PeakSplitter installation

Xiaoyang

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Dec 9, 2011, 4:37:19 PM12/9/11

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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

mali salmon

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Dec 11, 2011, 1:20:03 AM12/11/11

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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

- Xiaoyang

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sflprint.h

sfl.h

prelude.h

Xiaoyang Zhang

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Dec 11, 2011, 10:40:36 AM12/11/11

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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 <shal...@gmail.com>

mali salmon

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Dec 12, 2011, 1:06:55 AM12/12/11

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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

Xiaoyang Zhang

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Dec 12, 2011, 10:47:56 AM12/12/11

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Thank you, Mali!
It's working now!
- Xiaoyang

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

António Miguel de Jesus Domingues

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Aug 13, 2012, 11:52:50 AM8/13/12

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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

Yuuki Imai

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Aug 31, 2012, 2:50:06 AM8/31/12

to macs-ann...@googlegroups.com, Kazuki Inoue

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" <shal...@gmail.com> wrote:

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 <xyzxi...@gmail.com> wrote:

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 <shal...@gmail.com>

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")

To unsubscribe from this group, send email to macs-announcem...@googlegroups.com <mailto:macs-announcement%2Bunsu...@googlegroups.com> .

mali salmon

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Sep 1, 2012, 2:31:13 PM9/1/12

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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

> macs-announcem...@googlegroups.com.

Yuuki Imai

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Sep 1, 2012, 9:46:22 PM9/1/12

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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 <shal...@gmail.com>

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

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Yuuki Imai

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Sep 3, 2012, 4:22:43 AM9/3/12

to macs-ann...@googlegroups.com, Kazuki Inoue

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:

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 <shal...@gmail.com>

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

On Fri, Aug 31, 2012 at 9:50 AM, Yuuki Imai <yi...@iam.u-tokyo.ac.jp> wrote:
> 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" <shal...@gmail.com> wrote:
>
> 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)

> <mailto:macs-announcement%2Bunsu...@googlegroups.com <mailto:macs-announcement%252Buns...@googlegroups.com> > .

>
> For more options, visit this group at
> http://groups.google.com/group/macs-announcement?hl=en.
>
>
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Yuuki Imai

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Sep 3, 2012, 4:47:31 AM9/3/12

to macs-ann...@googlegroups.com, Kazuki Inoue

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

António Domingues

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Dec 26, 2012, 12:27:34 PM12/26/12

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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/BURRvZhOTCoJ
http://www.biostars.org/p/13350/

I hope it helps.
António

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

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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Mar 16, 2014, 11:18:33 PM3/16/14

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Hello, could you please give me some suggestion for avoid these warnings?

This is the step in PeakSplitter_v1 path.

[tianf@solar PeakSplitter_v1]$ make

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,

from SplitPeaks/BedGraphParser.h:2,

from SplitPeaks/BedGraphParser.cpp:1:

./SFL/sfl.h:192:1: warning: "__NO_CTYPE" redefined

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:1687,

from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:39,

from SplitPeaks/Shared.h:8,

from SplitPeaks/BedGraphParser.h:2,

from SplitPeaks/BedGraphParser.cpp:1:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:37:1: warning: this is the location of the previous definition

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/BedGraphParser.h:2,

from SplitPeaks/BedGraphParser.cpp:1:

./SFL/sfl.h:236:80: warning: iostream.h: No such file or directory

Finished building: SplitPeaks/BedGraphParser.cpp

Building file: SplitPeaks/Parser.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"Parser.d" -MT"Parser.d" -o"Parser.o" "SplitPeaks/Parser.cpp"

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/Parser.h:2,

from SplitPeaks/Parser.cpp:1:

./SFL/sfl.h:192:1: warning: "__NO_CTYPE" redefined

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:1687,

from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:39,

from SplitPeaks/Shared.h:8,

from SplitPeaks/Parser.h:2,

from SplitPeaks/Parser.cpp:1:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:37:1: warning: this is the location of the previous definition

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/Parser.h:2,

from SplitPeaks/Parser.cpp:1:

./SFL/sfl.h:236:80: warning: iostream.h: No such file or directory

SplitPeaks/Parser.cpp: In static member function ‘static std::string Parser::getFileFormat(std::ifstream*, int*)’:

