Re: [Rd] [R-sig-hpc] doMC - compiler - concatenate an expression vector into a single expression?
Thank you very much Steve.
Your suggestion works perfectly -- at least with doSEQ, doMC and doMPI.
Bests,
Renaud
On 28/06/2011 15:35, Stephen Weston wrote:
I think that the result of the concatenation should be a call object,
rather than an expression object. How about something along the
lines of:
'%dopar2%'- function(obj, ex) {
ex- as.call(list(as.name('{'),
quote({ a- i; message(Custom , a) }),
substitute(ex)))
do.call('%dopar%', list(obj, ex), envir=parent.frame())
}
- Steve
On Tue, Jun 28, 2011 at 8:26 AM, Renaud Gaujoux
ren...@mancala.cbio.uct.ac.za wrote:
Hi,
this post is about foreach operators, the compiler package and the last
update of doMC that includes support for the compiler functionality.
I am using a home-made %dopar%-like operator that adds some custom
expression to be executed before the foreach loop expression itself (see
sample code below).
It used to work perfectly with doMC 1.2.1, but with the introduction of
the compiler functionality, things do not work properly.
The change in the doMC package consists in evaluating a compiled
expression instead of the original R expression:
# from doMC:::doMC ...
c.expr- comp(expr, env = envir, options = list(suppressUndefined = TRUE))
and for R= 2.13.0 comp is defined as compiler::compile:
function (e, env = .GlobalEnv, options = NULL)
{
cenv- makeCenv(env)
cntxt- make.toplevelContext(cenv, options)
cntxt$env- addCenvVars(cenv, findLocals(e, cntxt))
genCode(e, cntxt)
}
environment: namespace:compiler
My guess is that the function findLocals or genCode can not handle a
2-length expression vector.
Maybe somebody who knows the internals of these functions could explain
better this behaviour?
How can I concatenate two expressions into a single one?
Thank you,
Renaud
##
# Sample code
##
`%dopar2%`- function(obj, ex){
# append custom code to the expression
ex- c(expression({ a- i; message(Custom , a);}), substitute(ex))
# call the standard %dopar% operator
do.call(`%dopar%`, list(obj, ex), envir=parent.frame() )
}
res- foreach(i=1:3) %dopar2% { print(i); i*2; }
res
#
# Output with doSEQ or doMC 1.2.1
#
Custom 1
[1] 1
Custom 2
[1] 2
Custom 3
[1] 3
res
[[1]]
[1] 2
[[2]]
[1] 4
[[3]]
[1] 6
#
# Output with doMC 1.2.2
#
[[1]]
expression({
a- i
message(Custom , a)
}, {
print(i)
i * 2
})
[[2]]
expression({
a- i
message(Custom , a)
}, {
print(i)
i * 2
})
[[3]]
expression({
a- i
message(Custom , a)
}, {
print(i)
i * 2
})
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[Rd] Compilation error Mac binary
Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel Digest, Vol 100, Issue 28
I get the same style of path as Hadley. This is on Windows 7 Home Premium with SP1. I start R by clicking on the R-2.31.0 icon. I'd assumed that it was a change that came with R-2.13.0! (On 32-bit Windows XP, which I have just checked, I do indeed get the 8.3 paths.) R.home() [1] C:/Programs/R/R-2.13.0 sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Australia.1252 [2] LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets [6] methods base John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. http://www.maths.anu.edu.au/~johnm From: Duncan Murdoch murdoch.dun...@gmail.com Date: 29 June 2011 10:17:46 AM AEST To: Hadley Wickham had...@rice.edu Cc: Simon Urbanek simon.urba...@r-project.org, r-devel@r-project.org Subject: Re: [Rd] Small bug in install.packages? On 28/06/2011 5:42 PM, Hadley Wickham wrote: Isn't R.home() 8.3 path anyway? I don't think so: R.home(bin) [1] C:/Program Files/R/R-2.13.0/bin/i386 Weird. Like others, I see 8.3 pathnames. R gets those from a Windows call; what version of Windows are you using? Duncan Murdoch [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/ Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/ include -I/usr/local/include -I/Library/Frameworks/R.framework/ Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/ library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius, MD West Hartford, CT __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius, MD West Hartford, CT __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Ref Classes: bug with using '.self' within initialize methods?
