Thanks for posting here, and showing complete references. Your earlier StackOverflow questions went nowhere. Hopefully we can tackle this here.
On 12 December 2016 at 17:32, khagay nagdimov wrote: | I am trying to create a package that uses Rcpp to translate code from SeqLib ( | https://github.com/walaj/SeqLib) into R. I have compiled SeqLib but, I still | have problems referencing the function definitions. The current structure of my | R package is shown here: https://github.com/KhagayN/SeqLibr A bit of a mess. The repo is full of object files (.o), editor backups (*~), editor temp files (#*#). But at least you are using the right editor. I have no experience with git submodules and cannot say wether SeqLib again in SeqLibR is a good idea. | My makevars links to the location of the header files and to the static | libraries. To my understanding, the header files linked via PKG_CXXFLAGS point | to the header files and PKG_LIBS points to the static libraries. Then, in The Makevars is suspicious: ## the following flags are for PreProcessor. PKG_CPPFLAGS= -I../bwa/ -I../ -I../src/SeqLib/* First, the ../bwa/ directory does not work. R includes _everything below inst/_ but only a few known directories at the top-level. This is why we all put headers into inst/include/ --- so I would make **very strongly** suggest you move bwa/ into inst/include/bwa and then use -I../inst/include/bwa. Second, you are in src/ so ../src/ makes no sense. Make that -ISeqLib/ Third, there is no notion of wildcards in include directories. So -ISeqLib/ Fourth, for SeqLib you do ( cd SeqLib; ./configure; make; make install; ) and you _almost surely_ should not run 'make install'. The rest of your src/Makevars is trying to use the static library from that directory; make install would attempt to write the library somewhere else. "Writing R Extensions* _explicitly_ prohibits that for good reason. I stop here. Other failures related to loading object are likely due to these issues which you probably want to correct first. Dirk | rcpp_hello_world.cpp, I reference a function called Open within the FastqReader | class within the SeqLib namespace but, when I run load_all() I get an effor | saying: | | | Error in dyn.load(dllfile); | | unable to load shared object 'subsetSeqLib.so': undefined symbol: | _ZN6SeqLib11FastqReader40OpenERKSs, which references that Open function from | FastqReader. I don't understand why this is happening since I am linked to the | static libraries that have the definition of that function. | | | Thanks for all the help. | | | | _______________________________________________ | 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 -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org _______________________________________________ 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
