[Rcpp-devel] Problem loading a binary package which links dynamically with Rcpp
Hi, I develop a binary R package (let's call it MyPack) which is not on the CRAN and which depends from Rcpp (0.10.2). This package is built in-house under linux using the R CMD INSTALL --build and a Makevars file containing : PKG_CPPFLAGS = -I$(R_HOME)/include -I$(R_HOME)/library/Rcpp/include PKG_LIBS = `$(R_HOME)/bin/Rscript -e Rcpp:::LdFlags()` The problem is that I cannot load my package on another linux computer: library(MyPack) Loading required package: Rcpp Error in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Path/To/R_Packs/MyPack/libs/MyPack.so': libRcpp.so: cannot open shared object file: No such file or directory Error: package/namespace load failed for ‘MyPack’ Both Rcpp and MyPack have been installed using: R CMD INSTALL Rcpp_0.10.2.tar.gz -l /Path/To/R_Packs/ R CMD INSTALL MyPack_1.0.0.tar.gz -l /Path/To/R_Packs/ And the path to R_Packs have been added to R_LIBS environment variable, so: .libPaths() [1] /Path/To/R_Packs /usr/local/lib64/R/library If I install both packages as root (inside /usr/local/lib64/R/library/), there is no problem. Any help would be greatly appreciated. Thanks. Fabien ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Re: [Rcpp-devel] Compiling packages using Rcpp code under R devel
Søren, On 28 January 2013 at 22:39, Søren Højsgaard wrote: | Dear all, | | I was checking one of my packages (gRbase) under R-devel and got | | * checking compiled code ... NOTE | File 'C:/Documents/stat/Rdevel/GMwR-DEVEL/gRbaseDEVEL/gRbase.Rcheck/gRbase/libs/i386/gRbase.dll': | Found non-API calls to R: 'Rf_EncodeComplex', 'Rf_EncodeReal', | 'Rf_formatComplex', 'Rf_formatReal' | File 'C:/Documents/stat/Rdevel/GMwR-DEVEL/gRbaseDEVEL/gRbase.Rcheck/gRbase/libs/x64/gRbase.dll': | Found non-API calls to R: 'Rf_EncodeComplex', 'Rf_EncodeReal', | 'Rf_formatComplex', 'Rf_formatReal' | | Compiled code should not call non-API entry points in R. | | I guess this is something related to Rcpp, but I am not sure. Any help on this? That is already taken care of in SVN for Rcpp: 2013-01-15 Dirk Eddelbuettel e...@debian.org * src/api.cpp (Rcpp): Commented-out coerce_to_string() for real and complex arguments as R-devel (as of today) dislikes use of non-API functions Rf_EncodeComplex’, ‘Rf_EncodeReal’, ‘Rf_formatComplex’ * .Rbuildignore: Added inst/include/Rcpp/preprocessor and sugar/functions/impl which are currently empty directories * src/Timer.cpp (Rcpp): Avoid a 'long long' warning from a const R Core added this test around Jan 13 or 14, or /way/ past our last release. So there is nothing we could have done in December when we released, and there is nothing to do here until our next release -- but I successfule urged Kurt to update his copy of Rcpp to our SVN which he did in order to suppress this. In short, gRbase is an innocent bystander and victim of a very zealous warning. Update Rcpp and this will be quieter. Dirk | | Regards | Søren | ___ | Rcpp-devel mailing list | Rcpp-devel@lists.r-forge.r-project.org | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Re: [Rcpp-devel] Problem loading a binary package which links dynamically with Rcpp