Dear list,
I'm wondering if the following error I'm getting is a small bug in the
Reference Class paradigm or if it makes perfect sense.
When you write an explicit initialize method for a Ref Class, can you
then make use of '.self' WITHIN this initialize method just as you would
once an object of the class has actually been initialized?
Because it seems to me that you can not.
Below is an example that shows that calling '.self$someInitFoo()' within
the initialize method for 'MyClass' does not work (see section METHODS
in example below). Instead I have to go with
'someInitFooRefInner(.self=.Object, ...)' (see section UPDATED METHOD
in example below). Yet, this is only possible because there actually IS
such a method (I try to stick to the recommendations at ?setRefClass
where it says: Reference methods should be kept simple; if they need to
do some specialized *R* computation, that computation should use a
separate *R* function that is called from the reference method)
The same problem occurs when, say 'someInitFoo()' calls yet another Ref
Class method (as is the case in the example below with a call to
'.self$someFoo()').
Is this a desired behavior?
Thanks for any clarifying comments!
Janko
# CODE EXAMPLE #
# CLASSES
setRefClass(
Class=MyVirtual,
contains=c(VIRTUAL),
methods=list(
initialize=function(...){
callSuper(...)
return(.self)
},
someInitFoo=function(flds, ...){
someInitFooRefInner(
.self=.self,
flds=flds
)
}
)
)
GENERATOR - setRefClass(
Class=MyClass,
contains=c(MyVirtual),
fields=list(
A=character,
B=numeric
),
methods=list(
someFoo=function(...){
someFooRefInner(.self=.self, ...)
}
)
)
# /
# GENERICS
setGeneric(name=someInitFooRefInner,
def=function(.self, ...) standardGeneric(someInitFooRefInner),
signature=c(.self)
)
setGeneric(name=someFooRefInner,
def=function(.self, ...) standardGeneric(someFooRefInner),
signature=c(.self)
)
# /
# METHODS
setMethod(
f=someInitFooRefInner,
signature=signature(.self=MyVirtual),
definition=function(.self, flds, ...){
print(Trying to call '.self$someFoo())
try(.self$someFoo())
print(Trying to call 'someFooRefInner(.self=.self))
try(someFooRefInner(.self=.self))
return(flds)
}
)
setMethod(
f=someFooRefInner,
signature=signature(.self=MyVirtual),
definition=function(.self, ...){
print(hello world!)
}
)
setMethod(
f=initialize,
signature=signature(.Object=MyVirtual),
definition=function(.Object, GENERATOR=NULL, ...){
# MESSAGE
if(class(.Object) == MyVirtual){
cat(paste(initializing object of class ', class(.Object),
',
sep=), sep=\n)
} else {
cat(paste(initializig object of class', class(.Object),
' inheriting from class 'MyVirtual', sep=), sep=\n)
}
# /
# GET GENERATOR OBJECT
if(is.null(GENERATOR)){
GENERATOR - getRefClass(class(.Object))
}
flds - names(GENERATOR$fields())
.Object$someInitFoo(
flds=flds,
...
)
return(.Object)
}
)
# /
x - GENERATOR$new()
# UPDATED METHOD
setMethod(
f=initialize,
signature=signature(.Object=MyVirtual),
definition=function(.Object, GENERATOR=NULL, ...){
# MESSAGE
if(class(.Object) == MyVirtual){
cat(paste(initializing object of class ', class(.Object),
',
sep=), sep=\n)
} else {
cat(paste(initializig object of class', class(.Object),
' inheriting from class 'MyVirtual', sep=),
sep=\n)
}
# /
# GET GENERATOR OBJECT
if(is.null(GENERATOR)){
GENERATOR - getRefClass(class(.Object))
}
flds - names(GENERATOR$fields())
someInitFooRefInner(.self=.Object, flds=flds, ...)
return(.Object)
}
)
# /
x - GENERATOR$new()
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Re: [Rd] Small bug in install.packages?
R.home(bin) [1] C:/Program Files/R/R-2.13.0/bin/i386 Weird. Like others, I see 8.3 pathnames. R gets those from a Windows call; what version of Windows are you using? ... and how are you starting R? Startup goes through some contortions to handle all the different possibilities; maybe one of them is missing the path-shortening step. Ok, this was coming from R running within eclipse, via rj. (This is not my setup, but a collaborator's) Hadley -- Assistant Professor / Dobelman Family Junior Chair Department of Statistics / Rice University http://had.co.nz/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel Digest, Vol 100, Issue 28
On 29.06.2011 13:41, John Maindonald wrote: I get the same style of path as Hadley. This is on Windows 7 Home Premium with SP1. I start R by clicking on the R-2.31.0 icon. I'd assumed that it was a change that came with R-2.13.0! (On 32-bit Windows XP, which I have just checked, I do indeed get the 8.3 paths.) R.home() [1] C:/Programs/R/R-2.13.0 No, you got the same as Duncan: This is 8.3 compatible. Uwe sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_Australia.1252 [2] LC_CTYPE=English_Australia.1252 [3] LC_MONETARY=English_Australia.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_Australia.1252 attached base packages: [1] stats graphics grDevices utils datasets [6] methods base John Maindonald email: john.maindon...@anu.edu.au phone : +61 2 (6125)3473fax : +61 2(6125)5549 Centre for Mathematics Its Applications, Room 1194, John Dedman Mathematical Sciences Building (Building 27) Australian National University, Canberra ACT 0200. http://www.maths.anu.edu.au/~johnm From: Duncan Murdochmurdoch.dun...@gmail.com Date: 29 June 2011 10:17:46 AM AEST To: Hadley Wickhamhad...@rice.edu Cc: Simon Urbaneksimon.urba...@r-project.org, r-devel@r-project.org Subject: Re: [Rd] Small bug in install.packages? On 28/06/2011 5:42 PM, Hadley Wickham wrote: Isn't R.home() 8.3 path anyway? I don't think so: R.home(bin) [1] C:/Program Files/R/R-2.13.0/bin/i386 Weird. Like others, I see 8.3 pathnames. R gets those from a Windows call; what version of Windows are you using? Duncan Murdoch [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). Best, Uwe Ligges On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius, MD West Hartford, CT __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-devel Digest, Vol 100, Issue 28
On 29/06/2011 1:09 PM, Uwe Ligges wrote: On 29.06.2011 13:41, John Maindonald wrote: I get the same style of path as Hadley. This is on Windows 7 Home Premium with SP1. I start R by clicking on the R-2.31.0 icon. I'd assumed that it was a change that came with R-2.13.0! (On 32-bit Windows XP, which I have just checked, I do indeed get the 8.3 paths.) R.home() [1] C:/Programs/R/R-2.13.0 No, you got the same as Duncan: This is 8.3 compatible. Yes, that's right. The documentation is pretty inaccurate. What actually is supposed to happen is that you get the actual path, with forward slashes in it, unless it contains spaces: then you get the 8.3 version. So John's path has no spaces, and doesn't get converted to 8.3. True 8.3 would also have uppercase PROGRAMS, and only one dot in R-2.13.0 (I forget how that is converted). Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R CMD check --force-multiarch does not install all the archs for testing
On 28.06.2011 23:11, Hervé Pagès wrote: Simon, On 11-06-28 01:44 PM, Simon Urbanek wrote: On Jun 28, 2011, at 3:45 PM, Hervé Pagès wrote: Hi Simon, On 11-06-28 12:19 PM, Simon Urbanek wrote: On Jun 28, 2011, at 3:01 PM, Hervé Pagès wrote: Hi Uwe, On 11-06-28 01:44 AM, Uwe Ligges wrote: On 28.06.2011 01:31, Hervé Pagès wrote: Hi, Why isn't 'R CMD check --force-multiarch' installing the package for all the architectures that are going to be checked? Hervé, no, since it cannot know that that you need --merge-multiarch as an additional install flag for this particular package. Why not just use this flag anyway? Does it hurt to use it on packages that don't strictly need it? It does for two reasons: a) everything is built twice That's exactly what I want when I do 'R CMD check --force-multiarch' No, that's not what it does (and I assume you mean --force-biarch). It builds the package just once, you're simply overriding the default behavior of checking for configure.win, that's all. The two flags are orthogonal, --force-biarch makes no sense with --merge-multiarch, they are for all practical purposes mutually exclusive by definition of what they do. I really mean --force-multiarch, not --force-biarch. AFAIK 'R CMD check' has no --force-biarch option. and b) package authors don't expect the necessity to support --libs-only if the package doesn't require separate build runs. When specifying --force-multiarch, the user really expects the package to be installed for all sub-archs. ... with the assumption that the package supports it even though it has a configure script which may to may not work unlike --merge-multiarch which will always work. Just to clarify: --force-multiarch is an 'R CMD check' option, not an 'R CMD INSTALL' option --merge-multiarch is an 'R CMD INSTALL' option, not an 'R CMD check' option Now you are saying that --merge-multiarch will always work (on Windows of course, all this discussion is about how to achieve multiarch check on Windows). Great, this is what I've been observing too so far! It does not always work, unfortunately. We need force-biarch on CRAN for: RGtk2 rgdal rphast SQLiteMap On packages with or without native codes, with or without configure.win scripts, etc... It always seems to work. So, again, why isn't 'R CMD check --force-multiarch' installing with --merge-multiarch? Note that I'm not attached to that solution in particular, just trying to suggest an easy fix for 'R CMD check --force-multiarch' (which right now is broken on some packages). Well, merge-multiarch will result in small overhead. It will try to compile the code in ./src for the other architecture and merge that into the same package. For packages without any compiled code, it does not make sense to ask R to do that since the packages are identical under 32-bit and 64-bit, hence you don't want the overhead. For packages that include compiled code, you still do not want it, since R does it automatically - unless there is a configure.win file. Therefore, the option is just an add on that is necessary for only 18 out of roughly 3000 CRAN packages. So we have 4 packages that require --force-biarch and 18 requiring --merge-multiarch on CRAN. All the others build automatically for both architectures if they need to. So no reason to do that all the time. Best wishes, Uwe --force-biarch is just a way to flag packages that have configure.win that has no effect on the binary settings (flags etc.). It forces R to try multi-arch build in one flight, but it may or may not work depending on the package. It is a way to save time by not running --merge-multiarch (and thus building the package twice). --force-biarch is an 'R CMD INSTALL' option that I don't use. Why would I use something that might fail when I can use --merge-multiarch which always works. Thanks, H. Cheers, Simon The cross-platform way is to not use --merge-multiarch but use --libs-only instead as needed (easy to check after the first arch run which will tell you whether it's needed or not). I suspect that --merge-multiarch is just a convenience shortcut (and it's unclear to me why it's Windows-only...). A great convenience indeed as it allows to do the multiarch install in a single step. And it's unclear to me too why it's Windows-only but I would have hoped you would know... Thanks, H. Cheers, Simon You will have to check it in repository maintainer's mode (as the CRAN maintainers do everywhere). Essentially this is for me (when also producing WIndows binaries): Step 1: Installation R CMD INSTALL --pkglock --compact-docs --build --merge-multiarch --library=D:/path/to/library fabia_1.5.0.tar.gz fabia-install.out 21 (where the merge-multiarch part applies only to this package, of course) Step 2: Check (without installation, since that happened before already, using the install log from step 1) R CMD check --library=D:/path/to/library --force-multiarch
Re: [Rd] Compilation error Mac binary
On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). Cheers, Simon On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. I ~ $: less /opt/local/include/boost/version.hpp // Boost version.hpp configuration header file --// [...] #define BOOST_VERSION 104601 #define BOOST_LIB_VERSION 1_46_1 [...] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius, MD West Hartford, CT __
Re: [Rd] R-devel Digest, Vol 100, Issue 28