SplitPeaks/Parser.cpp:115: warning: comparison between signed and unsigned integer expressions

SplitPeaks/Parser.cpp: In static member function ‘static std::string Parser::ToUpper(const std::string&)’:

SplitPeaks/Parser.cpp:155: warning: comparison between signed and unsigned integer expressions

Finished building: SplitPeaks/Parser.cpp

Building file: SplitPeaks/PeakParser.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"PeakParser.d" -MT"PeakParser.d" -o"PeakParser.o" "SplitPeaks/PeakParser.cpp"

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/PeakParser.h:2,

from SplitPeaks/PeakParser.cpp:1:

./SFL/sfl.h:192:1: warning: "__NO_CTYPE" redefined

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:1687,

from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:39,

from SplitPeaks/Shared.h:8,

from SplitPeaks/PeakParser.h:2,

from SplitPeaks/PeakParser.cpp:1:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:37:1: warning: this is the location of the previous definition

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/PeakParser.h:2,

from SplitPeaks/PeakParser.cpp:1:

./SFL/sfl.h:236:80: warning: iostream.h: No such file or directory

SplitPeaks/PeakParser.cpp:2:20: warning: extra tokens at end of #include directive

Finished building: SplitPeaks/PeakParser.cpp

Building file: SplitPeaks/Position.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"Position.d" -MT"Position.d" -o"Position.o" "SplitPeaks/Position.cpp"

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/Position.h:2,

from SplitPeaks/Position.cpp:1:

./SFL/sfl.h:192:1: warning: "__NO_CTYPE" redefined

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:1687,

from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:39,

from SplitPeaks/Shared.h:8,

from SplitPeaks/Position.h:2,

from SplitPeaks/Position.cpp:1:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:37:1: warning: this is the location of the previous definition

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/Position.h:2,

from SplitPeaks/Position.cpp:1:

./SFL/sfl.h:236:80: warning: iostream.h: No such file or directory

Finished building: SplitPeaks/Position.cpp

Building file: SplitPeaks/SequenceDownloader.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"SequenceDownloader.d" -MT"SequenceDownloader.d" -o"SequenceDownloader.o" "SplitPeaks/SequenceDownloader.cpp"

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/SequenceDownloader.h:1,

from SplitPeaks/SequenceDownloader.cpp:1:

./SFL/sfl.h:192:1: warning: "__NO_CTYPE" redefined

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:1687,

from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:39,

from SplitPeaks/Shared.h:8,

from SplitPeaks/SequenceDownloader.h:1,

from SplitPeaks/SequenceDownloader.cpp:1:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:37:1: warning: this is the location of the previous definition

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/SequenceDownloader.h:1,

from SplitPeaks/SequenceDownloader.cpp:1:

./SFL/sfl.h:236:80: warning: iostream.h: No such file or directory

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/strstream:47,

from SplitPeaks/SequenceDownloader.h:2,

from SplitPeaks/SequenceDownloader.cpp:1:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.

Finished building: SplitPeaks/SequenceDownloader.cpp

Building file: SplitPeaks/Split.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"Split.d" -MT"Split.d" -o"Split.o" "SplitPeaks/Split.cpp"

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/Split.h:2,

from SplitPeaks/Split.cpp:1:

./SFL/sfl.h:192:1: warning: "__NO_CTYPE" redefined

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:1687,

from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:39,

from SplitPeaks/Shared.h:8,

from SplitPeaks/Split.h:2,

from SplitPeaks/Split.cpp:1:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:37:1: warning: this is the location of the previous definition

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/Split.h:2,

from SplitPeaks/Split.cpp:1:

./SFL/sfl.h:236:80: warning: iostream.h: No such file or directory

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/strstream:47,

from SplitPeaks/SequenceDownloader.h:2,

from SplitPeaks/Split.cpp:2:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/backward/backward_warning.h:28:2: warning: #warning This file includes at least one deprecated or antiquated header which may be removed without further notice at a future date. Please use a non-deprecated interface with equivalent functionality instead. For a listing of replacement headers and interfaces, consult the file backward_warning.h. To disable this warning use -Wno-deprecated.

