David Ibarra Gómez
2014-Oct-22 08:22 UTC
[R-sig-Debian] Problems to compile examples of RInside
Hello,
I have some problems to migrate to R >3.0 my devel machine
(R.2.15.2). So I decided to start from scratch with a brand new virtual machine.
Downloaded latest network install of debian testing, not stable (jessie/sid, SMP
Debian 3.16.3-2 (2014-09-20) x86_64 GNU/Linux) installed only with ssh-server
and basic utilities (no X).
Then I installed R by:
apt-get install r-base-dev
Then from R, I installed the needed (for me) packages by:
install.packages(c("Rcpp","RInside","forecast",
"quadprog", "tseries", "fracdiff",
"zoo",
"RcppArmadillo","randomForest","RInside","lubridate","quantmod","nnet","caret"),type="source")
Session info extract (Rcpp and RInside libraries loaded):
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RInside_0.2.11 Rcpp_0.11.3
Afterwards I tried to compile RInside examples, by make on
/usr/local/lib/R/site-library/RInside/examples/standard. No problem for:
rinside_sample7,rinside_sample10,rinside_test0,rinside_sample0,rinside_sample14.
But when it comes to "rinside_module_sample0" I do get the following:
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:64:0,
from
/usr/local/lib/R/site-library/RInside/include/RInsideCommon.h:38,
from
/usr/local/lib/R/site-library/RInside/include/RInside.h:26,
from rinside_module_sample0.cpp:7:
rinside_module_sample0.cpp: In function ?int main(int, char**)?:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:5: error: ?Shield?
was not declared in this scope
Shield<SEXP> __load_module_call__( Rf_lang2( GET_MODULE_SYM,
_rcpp_module_boot_##NAME() ); \
^
rinside_module_sample0.cpp:27:18: note: in expansion of macro ?LOAD_RCPP_MODULE?
R["bling"] = LOAD_RCPP_MODULE(bling) ;
^
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:5: note: suggested
alternative:
Shield<SEXP> __load_module_call__( Rf_lang2( GET_MODULE_SYM,
_rcpp_module_boot_##NAME() ); \
^
rinside_module_sample0.cpp:27:18: note: in expansion of macro ?LOAD_RCPP_MODULE?
R["bling"] = LOAD_RCPP_MODULE(bling) ;
^
In file included from
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/protection/protection.h:21:0,
from
/usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:129,
from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
from
/usr/local/lib/R/site-library/RInside/include/RInsideCommon.h:38,
from
/usr/local/lib/R/site-library/RInside/include/RInside.h:26,
from rinside_module_sample0.cpp:7:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/protection/Shield.h:29:11: note:
?Rcpp::Shield?
class Shield{
^
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:64:0,
from
/usr/local/lib/R/site-library/RInside/include/RInsideCommon.h:38,
from
/usr/local/lib/R/site-library/RInside/include/RInside.h:26,
from rinside_module_sample0.cpp:7:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:16: error: expected
primary-expression before ?>? token
Shield<SEXP> __load_module_call__( Rf_lang2( GET_MODULE_SYM,
_rcpp_module_boot_##NAME() ); \
^
rinside_module_sample0.cpp:27:18: note: in expansion of macro ?LOAD_RCPP_MODULE?
R["bling"] = LOAD_RCPP_MODULE(bling) ;
^
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:94: error: expected
?)? before ?;? token
Shield<SEXP> __load_module_call__( Rf_lang2( GET_MODULE_SYM,
_rcpp_module_boot_##NAME() ); \
^
rinside_module_sample0.cpp:27:18: note: in expansion of macro ?LOAD_RCPP_MODULE?
R["bling"] = LOAD_RCPP_MODULE(bling) ;
^
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:452:13: error:
?__load_module_call__? was not declared in this scope
Rf_eval(__load_module_call__), R_GlobalEnv );
^
rinside_module_sample0.cpp:27:18: note: in expansion of macro ?LOAD_RCPP_MODULE?
R["bling"] = LOAD_RCPP_MODULE(bling) ;
^
<builtin>: recipe for target 'rinside_module_sample0' failed
make: *** [rinside_module_sample0] Error 1
Probably I'm missing something on installation, Could you please provide
some advice?
Regards
David Ibarra
________________________________
Disclaimer: http://disclaimer.aqualogy.net/
[[alternative HTML version deleted]]
Dirk Eddelbuettel
2014-Oct-22 11:38 UTC
[R-sig-Debian] Problems to compile examples of RInside
On 22 October 2014 at 10:22, David Ibarra G??mez wrote:
| Hello,
|
| I have some problems to migrate to R >3.0 my devel machine
(R.2.15.2). So I decided to start from scratch with a brand new virtual machine.
|
| Downloaded latest network install of debian testing, not stable (jessie/sid,
SMP Debian 3.16.3-2 (2014-09-20) x86_64 GNU/Linux) installed only with
ssh-server and basic utilities (no X).
|
| Then I installed R by:
|
| apt-get install r-base-dev
|
| Then from R, I installed the needed (for me) packages by:
|
| install.packages(c("Rcpp","RInside","forecast",
"quadprog", "tseries", "fracdiff",
"zoo",
"RcppArmadillo","randomForest","RInside","lubridate","quantmod","nnet","caret"),type="source")
|
| Session info extract (Rcpp and RInside libraries loaded):
|
| R version 3.1.1 (2014-07-10)
| Platform: x86_64-pc-linux-gnu (64-bit)
|
| locale:
| [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
| [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
| [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
| [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
| [9] LC_ADDRESS=C LC_TELEPHONE=C
| [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
|
| attached base packages:
| [1] stats graphics grDevices utils datasets methods base
|
| other attached packages:
| [1] RInside_0.2.11 Rcpp_0.11.3
|
| Afterwards I tried to compile RInside examples, by make on
| /usr/local/lib/R/site-library/RInside/examples/standard.
It does not hurt to be explicit as this is the _Debian_ list. I do
edd at max:~$ cd git/rinside/inst/examples/standard/ # my src
edd at max:~/git/rinside/inst/examples/standard(master)$ make
and
| No problem for:
|
rinside_sample7,rinside_sample10,rinside_test0,rinside_sample0,rinside_sample14.
I generally manage to build way more ...
| But when it comes to "rinside_module_sample0" I do get the
following:
... but not always all. Sources (in Rcpp) change, and we sometimes need to
retire examples here.
Right now I get:
edd at max:~/git/rinside/inst/examples/standard(master)$ find . -executable
-print | sort
.
./cmake
./rinside_axionator
./rinside_callbacks0
./rinside_callbacks1
./rinside_issue178
./rinside_module_sample0
./rinside_sample0
./rinside_sample1
./rinside_sample10
./rinside_sample11
./rinside_sample12
./rinside_sample13
./rinside_sample14
./rinside_sample15
./rinside_sample2
./rinside_sample3
./rinside_sample4
./rinside_sample5
./rinside_sample6
./rinside_sample7
./rinside_sample8
./rinside_sample9
./rinside_slava
./rinside_test0
./rinside_test1
./rinside_test2
./rinside_vertica
edd at max:~/git/rinside/inst/examples/standard(master)$
and this excludes a few example not part of the repo, sources or package
because they were just a quick hack in reply to someone on r-sig-debian,
StackOverflow or somewhere else.
| In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:64:0,
| from
/usr/local/lib/R/site-library/RInside/include/RInsideCommon.h:38,
| from
/usr/local/lib/R/site-library/RInside/include/RInside.h:26,
| from rinside_module_sample0.cpp:7:
| rinside_module_sample0.cpp: In function ?int main(int, char**)?:
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:5: error:
?Shield? was not declared in this scope
| Shield<SEXP> __load_module_call__( Rf_lang2( GET_MODULE_SYM,
_rcpp_module_boot_##NAME() ); \
| ^
| rinside_module_sample0.cpp:27:18: note: in expansion of macro
?LOAD_RCPP_MODULE?
| R["bling"] = LOAD_RCPP_MODULE(bling) ;
| ^
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:5: note:
suggested alternative:
| Shield<SEXP> __load_module_call__( Rf_lang2( GET_MODULE_SYM,
_rcpp_module_boot_##NAME() ); \
| ^
| rinside_module_sample0.cpp:27:18: note: in expansion of macro
?LOAD_RCPP_MODULE?
| R["bling"] = LOAD_RCPP_MODULE(bling) ;
| ^
| In file included from
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/protection/protection.h:21:0,
| from
/usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:129,
| from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
| from
/usr/local/lib/R/site-library/RInside/include/RInsideCommon.h:38,
| from
/usr/local/lib/R/site-library/RInside/include/RInside.h:26,
| from rinside_module_sample0.cpp:7:
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/protection/Shield.h:29:11:
note: ?Rcpp::Shield?
| class Shield{
| ^
| In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:64:0,
| from
/usr/local/lib/R/site-library/RInside/include/RInsideCommon.h:38,
| from
/usr/local/lib/R/site-library/RInside/include/RInside.h:26,
| from rinside_module_sample0.cpp:7:
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:16: error:
expected primary-expression before ?>? token
| Shield<SEXP> __load_module_call__( Rf_lang2( GET_MODULE_SYM,
_rcpp_module_boot_##NAME() ); \
| ^
| rinside_module_sample0.cpp:27:18: note: in expansion of macro
?LOAD_RCPP_MODULE?
| R["bling"] = LOAD_RCPP_MODULE(bling) ;
| ^
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:94: error:
expected ?)? before ?;? token
| Shield<SEXP> __load_module_call__( Rf_lang2( GET_MODULE_SYM,
_rcpp_module_boot_##NAME() ); \
|
^
| rinside_module_sample0.cpp:27:18: note: in expansion of macro
?LOAD_RCPP_MODULE?
| R["bling"] = LOAD_RCPP_MODULE(bling) ;
| ^
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:452:13: error:
?__load_module_call__? was not declared in this scope
| Rf_eval(__load_module_call__), R_GlobalEnv );
| ^
| rinside_module_sample0.cpp:27:18: note: in expansion of macro
?LOAD_RCPP_MODULE?
| R["bling"] = LOAD_RCPP_MODULE(bling) ;
| ^
| <builtin>: recipe for target 'rinside_module_sample0' failed
| make: *** [rinside_module_sample0] Error 1
This example works for me, but only because __we disabled it now__:
edd at max:~/git/rinside/inst/examples/standard(master)$ grep disable
rinside_module_sample0.cpp
Rcpp::Rcout << "** rinside_module_sample0 is currently
disabled.\n";
edd at max:~/git/rinside/inst/examples/standard(master)$
I think that was discussed just a few weeks ago on rcpp-devel.
| Probably I'm missing something on installation, Could you please provide
some advice?
This particular example is currently retired / unsupported.
There is no other Debian question here so if you have _Rcpp-related_
followups the other list may be better.
Dirk
| Regards
|
| David Ibarra
|
|
|
|
|
|
|
|
|
|
|
| ________________________________
| Disclaimer: http://disclaimer.aqualogy.net/
|
| [[alternative HTML version deleted]]
|
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org