[R-SIG-Mac] Build error - not sure where to look

Ben Madin lists at remoteinformation.com.au
Sun Mar 4 06:06:59 CET 2012 

Further to this, I am starting to think I missed some thing else : attempting to compile rgeos gives me :

install.packages(c('/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz'), type='soruce', configure.args = '--with-geos-config=/Library/Frameworks/GEOS.framework/unix/bin/geos-config', repos=NULL)
* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
geos-config: /Library/Frameworks/GEOS.framework/unix/bin/geos-config
GEOS: 3.3.2dev
./configure: line 1263: test: 332dev: integer expression expected
CPPFLAGS: -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include
LIBS: -L/Library/Frameworks/GEOS.framework/Versions/3/unix/lib -lgeos
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
gcc -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64 -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/sp/include"   -fPIC  -g -O2 -c init.c -o init.o
In file included from init.c:1:
/Library/Frameworks/R.framework/Resources/include/R.h:28:20: error: stdlib.h: No such file or directory
/Library/Frameworks/R.framework/Resources/include/R.h:29:73: error: stdio.h: No such file or directory
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:30,
                 from init.c:1:
/Developer/usr/bin/../lib/gcc/i686-apple-darwin10/4.2.1/include/limits.h:10:25: error: limits.h: No such file or directory
In file included from init.c:1:
/Library/Frameworks/R.framework/Resources/include/R.h:31:18: error: math.h: No such file or directory
In file included from /Library/Frameworks/R.framework/Resources/include/R.h:44,
                 from init.c:1:
/Library/Frameworks/R.framework/Resources/include/R_ext/RS.h:24:39: error: string.h: No such file or directory
In file included from init.c:2:
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:801: error: expected declaration specifiers or ‘...’ before ‘FILE’
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:804: error: expected declaration specifiers or ‘...’ before ‘FILE’
make: *** [init.o] Error 1
ERROR: compilation failed for package ‘rgeos’
* removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgeos’
Warning message:
In install.packages(c("/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz"),  :
  installation of package ‘/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz’ had non-zero exit status


NB: this is a different message to if I do it in the GUI :

install.packages(c('/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz'), type='soruce', configure.args = '--with-geos-config=/Library/Frameworks/GEOS.framework/unix/bin/geos-config', repos=NULL)
* installing *source* package ‘rgeos’ ...
** package ‘rgeos’ successfully unpacked and MD5 sums checked
geos-config: /Library/Frameworks/GEOS.framework/unix/bin/geos-config
GEOS: 3.3.2dev
./configure: line 1263: test: 332dev: integer expression expected
CPPFLAGS: -I/Library/Frameworks/GEOS.framework/Versions/3/unix/include
LIBS: -L/Library/Frameworks/GEOS.framework/Versions/3/unix/lib -lgeos
configure: creating ./config.status
config.status: creating src/Makevars
** libs
*** arch - x86_64
sh: make: command not found
ERROR: compilation failed for package ‘rgeos’
* removing ‘/Library/Frameworks/R.framework/Versions/2.14/Resources/library/rgeos’
Warning message:
In install.packages(c("/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz"),  :
  installation of package ‘/Users/benmadin/Desktop/rgeos_0.2-3.tar.gz’ had non-zero exit status



So I don't understand why different problems for each, and why problems at all. If any can suggest anything, I'd be very grateful.

FWIW - I installed the new Xcode, but still have the old one - is that likely to cause problems?

cheers

Ben



On 04/03/2012, at 12:06 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’
> 
>> 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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