On 29/06/2011 1:44 PM, Duncan Murdoch wrote: On 29/06/2011 1:09 PM, Uwe Ligges wrote: On 29.06.2011 13:41, John Maindonald wrote: I get the same style of path as Hadley. This is on Windows 7 Home Premium with SP1. I start R by clicking on the R-2.31.0 icon. I'd assumed that it was a change that came with R-2.13.0! (On 32-bit Windows XP, which I have just checked, I do indeed get the 8.3 paths.) R.home() [1] C:/Programs/R/R-2.13.0 No, you got the same as Duncan: This is 8.3 compatible. Yes, that's right. The documentation is pretty inaccurate. What actually is supposed to happen is that you get the actual path, with forward slashes in it, unless it contains spaces: then you get the 8.3 version. So John's path has no spaces, and doesn't get converted to 8.3. True 8.3 would also have uppercase PROGRAMS, and only one dot in R-2.13.0 (I forget how that is converted). I've now clarified the help page. R.home() just looks up the environment variable R_HOME, and then possibly adds some subdir to it. If your front end (e.g. Hadley's rj/Eclipse setup) doesn't initialize R_HOME properly, then you'll get whatever it put there. You can also mess with it using Sys.setenv(R_HOME=junk). Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
BTW: the build result is at http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html so you may want to have a look. I'm not a C++ expert so you may want to ask on the Rcpp list since it appears to be some issue triggered by Rcpp includes - as if boost and tr1 and somehow define the same things but differently ... Since Dirk uses the same boost (1.43 here) successfully in QuantLib he may know more ... Cheers, Simon On Jun 29, 2011, at 2:05 PM, Simon Urbanek wrote: On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). Cheers, Simon On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1 (GCC) 4.2.1 (Apple Inc. build 5666) (dot 3) Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO
Re: [Rd] R-devel Digest, Vol 100, Issue 28
On 06/29/2011 08:08 PM, Duncan Murdoch wrote: On 29/06/2011 1:44 PM, Duncan Murdoch wrote: On 29/06/2011 1:09 PM, Uwe Ligges wrote: On 29.06.2011 13:41, John Maindonald wrote: I get the same style of path as Hadley. This is on Windows 7 Home Premium with SP1. I start R by clicking on the R-2.31.0 icon. I'd assumed that it was a change that came with R-2.13.0! (On 32-bit Windows XP, which I have just checked, I do indeed get the 8.3 paths.) R.home() [1] C:/Programs/R/R-2.13.0 No, you got the same as Duncan: This is 8.3 compatible. Yes, that's right. The documentation is pretty inaccurate. What actually is supposed to happen is that you get the actual path, with forward slashes in it, unless it contains spaces: then you get the 8.3 version. So John's path has no spaces, and doesn't get converted to 8.3. True 8.3 would also have uppercase PROGRAMS, and only one dot in R-2.13.0 (I forget how that is converted). I've now clarified the help page. R.home() just looks up the environment variable R_HOME, and then possibly adds some subdir to it. If your front end (e.g. Hadley's rj/Eclipse setup) doesn't initialize R_HOME properly, then you'll get whatever it put there. You can also For the record, Eclipse/StatET makes use of an R_HOME variable as set by the user (not as initialized by the front-end) in a so called 'R Environment' under Window Preferences StatET Run/Debug R Environments Best, Tobias mess with it using Sys.setenv(R_HOME=junk). Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Compilation error Mac binary
Thanks Simon, Uwe and David for your helpful answers. English is not my primary language, so I was hypothesising a bit about the correct interpretation of inlining and supply inside. I thought it meant copying the headers inside the package. I was already inspecting RQuantlib but I did, so far, not get smarter. I think I will setup a VMware OS X 10.5 with an older boost. This approach seems more reliable to me than just trying around with a configure script which, eventually, I don't understand fully. Yet, interesting that GUTS builds on Win and Linux, but not on the CRAN OS X. Anyway, thanks for your help. Best Sören On 29.06.2011, at 20:05, Simon Urbanek wrote: On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). Cheers, Simon On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’ is not a member of ‘std’ GUTS.cpp:284: error: ‘cout’ was not declared in this scope make: *** [GUTS.o] Error 1 ERROR: compilation failed for package ‘GUTS’ * removing ‘/Library/Frameworks/R.framework/Versions/2.13/Resources/library/GUTS’ sessionInfo() R version 2.13.0 beta (2011-04-04 r55296) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] mgcv_1.7-6 sos_1.3-0 brew_1.0-6 lattice_0.19-26 loaded via a namespace (and not attached): [1] grid_2.13.0Matrix_0.999375-50 nlme_3.1-101 tools_2.13.0 -- David. R: version platform i386-apple-darwin9.8.0 arch i386 os darwin9.8.0 system i386, darwin9.8.0 status major 2 minor 13.0 year 2011 month 04 day13 svn rev55427 language R version.string R version 2.13.0 (2011-04-13) I ~ $: gcc --version i686-apple-darwin10-gcc-4.2.1
Re: [Rd] Compilation error Mac binary
On Jun 29, 2011, at 2:39 PM, soeren.vo...@uzh.ch wrote: Thanks Simon, Uwe and David for your helpful answers. English is not my primary language, so I was hypothesising a bit about the correct interpretation of inlining and supply inside. I thought it meant copying the headers inside the package. Yes, that is what I meant- pick the part of boost that you use and include it (boost has many parts so that's another reason to do that). I was already inspecting RQuantlib but I did, so far, not get smarter. The two comments were unrelated ;). I was just pointing out that Dirk has C++ expertise, uses boots himself and is the author of Rcpp so he may possibly know what the error is about. I did not have RQuantLib in mind for you to look at the boost inclusion - RQuantLib needs QuantLib in addition to boost, so it is not surprising that he doesn't include boost inside as he has additional dependencies (and he does declare them correctly). I think I will setup a VMware OS X 10.5 with an older boost. This approach seems more reliable to me than just trying around with a configure script which, eventually, I don't understand fully. Yet, interesting that GUTS builds on Win and Linux, but not on the CRAN OS X. Anyway, thanks for your help. It is a side-effect that GUTS builds at all, because the only reason it does is that some other package has probably required boost before. If that was not the case, your package would fail everywhere. [That is not the answer to the Mac error since the same applies - your failure to declare the dependency is masked by the fact that other packages do need boost. I suspect the answer will be in the interaction of tr1/boost/Rcpp, but your should fix GUTS regardless] Cheers, Simon On 29.06.2011, at 20:05, Simon Urbanek wrote: On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: Looks like a different boost version than the one you require. I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). Cheers, Simon On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: Hello David On 29.06.2011, at 15:56, David Winsemius wrote: On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. :-) Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. So thanks for the output, but the CRAN messages must point to something different... Regards Sören trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' Content type 'application/x-gzip' length 9842 bytes opened URL == downloaded 9842 bytes Loading required package: lattice Loading required package: sos Loading required package: brew [1] 2011-06-29 09:40:18 EDT * installing *source* package ‘GUTS’ ... ** libs *** arch - i386 g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o In file included from GUTS.cpp:12: GUTS.h:21:28: error: boost/random.hpp: No such file or directory GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory GUTS.cpp: In function ‘void to_print(double)’: GUTS.cpp:277: error: ‘cout’ was not declared in this scope GUTS.cpp: In member function ‘void GUTS::showObject()’: GUTS.cpp:281: error: ‘cout’
Re: [Rd] Compilation error Mac binary
On 29 June 2011 at 14:17, Simon Urbanek wrote: | BTW: the build result is at | | http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html | | so you may want to have a look. I'm not a C++ expert so you may want to ask on the Rcpp list since it appears to be some issue triggered by Rcpp includes - as if boost and tr1 and somehow define the same things but differently ... Since Dirk uses the same boost (1.43 here) successfully in QuantLib he may know more ... Well, I already told Soeren over there on rcpp-devel that his issues are a) totally homegrown (as he continues to ignore configure issues and just assumes things would work because they do on his), b) hence unrelated to Rcpp (as he just throws '#include boost/...' in his code without testing c) almost entirely solvable by copy-and-paste as e.g. my RQuantLib has a configure script using boost-config he could copy (but I acknowldged that the configure script does more and is hence not the easiest possible). Now, I do admit that learning configure is a bit of a pain, but that is the price of admission of CRAN if you use Boost -- or you choose the frequently done but very inelegant route of copying all your Boost headers into your package. My RcppBDT package does that too. Some of us have talked about creating a 'boost-headers' package for CRAN that the couple of Boost-using packages could have a 'Depends:' and 'LinkingTo:' on. Then his issues would be solved -- but we're not there yet. Soeren just shown resilience and persistence in getting his package written, built and now onto CRAN. The remaining step is to learn more