L", libPath), stdout = TRUE)</div><div> c(</div><div> "libc++"[any(grepl("libc++", otoolOutput, fixed = TRUE))],</div>
<div> "libstdc++"[any(grepl("libstdc++", otoolOutput, fixed = TRUE))]</div><div> )</div><div>})</div><div><br></div><div>pkgsWithLibStdCpp <- allPackages[sapply(stdLibsUsed, function(x) {</div><div>
"libstdc++" %in% x</div><div>})]</div><div><br></div><div>pkgsWithLibCpp <- allPackages[sapply(stdLibsUsed, function(x) {</div><div> "libc++" %in% x</div><div>})]</div><div> </div><div>list(</div>
<div> "libstdc++" = pkgsWithLibStdCpp,</div><div> "libc++" = pkgsWithLibCpp</div><div>)</div></blockquote><br><div>I'm not sure where this could live, but basically, Mavericks users who see any packages linking to `libstdc++` would probably want to reinstall those packages. There may be some packages that need to explicitly link to libstdc++ even on a Mavericks system for other reasons, though...<br>
<br>That said, most of the initial migration headaches seem to be over so this probably would have been more useful half a year ago ;)<br><br>Cheers,<br>Kevin</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Sun, Aug 3, 2014 at 1:10 PM, Kevin Ushey <span dir="ltr"><<a href="mailto:kevinushey@gmail.com" target="_blank">kevinushey@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">I think this bit:<div><br></div><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><div><div>The \texttt{clang} and \texttt{clang++} compilers from the LLVM project can</div></div><div><div>
also be used as they are inter-operable with \texttt{gcc} et al. The</div></div><div><div>\texttt{clang++} compiler is interesting as it emits much more</div></div><div><div>comprehensible error messages than \texttt{g++} (though \texttt{g++} 4.8 and 4.9</div>
</div><div><div>have caught up).</div></div></blockquote><div><br></div><div>needs to be amended. The standard library implementation used with gcc (libstdc++) is not ABI compatible with the one used with clang (libc++). This has been a common pain point for users running Snow Leopard who updated their operating system to Mavericks, and also installed Mavericks R, without re-installing any previously installed packages -- having a clang-compiled package with C++ code try to link to an older gcc-compiled package with C++ code caused many headaches for users, either with weird segfaults or errors on loading packages or (if lucky) errors at link time.<br>
</div><div><br></div><div>In addition:</div><div><br></div><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px"><div><div>OS X used to be a little more conservative with compiler versions as Apple</div></div>
<div><div>stuck with gcc-4.2. Following the 'Mavericks' release, it is the opposite as</div></div><div><div>only llvm is provide in Xcode---while the R build provided by CRAN still has</div></div><div><div>hardwired settings for the gcc/g++ combination. </div>
</div><div><div><br></div></div><div><div>Until that is resolved, users either need to create softlinks (say, in,</div></div><div><div>\code{/usr/local/bin}) or override the \code{CC} and \code{CXX} variables via a</div>
</div>
<div><div>file \code{~/.R/Makevars} or its system-equivalent in R's \code{etc/}</div></div><div><div>directory. Also see \faq{q:OSXArma} below. In general, consult the</div></div><div><div>\code{r-sig-mac} mailing list for further details.</div>
</div></blockquote><div><br></div><div>There are now two separate CRAN binaries, one compiled for Snow Leopard and above (using gcc-4.2.1), and one compiled for Mavericks (using the latest clang release distributed with Mavericks). Fortunately, since R doesn't include any C++ code, one can use Snow Leopard R with clang-compiled packages containing C++ code with no problems. However, packages containing C++ code should be compiled with the same compiler suite. This is a bit of a pain point for users of Snow Leopard R who might be using clang -- the binaries distributed by CRAN are compiled with gcc-4.2 and libstdc++ (by default) and those won't be compatible with packages compiled from source with clang++ and libc++.</div>
<div><br></div><div>Professor Ripley compiled a set of recommendations in a post on R-SIG-Mac that we could link to: <a href="https://stat.ethz.ch/pipermail/r-sig-mac/2014-April/010835.html" target="_blank">https://stat.ethz.ch/pipermail/r-sig-mac/2014-April/010835.html</a></div>
<div><br></div><div>We might also link to the BioConductor guidelines for Mavericks + C++11 development: <a href="http://www.bioconductor.org/developers/how-to/mavericks-howto/" target="_blank">http://www.bioconductor.org/developers/how-to/mavericks-howto/</a>; it's a nice overview of the state of the world there.<br>
<br>The general prescription, I think:<br><br></div><div>1. If you want to mix and match CRAN binaries with packages installed from source, make sure your compiler suite matches that of the CRAN R you've installed. Otherwise, the safer route is to compile all packages from source.<br>
</div><div><br>2. If you're running OS X Mavericks (or greater), and want to compile packages from source (ostensibly using clang), use the Mavericks CRAN R binary, otherwise you will run into frustrating ABI compatibility issues (as Snow Leopard R will grab CRAN package binaries compiled with gcc 4.2; again incompatible with those compiled with clang)*.<br>
</div><div><br></div><div>I can try to amend the vignette to this effect later and submit a PR. If anyone else on the list thinks I missed something here, let me know too.<br></div><div><br></div><div>Cheers,<br>Kevin<br>
<br>*I suppose someone running Mavericks with a Snow Leopard R could set the 'pkgType' option (see ?install.packages) to grab Mavericks binaries of packages, but I doubt this is recommended.<br><br>PS: A useful utility one could write would check what C++ standard library implementation each installed package links to. Maybe I'll write that...</div>
</div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Aug 3, 2014 at 9:17 AM, Dirk Eddelbuettel <span dir="ltr"><<a href="mailto:edd@debian.org" target="_blank">edd@debian.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
I noticed a post cross-referenced on R Bloggers about Rcpp(Armadillo), OS X<br>
and the need for an additional Fortran packages from Simon's site -- so I<br>
took this as opportunity to update the OS X answers in the Rcpp FAQ vignette.<br>
<br>
As I don't use OS X, I'd appreciate a second set of eyes by anyone with a<br>
moment to spare and some mad OS X "skillz".<br>
<br>
Current Rnw file<br>
<a href="https://github.com/RcppCore/Rcpp/blob/master/vignettes/Rcpp-FAQ.Rnw" target="_blank">https://github.com/RcppCore/Rcpp/blob/master/vignettes/Rcpp-FAQ.Rnw</a><br>
<br>
Link to the committed changes<br>
<a href="https://github.com/RcppCore/Rcpp/commit/e892622ce1c741f47b2e43b1d44ece32d44ee239" target="_blank">https://github.com/RcppCore/Rcpp/commit/e892622ce1c741f47b2e43b1d44ece32d44ee239</a><br>
<br>
Corrections and improvements to other parts are of course welcome as well :)<br>
<span><font color="#888888"><br>
Dirk<br>
<br>
--<br>
<a href="http://dirk.eddelbuettel.com" target="_blank">http://dirk.eddelbuettel.com</a> | @eddelbuettel | <a href="mailto:edd@debian.org" target="_blank">edd@debian.org</a><br>
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