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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