SplitPeaks/Split.cpp: In member function ‘std::string Split::getRelatedChrFile(std::string, std::string)’:

SplitPeaks/Split.cpp:310: warning: unused variable ‘res’

SplitPeaks/Split.cpp: In member function ‘void Split::splitPeak(Position*, Parser*, std::ofstream*)’:

SplitPeaks/Split.cpp:371: warning: comparison between signed and unsigned integer expressions

SplitPeaks/Split.cpp:447: warning: comparison between signed and unsigned integer expressions

SplitPeaks/Split.cpp: In member function ‘std::string Split::Unzip(std::string)’:

SplitPeaks/Split.cpp:591: warning: unused variable ‘pos’

SplitPeaks/Split.cpp: In member function ‘void Split::AddToSortedSet(SubPeak*)’:

SplitPeaks/Split.cpp:656: warning: comparison between signed and unsigned integer expressions

Finished building: SplitPeaks/Split.cpp

Building file: SplitPeaks/SplitPeaks.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"SplitPeaks.d" -MT"SplitPeaks.d" -o"SplitPeaks.o" "SplitPeaks/SplitPeaks.cpp"

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/SplitPeaks.cpp:7:

./SFL/sfl.h:192:1: warning: "__NO_CTYPE" redefined

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:1687,

from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/string:40,

from ./SplitPeaks/tclap/SwitchArg.h:27,

from SplitPeaks/tclap/CmdLine.h:26,

from SplitPeaks/SplitPeaks.cpp:5:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:37:1: warning: this is the location of the previous definition

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/SplitPeaks.cpp:7:

./SFL/sfl.h:236:80: warning: iostream.h: No such file or directory

Finished building: SplitPeaks/SplitPeaks.cpp

Building file: SplitPeaks/SubPeak.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"SubPeak.d" -MT"SubPeak.d" -o"SubPeak.o" "SplitPeaks/SubPeak.cpp"

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/SubPeak.h:2,

from SplitPeaks/SubPeak.cpp:1:

./SFL/sfl.h:192:1: warning: "__NO_CTYPE" redefined

In file included from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/c++config.h:1687,

from /usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/iostream:39,

from SplitPeaks/Shared.h:8,

from SplitPeaks/SubPeak.h:2,

from SplitPeaks/SubPeak.cpp:1:

/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../include/c++/4.4.7/x86_64-redhat-linux/bits/os_defines.h:37:1: warning: this is the location of the previous definition

In file included from SplitPeaks/Shared.h:17,

from SplitPeaks/SubPeak.h:2,

from SplitPeaks/SubPeak.cpp:1:

./SFL/sfl.h:236:80: warning: iostream.h: No such file or directory

Finished building: SplitPeaks/SubPeak.cpp

Building file: SplitPeaks/unzip.c

Invoking: GCC C Compiler

gcc -D__UNIX__ -D__64BIT__ -I./SFL -I./Zlib -O3 -Wall -c -fmessage-length=0 -MMD -MP -MF"unzip.d" -MT"unzip.d" -o"unzip.o" "SplitPeaks/unzip.c"

SplitPeaks/unzip.c: In function ‘unzlocal_GetCurrentFileInfoInternal’:

SplitPeaks/unzip.c:610: warning: suggest explicit braces to avoid ambiguous ‘else’

SplitPeaks/unzip.c:690: warning: suggest explicit braces to avoid ambiguous ‘else’

SplitPeaks/unzip.c:715: warning: suggest explicit braces to avoid ambiguous ‘else’

SplitPeaks/unzip.c: In function ‘unzlocal_CheckCurrentFileCoherencyHeader’:

SplitPeaks/unzip.c:979: warning: suggest explicit braces to avoid ambiguous ‘else’

SplitPeaks/unzip.c: In function ‘unzGetGlobalComment’:

SplitPeaks/unzip.c:1537: warning: unused variable ‘err’

SplitPeaks/unzip.c: In function ‘unzlocal_getLong’:

SplitPeaks/unzip.c:235: warning: ‘i’ may be used uninitialized in this function

SplitPeaks/unzip.c: In function ‘unzlocal_GetCurrentFileInfoInternal’: