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Xiaoyang  
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 More options Dec 9 2011, 4:37 pm
From: Xiaoyang <xyzxiaoy...@gmail.com>
Date: Fri, 9 Dec 2011 13:37:19 -0800 (PST)
Local: Fri, Dec 9 2011 4:37 pm
Subject: PeakSplitter installation
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Hi all,
I am installing PeakSplitter_Cpp_1.0 but after the first step I got
errors below:
Xiaoyang-Zhangs-MacBook-Pro:PeakSplitter_MacOS XiaoyangZhang$ cd /
Applications/PeakSplitter_Cpp/PeakSplitter_MacOS/PeakSplitter_v1/SFL/
Release
Xiaoyang-Zhangs-MacBook-Pro:Release XiaoyangZhang$ make
Building file: ../sflbits.c
Invoking: GCC C Compiler
gcc -D__UNIX__ -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"sflbits.d"
-MT"sflbits.d" -o"sflbits.o" "../sflbits.c"
In file included from ../sflbits.c:16:
../prelude.h:401:9: error: #error "Cannot compile: must change
definition of 'qbyte'."
make: *** [sflbits.o] Error 1

Could you please take a look at it and help me out?
Thanks,
- Xiaoyang


 
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mali salmon  
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 More options Dec 11 2011, 1:20 am
From: mali salmon <shalm...@gmail.com>
Date: Sun, 11 Dec 2011 08:20:03 +0200
Local: Sun, Dec 11 2011 1:20 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Xiaoyang
Sorry for the late reply.
I suppose you have Mac OS, unfortunately, SFL doesn't support Mac OS and
hence the problems with different Mac versions.
I added some lines in the code forcing the compiler to think your machine
is 64 bit.
Please replace the "sfl.h, prelude.h and sflprint.h"  files under SFL
folder with the attached files, then try to re-compile (go to SFL/Release
folder, type "make clean", then run "make")
Please tell me if this solved the problem
Thanks
Mali

  sflprint.h
2K Download

  sfl.h
237K Download

  prelude.h
32K Download

 
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Xiaoyang Zhang  
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 More options Dec 11 2011, 10:40 am
From: Xiaoyang Zhang <xyzxiaoy...@gmail.com>
Date: Sun, 11 Dec 2011 10:40:36 -0500
Local: Sun, Dec 11 2011 10:40 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Mali,
Thanks for your help!
The SFL problem seems solved now! But some errors come out when it comes to
the last step (PeakSplitter_v1):

kiel-telesfords-macbook-pro:PeakSplitter_v1 XiaoyangZhang$ make
Building file: SplitPeaks/BedGraphParser.cpp
Invoking: GCC C++ Compiler
g++ -D__UNIX__ -I./SplitPeaks -I./SFL -I./Zlib -O3 -Wall -c
-fmessage-length=0 -MMD -MP -MF"BedGraphParser.d" -MT"BedGraphParser.d"
-o"BedGraphParser.o" "SplitPeaks/BedGraphParser.cpp"
In file included from SplitPeaks/BedGraphParser.h:2,
                 from SplitPeaks/BedGraphParser.cpp:1:
SplitPeaks/Shared.h:3:1: warning: "__UNIX__" redefined
<command-line>: warning: this is the location of the previous definition
In file included from /usr/include/c++/4.2.1/backward/iostream.h:31,
                 from ./SFL/sfl.h:236,
                 from SplitPeaks/Shared.h:17,
                 from SplitPeaks/BedGraphParser.h:2,
                 from SplitPeaks/BedGraphParser.cpp:1:
/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.
In file included from SplitPeaks/BedGraphParser.cpp:1:
SplitPeaks/BedGraphParser.h:12: error: extra qualification
‘BedGraphParser::’ on member ‘nextPosition’
make: *** [BedGraphParser.o] Error 1

Thanks again for your help!
- Xiaoyang

2011/12/11 mali salmon <shalm...@gmail.com>


 
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mali salmon  
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 More options Dec 12 2011, 1:06 am
From: mali salmon <shalm...@gmail.com>
Date: Mon, 12 Dec 2011 08:06:55 +0200
Local: Mon, Dec 12 2011 1:06 am
Subject: Re: [macs-announscement] PeakSplitter installation
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 Hi Xiaovang
Please open the file BedGraphParser.h, and replace line 12 "wigPosition*
BedGraphParser::nextPosition();"
with  "wigPosition* nextPosition();" (so actually just remove the
BedGraphParser:: from that line)
Then re-compile and let me know how it goes
Thanks
Mali

On Sun, Dec 11, 2011 at 5:40 PM, Xiaoyang Zhang <xyzxiaoy...@gmail.com>wrote:


 
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Xiaoyang Zhang  
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 More options Dec 12 2011, 10:47 am
From: Xiaoyang Zhang <xyzxiaoy...@gmail.com>
Date: Mon, 12 Dec 2011 10:47:56 -0500
Local: Mon, Dec 12 2011 10:47 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Thank you, Mali!
It's working now!
- Xiaoyang

2011/12/12 mali salmon <shalm...@gmail.com>


 
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António Miguel de Jesus Domingues  
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 More options Aug 13 2012, 11:52 am
From: António Miguel de Jesus Domingues <amjdoming...@gmail.com>
Date: Mon, 13 Aug 2012 08:52:50 -0700 (PDT)
Local: Mon, Aug 13 2012 11:52 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Mali,

I am also struggling with the PeakSplitter instalation but in Ubuntu 11.04.
Compiling the libraries SFL and zlib went well but compiling peaksplitter
gave this error:

Building file: SplitPeaks/BedGraphParser.cpp
Invoking: GCC C++ Compiler
g++ -D__UNIX__ -D__64BIT__ -I./SplitPeaks -I./SFL -I./Zlib -O3 -Wall -c
-fmessage-length=0 -MMD -MP -MF"BedGraphParser.d" -MT"BedGraphParser.d"
-o"BedGraphParser.o" "SplitPeaks/BedGraphParser.cpp"
In file included from SplitPeaks/Shared.h:17:0,
                 from SplitPeaks/BedGraphParser.h:2,
                 from SplitPeaks/BedGraphParser.cpp:1:
./SFL/sfl.h:192:0: warning: "__NO_CTYPE" redefined
/usr/include/c++/4.5/x86_64-linux-gnu/bits/os_defines.h:37:0: note: this is
the location of the previous definition
./SFL/sfl.h:236:80: fatal error: iostream.h: No such file or directory
compilation terminated.
make: *** [BedGraphParser.o] Error 1

Do you know how to solve this?

Cheers,
António


 
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Yuuki Imai  
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 More options Aug 31 2012, 2:50 am
From: Yuuki Imai <yi...@iam.u-tokyo.ac.jp>
Date: Fri, 31 Aug 2012 15:50:06 +0900
Local: Fri, Aug 31 2012 2:50 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Mali,

I also have same problem for installing PeakSplitter as below,

Building file: SplitPeaks/BedGraphParser.cpp
Invoking: GCC C++ Compiler
g++ -D__UNIX__ -I./SplitPeaks -I./SFL -I./Zlib -O3 -Wall -c
-fmessage-length=0 -MMD -MP -MF"BedGraphParser.d" -MT"BedGraphParser.d"
-o"BedGraphParser.o" "SplitPeaks/BedGraphParser.cpp"
In file included from SplitPeaks/BedGraphParser.h:2,
                 from SplitPeaks/BedGraphParser.cpp:1:
SplitPeaks/Shared.h:3:1: warning: "__UNIX__" redefined
<command-line>: warning: this is the location of the previous definition
In file included from SplitPeaks/BedGraphParser.cpp:1:
SplitPeaks/BedGraphParser.h:12: error: extra qualification
‘BedGraphParser::’ on member ‘nextPosition’
make: *** [BedGraphParser.o] Error 1

I tried to solve the problem according to your comments for Xiaoyang as
below,
but only the BedGraphParser.d was generated in the PeakSplitter_v1 folder.
My Mac is Mac OS X10.6.8. (32 bit)

Could you give your advice to solve the problem?

Best,

Yuuki

On 11/12/12 15:06, "mali salmon" <shalm...@gmail.com> wrote:


 
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mali salmon  
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 More options Sep 1 2012, 2:31 pm
From: mali salmon <shalm...@gmail.com>
Date: Sat, 1 Sep 2012 21:31:13 +0300
Local: Sat, Sep 1 2012 2:31 pm
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Yuuki
So you actually removed the "BedGraphParser::" from "wigPosition*
BedGraphParser::nextPosition();"  line in BedGraphParser.h file right?
Have you changes anything else? Did you get any error?
Thanks
Mali


 
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Yuuki Imai  
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 More options Sep 1 2012, 9:46 pm
From: Yuuki Imai <yi...@iam.u-tokyo.ac.jp>
Date: Sun, 2 Sep 2012 10:46:22 +0900
Local: Sat, Sep 1 2012 9:46 pm
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Mali,

Thank you for your reply.
I could not find BedGraphParser.h file in the PeakSplitter_v1 folder.
So I did not removed it.

