[R-sig-Debian] Problems to compile examples of RInside

Dirk Eddelbuettel edd at debian.org
Wed Oct 22 13:38:18 CEST 2014


On 22 October 2014 at 10:22, David Ibarra Gómez 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 âint main(int, char**)â:
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:5: error: âShieldâ 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 âLOAD_RCPP_MODULEâ
|      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 âLOAD_RCPP_MODULEâ
|      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:   âRcpp::Shieldâ
|      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 â>â 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 âLOAD_RCPP_MODULEâ
|      R["bling"] = LOAD_RCPP_MODULE(bling) ;
|                   ^
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:451:94: error: expected â)â before â;â 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 âLOAD_RCPP_MODULEâ
|      R["bling"] = LOAD_RCPP_MODULE(bling) ;
|                   ^
| /usr/local/lib/R/site-library/Rcpp/include/Rcpp/Module.h:452:13: error: â__load_module_call__â was not declared in this scope
|      Rf_eval(__load_module_call__), R_GlobalEnv );
|              ^
| rinside_module_sample0.cpp:27:18: note: in expansion of macro âLOAD_RCPP_MODULEâ
|      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
| 
| 
| 
| 
| 
| 
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| 
| 
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