[Rcpp-devel] Rcpp build trouble with strings

Dirk Eddelbuettel edd at debian.org
Thu Aug 22 01:35:15 CEST 2013 

On 20 August 2013 at 15:09, jacob.a.russell.th at dartmouth.edu wrote:
| Hey Dirk,
| 
| I know that linking to a shared library is not enough, and that I need
| to runtime load the actual libraries that have their shared code stored
| separately. I wanted to do this in a way that when loaded by someone who
| installs the package, the shared libraries that I am including are
| available and the installer does the work for setting the ldconfig path

The installer (for R) does nothing to ldconfig. That is a systems issue. I do
not recommend mucking with that.

| for the libraries themselves. I looked at the RcppGSL package, but it
| doesn't actually include the library itself, but rather has you install
| it from an external source. I would like to include the libraries
| themselves, as they are not available from an external source. I settled
| on trying to include just the object files themselves (extracted them
| from the archives, they are all compiled with -fPIC). This got rid of
| the error that it can't find my shared library (obviously) but still has
| an error that it cannot find the symbols for one of the files that was
| in one of the libraries. 
| 
| Running the default build I get an error:
| 
| Error in dyn.load....
| ...undefined symbol:_Z20parse_options_createv
| 
| This is a function in a file that I only have an object for and not a
| cpp file (api.h and api.o)
| 
| Because I kept getting this error, I tried to add a target to Makevars
| to see if I could override the build options for only the
| SantosDartmouth.so file that I am trying to create. I created the build
| target (Note: $OBJS is a variable that I hand-made with ls *.o):
| 
| SantosDartmouth.so: $(OBJECTS)
|         $(CC) -shared $(PKG_LIBS) $(PKG_CPPFLAGS) $(OBJS) -Wl,--no-undefined -o SantosDartmouth.so
| 
| I got the same error, and the output of R CMD check SantosDartmouth was
| the same except that it output that it overrode my target and showed
| what it actually used to compile. So from the command line, I ran what I
| actually wanted to run to build the target.
| 
| g++ -shared `Rscript -e 'Rcpp:::LdFlags()'` `Rscript -e
| 'Rcpp:::CxxFlags()'` analyze-linkage.o and.o api.o build-disjuncts.o
| command-line.o constituents.o count.o DG_commonTypes.o
| DGG_graphComponents.o DGG_heuristics.o DGG_strings.o DGG_templates.o
| DGG_tree.o DG_objectTable.o diGraph.o DLL_commonTypes.o
| documentGraphGenerator.o error.o extract-links.o fast-match.o
| functions.o getDocGraph.o idiom.o linkset.o massage.o my_std.o parse.o
| post-process.o pp_knowledge.o pp_lexer.o pp_linkset.o preparation.o
| print.o print-util.o prune.o read-dict.o resources.o skip_exp.o
| string-set.o stringTable.o tokenize.o utilities.o word-file.o -o
| SantosDartmouth.so
| 
| Then I was able to load this in R with dyn.load("SantosDartmouth.so")
| and sourcing my R file in the R directory of my package, I could run the
| function. However, I would still like to be able to build the package
| and not manually distribute this. How can I force the package to accept
| my override for this target?

I would look at any of the packages including a local copy of a library. I
can't name a good one from the top of my head, but for example a little while
back I helped the folks of the phylobase package to rationalize / rework
their package build. 

Long story short, instead of mucking with local libraries (which, as I
recall, invariably failed on one of the platforms) we just rearranged things
so that all required sources are in src/ -- and the R knows how to do the
right thing in that case.

Otherwise, your long-road approach would be to learn how to build a library
(outside of R), have it installed and use that.  

