[R] R CMD SHLIB changes function name when compiling
Hi,
I'm trying to write a function in C for implementation with .Call. When
compiling using R CMD SHLIB characters seem to be added to the function
name.
Here's the complete C code from the file summariseMCMC.c:
#includeR.h
#includeRdefines.h
#includeRinternals.h
void summariseMCMC(SEXP data) {
PROTECT(data=AS_NUMERIC(data));
UNPROTECT(1);
}
Then after compiling (R CMD SHLIB summariseMCMC.c) loading the .dll
dyn.load(C:/R/R-2.11.1/bin/summariseMCMC.dll)
is.loaded(_Z13summariseMCMCP7SEXPREC)
[1] TRUE
is.loaded(summariseMCMC)
[1] FALSE
Just wondering if anyone had any pointers for getting rid of this, or
have I missed something outrageously obvious?
Thanks,
Steve
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.4.4Biobase_2.8.0 aroma.affymetrix_1.7.0
[4] aroma.apd_0.1.7affxparser_1.20.0 R.huge_0.2.0
[7] aroma.core_1.7.0 aroma.light_1.16.0 matrixStats_0.2.1
[10] R.rsp_0.3.6R.cache_0.3.0 R.filesets_0.8.3
[13] digest_0.4.2 R.utils_1.4.4 R.oo_1.7.3
[16] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD SHLIB changes function name when compiling
On Fri, 8 Oct 2010, Steve Pederson wrote:
Hi,
I'm trying to write a function in C for implementation with .Call. When
compiling using R CMD SHLIB characters seem to be added to the function name.
Here's the complete C code from the file summariseMCMC.c:
#includeR.h
#includeRdefines.h
#includeRinternals.h
void summariseMCMC(SEXP data) {
PROTECT(data=AS_NUMERIC(data));
UNPROTECT(1);
}
Then after compiling (R CMD SHLIB summariseMCMC.c) loading the .dll
dyn.load(C:/R/R-2.11.1/bin/summariseMCMC.dll)
is.loaded(_Z13summariseMCMCP7SEXPREC)
[1] TRUE
is.loaded(summariseMCMC)
[1] FALSE
Just wondering if anyone had any pointers for getting rid of this, or have I
missed something outrageously obvious?
You have. This was not done by'R CMD SHLIB', but by a C++ compiler --
it is called 'name mangling'. Unfortunately you didn't show us the
output from that command, when the cause would probably have been
'outrageously obvious'.
The fix is to make sure you use a C compiler to compile C code, and
we've almost no idea why that is not being done on your system.
But as a guess, check that the environment variable CC is not set.
Thanks,
Steve
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.4.4Biobase_2.8.0 aroma.affymetrix_1.7.0
[4] aroma.apd_0.1.7affxparser_1.20.0 R.huge_0.2.0
[7] aroma.core_1.7.0 aroma.light_1.16.0 matrixStats_0.2.1
[10] R.rsp_0.3.6R.cache_0.3.0 R.filesets_0.8.3
[13] digest_0.4.2 R.utils_1.4.4 R.oo_1.7.3
[16] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD SHLIB changes function name when compiling
Hi Prof Ripley,
Thanks for the response the use of the correct terminology. I've
checked the environment variables there is none set called CC.
The .dll was definitely compiled using R CMD SHLIB. I'm not quite sure
what output you're referring to but at the command prompt when I enter:
...\bin R CMD SHLIB summariseMCMC.C
I get the output:
g++ -IC:/R/R-2.11.1/include-02 -Wall summariseMCMC.c
summariseMCMC.o
g++ -shared -s -static-libgcc -o summariseMCMC.dll tmp.def
summariseMCMC.0 -LC:/R/R-2.11.1/bin -1R
Please let me know if I can try anything different provide any more
useful output.
Another source file I have (runUniformMCMC.C) compiles runs perfectly
using the same approach, so I'm rather perplexed as to why this one gets
it's name mangled. It originally had actual code in it that did useful
things, but I stripped it back while I was trying to figure out what is
happening.
