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<p><span style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">Thank you Dirk for all the help, it is very much appreciated. </span></p>
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<p><span style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">I have made the changes you recommend and pushed them onto the GitHub page (</span><a href="https://github.com/KhagayN/SeqLibr" class="x_OWAAutoLink" id="LPlnk97557"><span style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">https://github.com/KhagayN/SeqLibr</span></a><span style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">).
I realized that the bwa directory isn't necessary because src/SeqLib/bwa is an entire copy of it. I changed the PKG_CPPFLAGS to reflect that bwa directory via -ISeqLib/bwa/</span></p>
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<p><span style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">Do you think that is acceptable? I will follow your guidance. </span></p>
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<p><span style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">If so,</span><font color="#212121"><span style="font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif"> I get an error after running load_all() </span></font><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif"> Error in dyn.load(dllfile)</span></p>
<p><span style="color:rgb(33,33,33); font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">unable to load shared object 'subsetSeqLib.so': mem_opt_init </span></p>
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<p><span style="color:rgb(33,33,33); font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">That function is defined in src/SeqLib/bwa/bwamem.c. </span></p>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Dirk Eddelbuettel <edd@debian.org><br>
<b>Sent:</b> Tuesday, December 13, 2016 8:31:11 AM<br>
<b>To:</b> khagay nagdimov<br>
<b>Cc:</b> rcpp-devel@lists.r-forge.r-project.org<br>
<b>Subject:</b> Re: [Rcpp-devel] Rcpp question regarding compilation of another package</font>
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Thanks for posting here, and showing complete references. Your earlier<br>
StackOverflow questions went nowhere. Hopefully we can tackle this here.<br>
<br>
On 12 December 2016 at 17:32, khagay nagdimov wrote:<br>
| I am trying to create a package that uses Rcpp to translate code from SeqLib ( <br>
| <a href="https://github.com/walaj/SeqLib">https://github.com/walaj/SeqLib</a>) into R. I have compiled SeqLib but, I still<br>
| have problems referencing the function definitions. The current structure of my<br>
| R package is shown here: <a href="https://github.com/KhagayN/SeqLibr">https://github.com/KhagayN/SeqLibr</a><br>
<br>
A bit of a mess. The repo is full of object files (.o), editor backups (*~),<br>
editor temp files (#*#). But at least you are using the right editor.<br>
<br>
I have no experience with git submodules and cannot say wether SeqLib again<br>
in SeqLibR is a good idea.<br>
<br>
| My makevars links to the location of the header files and to the static<br>
| libraries. To my understanding, the header files linked via PKG_CXXFLAGS point<br>
| to the header files and PKG_LIBS points to the static libraries. Then, in<br>
<br>
The Makevars is suspicious:<br>
<br>
## the following flags are for PreProcessor.<br>
PKG_CPPFLAGS= -I../bwa/ -I../ -I../src/SeqLib/* <br>
<br>
First, the ../bwa/ directory does not work. R includes _everything below<br>
inst/_ but only a few known directories at the top-level. This is why we all<br>
put headers into inst/include/ --- so I would make **very strongly** suggest<br>
you move bwa/ into inst/include/bwa and then use -I../inst/include/bwa.<br>
<br>
Second, you are in src/ so ../src/ makes no sense. Make that -ISeqLib/<br>
<br>
Third, there is no notion of wildcards in include directories. So -ISeqLib/<br>
<br>
Fourth, for SeqLib you do<br>
<br>
( cd SeqLib; ./configure; make; make install; )<br>
<br>
and you _almost surely_ should not run 'make install'. The rest of your<br>
src/Makevars is trying to use the static library from that directory; make<br>
install would attempt to write the library somewhere else. "Writing R<br>
Extensions* _explicitly_ prohibits that for good reason.<br>
<br>
I stop here. Other failures related to loading object are likely due to<br>
these issues which you probably want to correct first.<br>
<br>
Dirk<br>
<br>
<br>
| rcpp_hello_world.cpp, I reference a function called Open within the FastqReader<br>
| class within the SeqLib namespace but, when I run load_all() I get an effor<br>
| saying:<br>
| <br>
| <br>
| Error in dyn.load(dllfile);<br>
| <br>
| unable to load shared object 'subsetSeqLib.so': undefined symbol:<br>
| _ZN6SeqLib11FastqReader40OpenERKSs, which references that Open function from<br>
| FastqReader. I don't understand why this is happening since I am linked to the<br>
| static libraries that have the definition of that function.<br>
| <br>
| <br>
| Thanks for all the help. <br>
| <br>
| <br>
| <br>
| _______________________________________________<br>
| Rcpp-devel mailing list<br>
| Rcpp-devel@lists.r-forge.r-project.org<br>
| <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel">
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/rcpp-devel</a><br>
<br>
-- <br>
<a href="http://dirk.eddelbuettel.com">http://dirk.eddelbuettel.com</a> | @eddelbuettel | edd@debian.org<br>
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