Build error - not sure where to look
On Mar 3, 2012, at 11:06 PM, Ben Madin wrote:
G'day all, this is hopefully straightforward, but I'm not sure where to look. I am trying to build the surveillance package (which is excluded from the binaries because of a memory problem). I have successfully built it previously on Snow Leopard, but I have recently upgraded to Lion (7.3). I have installed the developer tools and the gfortran from r.research.att.com When I use the GUI it gets this far : * installing *source* package ?surveillance? ... ** package ?surveillance? successfully unpacked and MD5 sums checked ** Creating default NAMESPACE file ** libs *** arch - i386 sh: make: command not found ERROR: compilation failed for package ?surveillance?
You don't have Xcode command line tools installed. Note that Xcode 4.3 and later no longer work since they do not install tools in the system anymore. You can modify your PATH to include the tools that are now inside Xcode.app, but probably easier is to install the command line tools (either from Xcode's Preferences or from ADC). Cheers, Simon
sessionInfo()
R version 2.14.1 Patched (2012-02-16 r58370) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base thinking that this might be an architecture issue (I'm in R64 and it's trying to build -386) I try from the command line using --no-multiarch, but it fails saying no such file or directory (output below). Knowing just enough to be dangerous, I think that it means the lines in the src file stcd-assuncaocorea.h : #include <list> #include <valarray> are trying to include some sort of resource (library?), but not looking in the right place. This being the case, I'm not sure how to direct it to the right place, nor where that place is. If I'm correct, can someone please help me with this? cheers Ben $ R CMD INSTALL --no-multiarch --build -d surveillance_1.2-1.tar.gz processing ?surveillance_1.2-1.tar.gz? a file * installing to library ?/Library/Frameworks/R.framework/Versions/2.14/Resources/library? * build_help_types= * DBG: 'R CMD INSTALL' now doing do_install() * created lock directory ?/Library/Frameworks/R.framework/Versions/2.14/Resources/library/00LOCK-surveillance? * installing *source* package ?surveillance? ... ** package ?surveillance? successfully unpacked and MD5 sums checked ** Creating default NAMESPACE file ** libs *** arch - x86_64 about to run R CMD SHLIB -o surveillance.so stcd-assuncaocorrea.cc surveillance.c twins.cc g++ -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/usr/local/include -fPIC -g -O2 -c stcd-assuncaocorrea.cc -o stcd-assuncaocorrea.o In file included from stcd-assuncaocorrea.cc:8: stcd-assuncaocorrea.h:14:16: error: list: No such file or directory stcd-assuncaocorrea.h:15:20: error: valarray: No such file or directory stcd-assuncaocorrea.cc:9:17: error: cmath: No such file or directory stcd-assuncaocorrea.cc:10:20: error: iostream: No such file or directory In file included from stcd-assuncaocorrea.cc:8: stcd-assuncaocorrea.h:25: error: expected initializer before ?<? token stcd-assuncaocorrea.h:33: error: ?SVEventLst? was not declared in this scope stcd-assuncaocorrea.h:33: error: ?ev? was not declared in this scope stcd-assuncaocorrea.h:34: error: expected primary-expression before ?const? stcd-assuncaocorrea.h:34: error: expected primary-expression before ?const? stcd-assuncaocorrea.h:35: error: expected primary-expression before ?const? stcd-assuncaocorrea.h:35: error: expected primary-expression before ?double? stcd-assuncaocorrea.h:36: error: expected primary-expression before ?const? stcd-assuncaocorrea.h:36: error: ?valarray? is not a member of ?std? stcd-assuncaocorrea.h:36: error: expected primary-expression before ?double? stcd-assuncaocorrea.h:36: error: initializer expression list treated as compound expression stcd-assuncaocorrea.h:37: error: ?SVEventLst? was not declared in this scope stcd-assuncaocorrea.h:37: error: ?ev? was not declared in this scope stcd-assuncaocorrea.h:37: error: expected primary-expression before ?const? stcd-assuncaocorrea.h:37: error: expected primary-expression before ?const? stcd-assuncaocorrea.h:38: error: ?valarray? is not a member of ?std? stcd-assuncaocorrea.h:38: error: expected primary-expression before ?double? stcd-assuncaocorrea.h:38: error: expected primary-expression before ?unsigned? stcd-assuncaocorrea.h:38: error: initializer expression list treated as compound expression stcd-assuncaocorrea.cc:61: error: redefinition of ?int SistemadeVigilancia? stcd-assuncaocorrea.h:33: error: ?int SistemadeVigilancia? previously defined here stcd-assuncaocorrea.cc:61: error: ?SVEventLst? was not declared in this scope stcd-assuncaocorrea.cc:61: error: ?ev? was not declared in this scope stcd-assuncaocorrea.cc:62: error: expected primary-expression before ?const? stcd-assuncaocorrea.cc:62: error: expected primary-expression before ?const? stcd-assuncaocorrea.cc:63: error: expected primary-expression before ?const? stcd-assuncaocorrea.cc:63: error: expected primary-expression before ?double? stcd-assuncaocorrea.cc:64: error: expected primary-expression before ?const? stcd-assuncaocorrea.cc:64: error: ?valarray? is not a member of ?std? stcd-assuncaocorrea.cc:64: error: expected primary-expression before ?double? make: *** [stcd-assuncaocorrea.o] Error 1 ERROR: compilation failed for package ?surveillance? * removing ?/Library/Frameworks/R.framework/Versions/2.14/Resources/library/surveillance?
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