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Old 11-11-2010, 02:27 PM   #1
ewilbanks
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Unhappy 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);
    }
  }
}
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Old 11-12-2010, 01:30 AM   #2
mudshark
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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.
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Old 11-12-2010, 11:16 AM   #3
ewilbanks
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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!
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Old 01-24-2011, 12:47 PM   #4
ewilbanks
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For folks looking for the patch we wrote, here's a link!

http://dl.dropbox.com/u/2796343/bed2vector.C
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Old 02-10-2011, 07:30 AM   #5
Bardj
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Thanks for posting the patch, i've been stuck with this problem on my mac for ages!
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Old 02-10-2011, 07:43 AM   #6
ewilbanks
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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.
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Old 03-15-2012, 07:45 AM   #7
qwzhang61
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Default 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.

Quote:
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
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Old 08-22-2012, 12:04 PM   #8
arecht
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Default 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!

Quote:
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
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Old 08-22-2012, 12:37 PM   #9
ewilbanks
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This should work!

https://dl.dropbox.com/u/2796343/bed2vector.C
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Old 08-22-2012, 02:52 PM   #10
arecht
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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>

Quote:
Originally Posted by ewilbanks View Post
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Old 06-19-2013, 06:41 AM   #11
Bardj
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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
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