Salut Fabien, This is not a reproducible report ... On 28 January 2013 at 10:19, Fabien Ors wrote: | Hi, | | I develop a binary R package (let's call it MyPack) which is not on the | CRAN and which depends from Rcpp (0.10.2). | This package is built in-house under linux using the R CMD INSTALL | --build and a Makevars file containing : | | PKG_CPPFLAGS = -I$(R_HOME)/include -I$(R_HOME)/library/Rcpp/include | PKG_LIBS = `$(R_HOME)/bin/Rscript -e Rcpp:::LdFlags()` | | The problem is that I cannot load my package on another linux computer: | | library(MyPack) | Loading required package: Rcpp | Error in dyn.load(file, DLLpath = DLLpath, ...): | unable to load shared object '/Path/To/R_Packs/MyPack/libs/MyPack.so': | libRcpp.so: cannot open shared object file: No such file or directory | Error: package/namespace load failed for ‘MyPack’ | | Both Rcpp and MyPack have been installed using: | R CMD INSTALL Rcpp_0.10.2.tar.gz -l /Path/To/R_Packs/ | R CMD INSTALL MyPack_1.0.0.tar.gz -l /Path/To/R_Packs/ | | And the path to R_Packs have been added to R_LIBS environment variable, so: | .libPaths() | [1] /Path/To/R_Packs /usr/local/lib64/R/library | | If I install both packages as root (inside /usr/local/lib64/R/library/), | there is no problem. That would indicate there is no problem per se with your or our code, but rather with the setup of your computer. Maybe /etc/ld.so.conf is out of sync with where you keep dynamic libraries -- hard to say without anything reproducible. Dirk | Any help would be greatly appreciated. | | Thanks. | Fabien | ___ | Rcpp-devel mailing list | Rcpp-devel@lists.r-forge.r-project.org | https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel -- Dirk Eddelbuettel | e...@debian.org | http://dirk.eddelbuettel.com ___ Rcpp-devel mailing list Rcpp-devel@lists.r-forge.r-project.org https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel
Re: [Rcpp-devel] an error message from RcppArmadillo
The main error that pops out is that 'g++', the compiler used to compile
the C++ code, was not found.
Best guess: Rtools isn't in your PATH. I believe the Windows Rtools
installer automatically adds itself to your system PATH, so if you just
installed with default settings you'd be fine there. If not, you're going
to have to change your PATH to point to both Rtools and the gcc
installation subdir in Rtools. You might consider using something like
RStudio as well, since it'll do some magic behind the scenes to ensure
Rtools is found and called whenever compiling code.
Other potential problem: you have R installed in 'C:/Program Files', and
that space in the path can potentially cause problems. You might consider
reinstalling R in a directory with no spaces. Frustrating and silly, I know
:P
Hope it helps,
-Kevin
On Mon, Jan 28, 2013 at 3:23 PM, Aileen Lin aileenshanhong@gmail.comwrote:
Hi there,
I am trying the package of RcppArmadillo. This is the code I copied from
your website. I am not sure what went wrong.
suppressMessages(require(inline))
code - '
+arma::mat coeff = Rcpp::asarma::mat(a);
+arma::mat errors = Rcpp::asarma::mat(e);
+int m = errors.n_rows; int n = errors.n_cols;
+arma::mat simdata(m,n);
+simdata.row(0) = arma::zerosarma::mat(1,n);
+for (int row=1; rowm; row++) {
+ simdata.row(row) = simdata.row(row-1)*trans(coeff)+errors.row(row);
+}
+return Rcpp::wrap(simdata);
+ '
## create the compiled function
rcppSim - cxxfunction(signature(a=numeric,e=numeric),
+code,plugin=RcppArmadillo)
tty option detected in CYGWIN environment variable.
CYGWIN=tty is no longer supported. Please remove it from your
CYGWIN environment variable and use a terminal emulator like mintty,
xterm, or rxvt.
cygwin warning:
MS-DOS style path detected: C:/PROGRA~1/R/R-215~1.2/etc/i386/Makeconf
Preferred POSIX equivalent is:
/cygdrive/c/PROGRA~1/R/R-215~1.2/etc/i386/Makeconf
CYGWIN environment variable option nodosfilewarning turns off this
warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
/usr/bin/sh: g++: command not found
make: *** [filee245f631629.o] Error 127
ERROR(s) during compilation: source code errors or compiler configuration
errors!
Program source:
1:
2: // includes from the plugin
3: #include RcppArmadillo.h
4: #include Rcpp.h
5:
6:
7: #ifndef BEGIN_RCPP
8: #define BEGIN_RCPP
9: #endif
10:
11: #ifndef END_RCPP
12: #define END_RCPP
13: #endif
14:
15: using namespace Rcpp;
16:
17:
18: // user includes
19:
20:
21: // declarations
22: extern C {
23: SEXP filee245f631629( SEXP a, SEXP e) ;
24: }
25:
26: // definition
27:
28: SEXP filee245f631629( SEXP a, SEXP e ){
29: BEGIN_RCPP
30:
31:arma::mat coeff = Rcpp::asarma::mat(a);
32:arma::mat errors = Rcpp::asarma::mat(e);
33:int m = errors.n_rows; int n = errors.n_cols;
34:arma::mat simdata(m,n);
35:simdata.row(0) = arma::zerosarma::mat(1,n);
36:for (int row=1; rowm; row++) {
37: simdata.row(row) =
simdata.row(row-1)*trans(coeff)+errors.row(row);
38:}
39:return Rcpp::wrap(simdata);
40:
41: END_RCPP
42: }
43:
44:
Error in compileCode(f, code, language = language, verbose = verbose) :
Compilation ERROR, function(s)/method(s) not created! tty option
detected in CYGWIN environment variable.
CYGWIN=tty is no longer supported. Please remove it from your
CYGWIN environment variable and use a terminal emulator like mintty,
xterm, or rxvt.
cygwin warning:
MS-DOS style path detected: C:/PROGRA~1/R/R-215~1.2/etc/i386/Makeconf
Preferred POSIX equivalent is:
/cygdrive/c/PROGRA~1/R/R-215~1.2/etc/i386/Makeconf
CYGWIN environment variable option nodosfilewarning turns off this
warning.
Consult the user's guide for more details about POSIX paths:
http://cygwin.com/cygwin-ug-net/using.html#using-pathnames
/usr/bin/sh: g++: command not found
make: *** [filee245f631629.o] Error 127
My inline package is 0.3.10, RcppArmadillo is 0.3.6.1, Rcpp is 0.10.2. I
also installed Rtools216.exe. Please let me know what I did wrongly. Thank
you.
Regards,
Aileen L.
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[Rcpp-devel] an error message from RcppArmadillo: sourceRcpp
Hi there,
I get RcppArmadillo running, but still has a problem
with Rcpp::sourceCpp(). My code is here:
#include Rcpp.h
#include RcppArmadillo.h
using namespace Rcpp;
//[[Rcpp::export]]
NumericMatrix add(NumericMatrix b){
return b.n_cols;
}
Rcpp::sourceCpp('add.cpp')
g++ -m64 -IC:/R/R-215~1.2/include -DNDEBUG
-IC:/Users/Aileen/Documents/R/win-library/2.15/Rcpp/include
-Id:/RCompile/CRANpkg/extralibs64/local/include -O2 -Wall
-mtune=core2 -c add.cpp -o add.o add.cpp:2:27: fatal error:
RcppArmadillo.h: No such file or directory compilation terminated. make:
*** [add.o] Error 1
Error in Rcpp::sourceCpp(add.cpp) :
Error 1 occurred building shared library.
Could anyone tell me what I did wrongly? Thank you.
Regards,
Aileen
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Re: [Rcpp-devel] an error message from RcppArmadillo: sourceRcpp
Hi,
I believe you're missing this line:
// [[Rcpp::depends(RcppArmadillo)]]
HTH,
baptiste
On 29 January 2013 19:08, Aileen Lin aileenshanhong@gmail.com wrote:
Hi there,
I get RcppArmadillo running, but still has a problem
with Rcpp::sourceCpp(). My code is here:
#include Rcpp.h
#include RcppArmadillo.h
using namespace Rcpp;
//[[Rcpp::export]]
NumericMatrix add(NumericMatrix b){
return b.n_cols;
}
Rcpp::sourceCpp('add.cpp')
g++ -m64 -IC:/R/R-215~1.2/include -DNDEBUG
-IC:/Users/Aileen/Documents/R/win-library/2.15/Rcpp/include
-Id:/RCompile/CRANpkg/extralibs64/local/include -O2 -Wall
-mtune=core2 -c add.cpp -o add.o add.cpp:2:27: fatal error:
RcppArmadillo.h: No such file or directory compilation terminated. make:
*** [add.o] Error 1
Error in Rcpp::sourceCpp(add.cpp) :
Error 1 occurred building shared library.
Could anyone tell me what I did wrongly? Thank you.
Regards,
Aileen
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