Hi Erik, Erik Wright wrote: > Hi Herv? & Chuck, > > Thanks for the help to get me started with the C interface. > > I have eventually figured out how to get the example working with functions in the Biostrings interface rather than the IR_Ranges interface: > > SEXP print_XString_bytes(SEXP x) > { > cachedXStringSet x_set; > cachedCharSeq x_i; > int i, j, x_length; > > x_set = cache_XStringSet(x); > > // number of XStrings in the XStringSet > x_length = get_cachedXStringSet_length(&x_set); > > for (i = 0; i < x_length; i++) { > // extract XString i from the XStringSet > x_i = get_cachedXStringSet_elt(&x_set, i); > > // print each character along the XString > for (j = 0; j < x_i.length; j++) > Rprintf("%c", DNAdecode(x_i.seq[j])); > > Rprintf("\n"); > } > return R_NilValue; > } That's indeed the right way to "walk" on an XStringSet object at the C level. Glad your figured it out! H. > > Cheers, > Erik > > > > > On Apr 5, 2010, at 1:39 AM, Hervé Pagès wrote: > >> Hi Erik, >> >> Erik Wright wrote: >>> Hello again, >>> It looks like my problem is that the function listed in the example code, "cache_XRaw()", is deprecated. >> cache_XRaw() has been moved to the IRanges package a long time ago >> and has since then been part of the IRanges C interface. The example >> given in the header of Biostrings_interface.h needs to be updated to >> reflect this change. Thanks for catching this and sorry for the >> confusion. >> >> For your GoneFISHing package that means that you need to do steps a., >> b. and c. for both, Biostrings and IRanges. For step d., add: >> >> #include "IRanges_interface.h" >> >> just before >> >> #include "Biostrings_interface.h" >> >> Then try to compile again and let me know if that still doesn't work. >> >>> Is there any source of information about how to use the functions listed in Biostrings_interface.h? >> There is nothing like that and no plans at the moment to formally >> document the C-level interfaces. For now the best way to learn >> about these functions is to see how they are used in >> IRanges/Biostrings themselves (they are prefixed with an >> underscore when they are used from within the package where >> they are defined). The authors have made some efforts to use consistent >> naming, and, I think, a clean and consistent C coding style across >> the 2 packages so hopefully the code is not too hard to understand >> (some parts of the code are tricky but most are not). They will be >> happy to help you with any specific questions you have. >> >> Cheers, >> H. >> >>> Thanks again, >>> Erik >>> On Apr 2, 2010, at 11:00 AM, Erik Wright wrote: >>>> Hello all, >>>> >>>> I am trying to interface Biostrings from C for the first time. I followed the example given in the header of Biostrings_interface.h to the letter (quite literally). In step "e" I paste the example function into myFile.c, register it as a .Call entry point and compile with R CMD CHECK. I get the following errors: >>>> >>>> myFile.c:13: warning: implicit declaration of function ?cache_XRaw? >>>> myFile.c:13: error: incompatible types in assignment >>>> myFile.c:14: error: ?cachedCharSeq? has no member named ?elts? >>>> myFile.c:14: error: ?cachedCharSeq? has no member named ?nelt? >>>> >>>> Based on the error, it seems like I still don't have access to any of the Biostrings variable definitions. I have tried everything that I can think of, so I am quite stuck. Does anyone know what I am doing incorrectly? I have pasted myFile.c below for reference. >>>> >>>> Thanks!, >>>> Erik >>>> >>>> >>>> >>>> >>>> //myFile.c >>>> >>>> #include <rdefines.h> >>>> #include <r_ext rdynload.h=""> >>>> #include <stdio.h> >>>> #include <stdlib.h> >>>> #include "Biostrings_interface.h" >>>> >>>> SEXP print_XString_bytes(SEXP xstring) >>>> { >>>> cachedCharSeq x; >>>> int i; >>>> const char *x_char; >>>> >>>> x = cache_XRaw(xstring); >>>> for (i = 0, x_char = x.elts; i < x.nelt; i++, x_char++) >>>> Rprintf("%x ", *x_char); >>>> Rprintf("\n"); >>>> return R_NilValue; >>>> } >>>> >>>> /* >>>> * -- REGISTRATION OF THE .Call ENTRY POINTS --- >>>> */ >>>> static const R_CallMethodDef callMethods[] = { >>>> {"print_XString_bytes", (DL_FUNC) &print_XString_bytes, 1}, >>>> {NULL, NULL, 0} >>>> }; >>>> >>>> void R_init_GoneFISHing(DllInfo *info) >>>> { >>>> R_registerRoutines(info, NULL, callMethods, NULL, NULL); >>>> } >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> -- >> Hervé Pagès >> >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> P.O. Box 19024 >> Seattle, WA 98109-1024 >> >> E-mail: hpages at fhcrc.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319