Dirk

| 
| Thanks again, sorry to be so long winded.
| 
| Jacob
| On Mon, Aug 19, 2013 at 06:58:06PM -0500, Dirk Eddelbuettel wrote:
| > 
| > Hi Jacob,
| > 
| > On 19 August 2013 at 13:10, jacob.a.russell.th at dartmouth.edu wrote:
| > | Hey again,
| > | 
| > | I built the default Rcpp.package.skeleton rcpp_hello_world to take in
| > | strings and it worked fine. My problems seem to be from the libraries
| > | themselves. I recompiled the libraries that I could to be shared
| > | libraries and now the package builds the .so file, but I still get an
| > | error when checking the package.
| > | 
| > | Error in dyn.load(file, DLLpath = DLLpath, ...) : 
| > |   unable to load shared object
| > |   '/home/jrussell/src/C++/NLP/RDGGDriver/SantosDartmouth.Rcheck/SantosDartmouth/libs/SantosDartmouth.so':
| > |     liblink_4_1b.so: cannot open shared object file: No such file or directory
| > 
| > Do you know about ldconfig and all that?  "Just linking" to a shared library
| > is usually not enough.
| > 
| > If all that is way too confusing, then don't build a library but rather
| > including all src/*.o directly into your package library -- R knows how to
| > find that.
| > | 
| > | The library liblink_4_1b.so is link grammar with slight modifications to
| > | work with C++ code instead of C code and doesn't have an R package. I
| > | have placed all libs in the src directory of the package, and they can
| > | all be found at build time, and the .so file seems to be correctly
| > | built, but then when it is checked, it seems not to use the same
| > | ldflags that it uses when building (PKG_LIBS). Is this something that I
| > | need to set separately? I have tried ??Makevars and google searches for
| > | "R Makevars" and "external libraries Rcpp" and not found much. Are there
| > | any concrete examples of packaging external libraries inside of R
| > 
| > Of course. For example RcppGSL has done it for years. Here GSL is assumed to
| > be a standard system library (but gsl-config --libs is queried to get the -L
| > argument). 
| > 
| > There are now 130 packages on CRAN that deploy Rcpp. Maybe you can find one
| > that suits your setup.
| > 
| > | packages? I have gone through all of the vignettes that I could find and
| > | can't seem to find anything about including pre-built .so files in
| > | packages. I suspect this is to keep source-only, but the libraries are
| > | not all mine and I don't have this option available.
| > | 
| > | Thanks!
| > | 
| > | Jacob Russell
| > | 
| > | P.S. Time-To-Response on this mailing list is probably the best that I
| > | have ever seen on a mailing list. Congrats!
| > 
| > :)
| > 
| > Had a busy day at work or else I would have replied earlier.
| > 
| > Dirk
| > 
| > | 
| > | On Fri, Aug 16, 2013 at 12:52:37PM -0500, Dirk Eddelbuettel wrote:
| > | > 
| > | > On 16 August 2013 at 13:45, jacob.a.russell.th at dartmouth.edu wrote:
| > | > | Hello,
| > | > | 
| > | > | I am trying to build a package but I have quite a few dependencies. As such, I
| > | > | have modified Makevars to be (I don't like backticks because I find them too
| > | > | similar to single quotes):
| > | > | 
| > | > | PKG_LIBS = $($(R_HOME)/bin/Rscript -e 'Rcpp:::LdFlags()') -L. -llink_4_1b -lDGG -lSTR -lDLL -lAF -lmy_std -lm
| > | > | PKG_CPPFLAGS=-I. -g
| > | > | 
| > | > | Which seems to compile when my R wrapper is (incorrectly):
| > | > | 
| > | > | RcppExport SEXP getDocGraph(std::string input){
| > | > |     
| > | > |     std::string testStr = input;
| > | > |     std::string output=getDG(testStr);
| > | > |     return(Rcpp::wrap(output));
| > | > | }
| > | > | 
| > | > | but then it gives me a segmentation fault because it cannot access the
| > | > | underlying character array (or general object) passed in by R.
| > | > | 
| > | > | Then if I change the function protoype to:
| > | > | 
| > | > | RcppExport SEXP getDocGraph(SEXP input){
| > | > |     
| > | > |     std::string testStr = Rcpp::as<std::string>(input);
| > | > |     std::string output=getDG(testStr);
| > | > |     return(Rcpp::wrap(output));
| > | > | }
| > | > | 
| > | > | it seems to compile, but when I go to check the package, the .Rcheck directory
| > | > | gives me an error:
| > | > | 
| > | > | ** testing if installed package can be loaded
| > | > | Error in dyn.load(file, DLLpath = DLLpath, ...) : 
| > | > |   unable to load shared object ...<packagename>.so':
| > | > | 
| > | > | and the .so file is not in the tgz package, but no error was given during
| > | > | compilation.
| > | > | 
| > | > | Any help is greatly appreciated.
| > | > 
| > | > Simplify. 
| > | > 
| > | > I would start by removing your six additional libraries and convince myself
| > | > that accessing a string via Rcpp works (and as our unit tests do that a lot,
| > | > you would have to be in a very unusual situation to not have it work).
| > | > 
| > | > Once that works, add your libraries. If and when things break again, examine
| > | > the differences.
| > | > 
| > | > Dirk
| > | > 
| > | > -- 
| > | > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
| > 
| > -- 
| > Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com
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-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com

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