Thanks again,
Steve
On 8/10/2010 8:06 PM, Prof Brian Ripley wrote:
On Fri, 8 Oct 2010, Steve Pederson wrote:
Hi,
I'm trying to write a function in C for implementation with .Call.
When compiling using R CMD SHLIB characters seem to be added to the
function name.
Here's the complete C code from the file summariseMCMC.c:
#includeR.h
#includeRdefines.h
#includeRinternals.h
void summariseMCMC(SEXP data) {
PROTECT(data=AS_NUMERIC(data));
UNPROTECT(1);
}
Then after compiling (R CMD SHLIB summariseMCMC.c) loading the .dll
dyn.load(C:/R/R-2.11.1/bin/summariseMCMC.dll)
is.loaded(_Z13summariseMCMCP7SEXPREC)
[1] TRUE
is.loaded(summariseMCMC)
[1] FALSE
Just wondering if anyone had any pointers for getting rid of this, or
have I missed something outrageously obvious?
You have. This was not done by'R CMD SHLIB', but by a C++ compiler -- it
is called 'name mangling'. Unfortunately you didn't show us the output
from that command, when the cause would probably have been 'outrageously
obvious'.
The fix is to make sure you use a C compiler to compile C code, and
we've almost no idea why that is not being done on your system.
But as a guess, check that the environment variable CC is not set.
Thanks,
Steve
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.4.4 Biobase_2.8.0 aroma.affymetrix_1.7.0
[4] aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0
[7] aroma.core_1.7.0 aroma.light_1.16.0 matrixStats_0.2.1
[10] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3
[13] digest_0.4.2 R.utils_1.4.4 R.oo_1.7.3
[16] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD SHLIB changes function name when compiling
I think I should also add that I have compiled R from source so am
pretty confident that I have the correct set of Rtools.
On 8/10/2010 8:06 PM, Prof Brian Ripley wrote:
On Fri, 8 Oct 2010, Steve Pederson wrote:
Hi,
I'm trying to write a function in C for implementation with .Call.
When compiling using R CMD SHLIB characters seem to be added to the
function name.
Here's the complete C code from the file summariseMCMC.c:
#includeR.h
#includeRdefines.h
#includeRinternals.h
void summariseMCMC(SEXP data) {
PROTECT(data=AS_NUMERIC(data));
UNPROTECT(1);
}
Then after compiling (R CMD SHLIB summariseMCMC.c) loading the .dll
dyn.load(C:/R/R-2.11.1/bin/summariseMCMC.dll)
is.loaded(_Z13summariseMCMCP7SEXPREC)
[1] TRUE
is.loaded(summariseMCMC)
[1] FALSE
Just wondering if anyone had any pointers for getting rid of this, or
have I missed something outrageously obvious?
You have. This was not done by'R CMD SHLIB', but by a C++ compiler -- it
is called 'name mangling'. Unfortunately you didn't show us the output
from that command, when the cause would probably have been 'outrageously
obvious'.
The fix is to make sure you use a C compiler to compile C code, and
we've almost no idea why that is not being done on your system.
But as a guess, check that the environment variable CC is not set.
Thanks,
Steve
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.4.4 Biobase_2.8.0 aroma.affymetrix_1.7.0
[4] aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0
[7] aroma.core_1.7.0 aroma.light_1.16.0 matrixStats_0.2.1
[10] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3
[13] digest_0.4.2 R.utils_1.4.4 R.oo_1.7.3
[16] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD SHLIB changes function name when compiling
Date: Sat, 9 Oct 2010 01:21:47 +1030
From: stephen.peder...@adelaide.edu.au
To: rip...@stats.ox.ac.uk
CC: r-help@r-project.org
Subject: Re: [R] R CMD SHLIB changes function name when compiling
I think I should also add that I have compiled R from source so am
pretty confident that I have the correct set of Rtools.
Assuming the problem is name mangling or symbol export,
how about extern C ? I haven't done this lately my memory
is bad but quick goog search suggests this is the header and IIRC
it sound about right.
On 8/10/2010 8:06 PM, Prof Brian Ripley wrote:
On Fri, 8 Oct 2010, Steve Pederson wrote:
Hi,
I'm trying to write a function in C for implementation with .Call.
When compiling using R CMD SHLIB characters seem to be added to the
function name.
Here's the complete C code from the file summariseMCMC.c:
#include
#include
#include
void summariseMCMC(SEXP data) {
PROTECT(data=AS_NUMERIC(data));
UNPROTECT(1);
}
Then after compiling (R CMD SHLIB summariseMCMC.c) loading the .dll
dyn.load(C:/R/R-2.11.1/bin/summariseMCMC.dll)
is.loaded(_Z13summariseMCMCP7SEXPREC)
[1] TRUE
is.loaded(summariseMCMC)
[1] FALSE
Just wondering if anyone had any pointers for getting rid of this, or
have I missed something outrageously obvious?
You have. This was not done by'R CMD SHLIB', but by a C++ compiler -- it
is called 'name mangling'. Unfortunately you didn't show us the output
from that command, when the cause would probably have been 'outrageously
obvious'.
The fix is to make sure you use a C compiler to compile C code, and
we've almost no idea why that is not being done on your system.
But as a guess, check that the environment variable CC is not set.
Thanks,
Steve
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.4.4 Biobase_2.8.0 aroma.affymetrix_1.7.0
[4] aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0
[7] aroma.core_1.7.0 aroma.light_1.16.0 matrixStats_0.2.1
[10] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3
[13] digest_0.4.2 R.utils_1.4.4 R.oo_1.7.3
[16] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD SHLIB changes function name when compiling
Is the file .c or .C? You said .c, but then you said a .C file
worked (which it should not have), and I wonder if you have this
backwards.
A .c file is C, a .C file is C++ (in R 2.11.1 but not R 2.12.0).
extern C would be required if this were a C++ source, but we were
told otherwise.
On Sat, 9 Oct 2010, Steve Pederson wrote:
Hi Prof Ripley,
Thanks for the response the use of the correct terminology. I've checked
the environment variables there is none set called CC.
The .dll was definitely compiled using R CMD SHLIB. I'm not quite sure what
output you're referring to but at the command prompt when I enter:
...\bin R CMD SHLIB summariseMCMC.C
I get the output:
g++ -IC:/R/R-2.11.1/include-02 -Wall summariseMCMC.c
summariseMCMC.o
g++ -shared -s -static-libgcc -o summariseMCMC.dll tmp.def summariseMCMC.0
-LC:/R/R-2.11.1/bin -1R
Exactly that -- g++ is a C++ compiler.
Please let me know if I can try anything different provide any more useful
output.
Another source file I have (runUniformMCMC.C) compiles runs perfectly using
the same approach, so I'm rather perplexed as to why this one gets it's name
mangled. It originally had actual code in it that did useful things, but I
stripped it back while I was trying to figure out what is happening.
Thanks again,
Steve
On 8/10/2010 8:06 PM, Prof Brian Ripley wrote:
On Fri, 8 Oct 2010, Steve Pederson wrote:
Hi,
I'm trying to write a function in C for implementation with .Call.
When compiling using R CMD SHLIB characters seem to be added to the
function name.
Here's the complete C code from the file summariseMCMC.c:
#includeR.h
#includeRdefines.h
#includeRinternals.h
void summariseMCMC(SEXP data) {
PROTECT(data=AS_NUMERIC(data));
UNPROTECT(1);
}
Then after compiling (R CMD SHLIB summariseMCMC.c) loading the .dll
dyn.load(C:/R/R-2.11.1/bin/summariseMCMC.dll)
is.loaded(_Z13summariseMCMCP7SEXPREC)
[1] TRUE
is.loaded(summariseMCMC)
[1] FALSE
Just wondering if anyone had any pointers for getting rid of this, or
have I missed something outrageously obvious?
You have. This was not done by'R CMD SHLIB', but by a C++ compiler -- it
is called 'name mangling'. Unfortunately you didn't show us the output
from that command, when the cause would probably have been 'outrageously
obvious'.
