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  • SPP -- ChIP-seq program installation??

    Hi all,

    I've been using Kharchenko et al's spp R package for calling peaks in ChIP-seq data for sometime. I've been really happy with it, and was trying to update to their latest version and am running into some real trouble

    I'm using a Mac OSX 10.6 machine, and I seem to be getting an error involving the use of a C "getline" function. I've gathered from researching the error I'm getting that this is because the function isn't supported by MacOS. Does anyone have ideas for a hack to fix this??? I've tried to do a few things myself but I'm in way over my head

    Below is the error I'm getting. Any help much appreciated!!!

    Code:
    $ sudo R CMD INSTALL spp_1.8.gz 
    Password:
    * Installing to library '/Library/Frameworks/R.framework/Resources/library'
    * Installing *source* package 'spp' ...
    checking for gcc... gcc
    checking for C compiler default output file name... a.out
    checking whether the C compiler works... yes
    checking whether we are cross compiling... no
    checking for suffix of executables... 
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for BZ2_bzDecompressInit in -lbz2... yes
    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    ** arch - i386
    g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include   -D_FASTMAP -DMAQ_LONGREADS	  -fPIC  -g -O2 -c bed2vector.C -o bed2vector.o
    In file included from /usr/include/c++/4.2.1/backward/strstream:51,
                     from bed2vector.C:8:
    /usr/include/c++/4.2.1/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <iostream> instead of the deprecated header <iostream.h>. To disable this warning use -Wno-deprecated.
    bed2vector.C: In function ‘int get_a_line(FILE*, BZFILE*, int, std::string&)’:
    bed2vector.C:74: error: no matching function for call to ‘getline(char**, size_t*, FILE*&)’
    make: *** [bed2vector.o] Error 1
    chmod: /Library/Frameworks/R.framework/Resources/library/spp/libs/i386/*: No such file or directory
    ERROR: compilation failed for package 'spp'
    ** Removing '/Library/Frameworks/R.framework/Resources/library/spp'
    ** Restoring previous '/Library/Frameworks/R.framework/Resources/library/spp'
    The parts of the bed2vector.C file that seemed relevant I've reproduced below (the whole file was too big to attach!):
    Code:
    int get_a_line(FILE *f,BZFILE *b,int bz2file,string& line) {
      line="";
      if(bz2file) {
        int bzerror=get_bzline(b,line);
        if(bzerror==BZ_OK) {
          return(1);
        } else {
          if(bzerror!=BZ_STREAM_END) {
    	cerr<<"encountered BZERROR="<<bzerror<<endl;
          }
          return(0);
        }
      } else {
        char *cline=NULL;
        size_t n;
        if(getline(&cline,&n,f) != -1) {
          if(cline) {
    	cline[strlen(cline)-1]='\0';
    	line+=cline;
    	free(cline);
          }
          return(1);
        } else {
          return(0);
        }
      }
    }

  • #2
    I hope I'm not totally mistaken but it rather looks like C is mixed with C++ and this has nothing to do with OSX. the getline function is coded in C-sytle within a C++ source.

    you should ask the author to correct it in case this package is considered a maintained package.

    Comment


    • #3
      Hi all,

      Have figured out a patch for this problem. If anyone has the same issue, just ask and I'll pass the file along!

      Comment


      • #4
        For folks looking for the patch we wrote, here's a link!

        Comment


        • #5
          Thanks for posting the patch, i've been stuck with this problem on my mac for ages!

          Comment


          • #6
            No problem -- you may want to check out the new version that just came out. I haven't had a chance to try installing it yet, but looks like it should have some good new features.

            Comment


            • #7
              patch for getline function in spp

              I met the same problem with the getline function, but I can not open the link to the patch. Would anyone provide it to me. Many thanks.

              Originally posted by ewilbanks View Post
              For folks looking for the patch we wrote, here's a link!

              http://dl.dropbox.com/u/2796343/bed2vector.C

              Comment


              • #8
                patch for getline function for spp on MAC OS X

                Hello, I came across the same problem but couldn't access the posted patch anymore. Could anybody please provide it again?
                Many thanks!

                Originally posted by ewilbanks View Post
                For folks looking for the patch we wrote, here's a link!

                http://dl.dropbox.com/u/2796343/bed2vector.C

                Comment


                • #9
                  This should work!

                  Comment


                  • #10
                    Thanks!
                    I renamed the file to bed2vector.cpp and placed it into spp/src/
                    I also needed to add the following include line to the file for the spp package to compile and install on my system:
                    #include <errno.h>

                    Originally posted by ewilbanks View Post

                    Comment


                    • #11
                      Just wanted to note, upgrading to SPP 1.11 version fixes this issue on the mac, so no patch needed. Just installed on OSX 10.6.8 with no issue

                      Comment

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