Thanks,

Yuuki

2012/9/2 mali salmon <shalm...@gmail.com>

--
********************************************************
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Lecturer
Institute of Molecular and Cellular Biosciences,
The University of Tokyo

1-1-1 Yoyoi, Bunkyo-ku, Tokyo, Japan 113-0032

Tel: +81-3-5841-7891
Fax: +81-3-5841-8477
email: yi...@iam.u-tokyo.ac.jp
http://www.iam.u-tokyo.ac.jp/boneandjoint
********************************************************


 
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Yuuki Imai  
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 More options Sep 3 2012, 4:22 am
From: Yuuki Imai <yi...@iam.u-tokyo.ac.jp>
Date: Mon, 03 Sep 2012 17:22:43 +0900
Local: Mon, Sep 3 2012 4:22 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Mali,

I found BedGraphParser.h file in the SplitPeaks folder and removed
“BedGraphParser::” from line 12.
Then, now it works!

Thank you for your kind help. Sorry for bothering you.

Best,

Yuuki

On 12/09/02 10:46, "Yuuki Imai" <yi...@iam.u-tokyo.ac.jp> wrote:


 
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Yuuki Imai  
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 More options Sep 3 2012, 4:47 am
From: Yuuki Imai <yi...@iam.u-tokyo.ac.jp>
Date: Mon, 03 Sep 2012 17:47:31 +0900
Local: Mon, Sep 3 2012 4:47 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Mali,

I found that an executable file named "PeakSplitter" was generated in the
folder.
Then, type ./peaksplitter in the command line, but there was a “PARSE ERROR”
as below,

imai-hiroshiki-no-iMac:MACS14 Yuuki$ ./peaksplitter
PARSE ERROR:  
             One or more required arguments missing!

Brief USAGE:
   ./peaksplitter  -p <string> -w <string> -o <string> [-c <int>] [-v
                   <float>] [-f] [-u <string>] [-n <int>] [-l <int>] [--]
                   [--version] [-h]

For complete USAGE and HELP type:
   ./peaksplitter --help

Could you help me again?

Thanks,

Yuuki

On 12/09/03 17:22, "Yuuki Imai" <yi...@iam.u-tokyo.ac.jp> wrote:


 
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Jancho Wang  
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 More options Dec 21 2012, 10:43 am
From: Jancho Wang <jancho.w...@gmail.com>
Date: Fri, 21 Dec 2012 07:43:16 -0800 (PST)
Local: Fri, Dec 21 2012 10:43 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Antonio,
   I met the same problem with you when installing the PeakSplitter on
Ubuntu 12.10. So could you tell me how to solve it? Appreciated very much.

Jancho

在 2012年8月13日星期一UTC+8下午11时52分50秒，António Miguel de Jesus Domingues写道：


 
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Jancho Wang  
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 More options Dec 22 2012, 3:16 am
From: Jancho Wang <jancho.w...@gmail.com>
Date: Sat, 22 Dec 2012 00:16:57 -0800 (PST)
Local: Sat, Dec 22 2012 3:16 am
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi, Antonio,
    Have u solved the problem. I also met the same one. So could u tell me
how to solve it?
Jancho

在 2012年8月13日星期一UTC+8下午11时52分50秒，António Miguel de Jesus Domingues写道：


 
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António Domingues  
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 More options Dec 26 2012, 12:27 pm
From: António Domingues <amjdoming...@gmail.com>
Date: Wed, 26 Dec 2012 18:27:34 +0100
Local: Wed, Dec 26 2012 12:27 pm
Subject: Re: [macs-announscement] PeakSplitter installation
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Hi Jancho,

I did solve the problem but I can remenber the details. I think the
compiling of SFL and zlib that were not complete and so I did them again
and then proceed with the compilation of PeakSplitter. In this step I
also had to fiddle with the files - there is also a bit more of
information here:
https://groups.google.com/forum/#!msg/macs-announcement/V2d8HdCJmRA/B...
http://www.biostars.org/p/13350/

I hope it helps.
António

On 22/12/12 09:16, Jancho Wang wrote:

--
---------------------------------------------------------------------
António Miguel de Jesus Domingues, PhD
Neugebauer group
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 Dresden
Germany

http://people.mpi-cbg.de/domingue/home.html
e-mail: domin...@mpi-cbg.de
tel. +49 351 210 2481
The Unbearable Lightness of Molecular Biology


 
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