The fix is to make sure you use a C compiler to compile C code, and
we've almost no idea why that is not being done on your system.
But as a guess, check that the environment variable CC is not set.
Thanks,
Steve
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.4.4 Biobase_2.8.0 aroma.affymetrix_1.7.0
[4] aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0
[7] aroma.core_1.7.0 aroma.light_1.16.0 matrixStats_0.2.1
[10] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3
[13] digest_0.4.2 R.utils_1.4.4 R.oo_1.7.3
[16] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] R CMD SHLIB changes function name when compiling
It seems that was the problem. My apologies as I was unaware of the
difference between a .c file a .C file.
Thanks again for your help,
Steve
On 9/10/2010 1:37 AM, Prof Brian Ripley wrote:
Is the file .c or .C? You said .c, but then you said a .C file worked
(which it should not have), and I wonder if you have this backwards.
A .c file is C, a .C file is C++ (in R 2.11.1 but not R 2.12.0).
extern C would be required if this were a C++ source, but we were told
otherwise.
On Sat, 9 Oct 2010, Steve Pederson wrote:
Hi Prof Ripley,
Thanks for the response the use of the correct terminology. I've
checked the environment variables there is none set called CC.
The .dll was definitely compiled using R CMD SHLIB. I'm not quite sure
what output you're referring to but at the command prompt when I enter:
...\bin R CMD SHLIB summariseMCMC.C
I get the output:
g++ -IC:/R/R-2.11.1/include -02 -Wall summariseMCMC.c summariseMCMC.o
g++ -shared -s -static-libgcc -o summariseMCMC.dll tmp.def
summariseMCMC.0 -LC:/R/R-2.11.1/bin -1R
Exactly that -- g++ is a C++ compiler.
Please let me know if I can try anything different provide any more
useful output.
Another source file I have (runUniformMCMC.C) compiles runs
perfectly using the same approach, so I'm rather perplexed as to why
this one gets it's name mangled. It originally had actual code in it
that did useful things, but I stripped it back while I was trying to
figure out what is happening.
Thanks again,
Steve
On 8/10/2010 8:06 PM, Prof Brian Ripley wrote:
On Fri, 8 Oct 2010, Steve Pederson wrote:
Hi,
I'm trying to write a function in C for implementation with .Call.
When compiling using R CMD SHLIB characters seem to be added to the
function name.
Here's the complete C code from the file summariseMCMC.c:
#includeR.h
#includeRdefines.h
#includeRinternals.h
void summariseMCMC(SEXP data) {
PROTECT(data=AS_NUMERIC(data));
UNPROTECT(1);
}
Then after compiling (R CMD SHLIB summariseMCMC.c) loading the .dll
dyn.load(C:/R/R-2.11.1/bin/summariseMCMC.dll)
is.loaded(_Z13summariseMCMCP7SEXPREC)
[1] TRUE
is.loaded(summariseMCMC)
[1] FALSE
Just wondering if anyone had any pointers for getting rid of this, or
have I missed something outrageously obvious?
You have. This was not done by'R CMD SHLIB', but by a C++ compiler -- it
is called 'name mangling'. Unfortunately you didn't show us the output
from that command, when the cause would probably have been 'outrageously
obvious'.
The fix is to make sure you use a C compiler to compile C code, and
we've almost no idea why that is not being done on your system.
But as a guess, check that the environment variable CC is not set.
Thanks,
Steve
sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
[3] LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
[5] LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] limma_3.4.4 Biobase_2.8.0 aroma.affymetrix_1.7.0
[4] aroma.apd_0.1.7 affxparser_1.20.0 R.huge_0.2.0
[7] aroma.core_1.7.0 aroma.light_1.16.0 matrixStats_0.2.1
[10] R.rsp_0.3.6 R.cache_0.3.0 R.filesets_0.8.3
[13] digest_0.4.2 R.utils_1.4.4 R.oo_1.7.3
[16] R.methodsS3_1.2.0
loaded via a namespace (and not attached):
[1] tools_2.11.1
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