about cross-platform build issues. Because that is the (high) standard of CRAN, and if you want to be part of it, you are expected to conform. No shortcuts. Dirk | Cheers, | Simon | | | On Jun 29, 2011, at 2:05 PM, Simon Urbanek wrote: | | | On Jun 29, 2011, at 1:12 PM, Uwe Ligges wrote: | | Looks like a different boost version than the one you require. | I'd suggest to talk to the Mac maintainer, Simon Urbanek (CCing). | | | GUTS doesn't specify any system requirements, so obviously it has no business trying to use boost from the system. Also note boost is inlined in the vast majority of cases, so most packages simply supply the headers inside as to guarantee the required version is used (which I would certainly expect GUTS to do since it doesn't depend on boost according to the DESCRIPTION). | | Cheers, | Simon | | | | On 29.06.2011 17:14, soeren.vo...@uzh.ch wrote: | Hello David | | On 29.06.2011, at 15:56, David Winsemius wrote: | | On Jun 29, 2011, at 5:33 AM, soeren.vo...@uzh.ch wrote: | | Hello, the compilation of the GUTS package on CRAN for Mac produces the following error messages: | | http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/GUTS-00install.html | | I guess it is some namespace collision, but I can not reproduce it on my machine, it compiles fine here. What is the cause and which setup do I need to reproduce the errors? | | I was going to suggest you take this up with the maintainers... but you _are_ one of the maintainers. | | :-) | | Here is the output from an attempt to compile from source, version 0.1.45, with a relatively recent version of R 2.13.0 (but not the most recent and I still use Mac OSX 10.5.8). Perhaps its brevity will be helpful, and the fact that it seems to identify different error than those flagged in the log at CRAN. | | Thanks for your answer. The failure on your side is clear to me: there is no installation of the boost C++ library in any of the standard include locations. I have added /opt/local/include in Makevars (Mac Ports installation of C source packages), however, I know I should but still I am reluctant to write a configure script that could circumvent non-standard installations of boost on UNIX machines. | | So thanks for the output, but the CRAN messages must point to something different... | | Regards | Sören | | trying URL 'http://lib.stat.cmu.edu/R/CRAN/src/contrib/GUTS_0.1.45.tar.gz' | Content type 'application/x-gzip' length 9842 bytes | opened URL | == | downloaded 9842 bytes | | Loading required package: lattice | Loading required package: sos | Loading required package: brew | [1] 2011-06-29 09:40:18 EDT | * installing *source* package ‘GUTS’ ... | ** libs | *** arch - i386 | g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -I/opt/local/include -I/usr/local/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include -fPIC -g -O2 -c GUTS.cpp -o GUTS.o | In file included from GUTS.cpp:12: | GUTS.h:21:28: error: boost/random.hpp: No such file or directory | GUTS.h:22:40: error: boost/math/distributions.hpp: No such file or directory |
Re: [Rd] Compilation error Mac binary
On 29.06.2011, at 21:19, Dirk Eddelbuettel wrote: Soeren just shown resilience and persistence in getting his package written, built and now onto CRAN. The remaining step is to learn more about cross-platform build issues. Because that is the (high) standard of CRAN, and if you want to be part of it, you are expected to conform. No shortcuts. Hehehe :-D Okay, Dirk, I'll try my best :-)! Cheers Sören __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] invalid body argument for function
Hi guys, Looks like mkCLOSXP cannot handle external pointers as the function body. Work around is obvious, but I guess it's a bug nonetheless. library(RGtk2) fun - eval(substitute(function() x, list(x = gtkWindow( Error in eval(expr, envir, enclos) : invalid body argument for function Should NEVER happen; please bug.report() [mkCLOSXP] sessionInfo() R version 2.14.0 Under development (unstable) (--) Platform: i686-pc-linux-gnu (32-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RGtk2_2.20.13 qtbase_0.8-16 visnab_0.0.1 loaded via a namespace (and not attached): [1] BSgenome_1.21.3 Biobase_2.11.10 Biostrings_2.21.6 [4] DBI_0.2-5 GenomicFeatures_1.5.5 GenomicRanges_1.3.39 [7] IRanges_1.11.11 MutableRanges_0.2.0 RColorBrewer_1.0-2 [10] RCurl_1.5-0 RSQLite_0.9-4 Rsamtools_1.5.13 [13] XML_3.2-0 biomaRt_2.7.2 colorspace_1.0-1 [16] dichromat_1.2-3 munsell_0.2 objectSignals_0.5.1 [19] plumbr_0.6.2 plyr_1.4.1qtpaint_0.7.22 [22] rtracklayer_1.13.3scales_0.1.0 stringr_0.4 [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
