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’
Because it says that make is not found it would suggest that you need
to provide more details about which version and where the developer
tools were installed. I'm wondering if the PATH for R may not include
the proper location.
This package also require package:spc. The one that was used when I
just compiled from source on a Leopard machine was spc_0.4.1.
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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David Winsemius, MD
West Hartford, CT
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