compiling peakseq

[wudai]

I have been trying to compile peakseq 1.1 (http://info.gersteinlab.org/PeakSeq) however I get an error:
$make
...
src/genomics/chip_seq/peak_selector/peakseq.cpp:67:54: error: ‘strlen’ was not declared in this scope
src/genomics/chip_seq/peak_selector/peakseq.cpp:68:38: error: ‘strcpy’ was not declared in this scope
...
after adding in #include <string.h> to peakseq.cpp I get the following error:
...
src/lib/utils/ansi_string/ansi_string.cpp:122:34: error: ‘memset’ was not declared in this scope
src/lib/utils/ansi_string/ansi_string.cpp: In static member function ‘static void t_string::replace_avoid_list(char*, char*, char)’:
src/lib/utils/ansi_string/ansi_string.cpp:262:44: error: ‘memset’ was not declared in this scope
...
I was tempted to add <string.h> to ansi_string.cpp but i noticed a comment saying not to add it.

Thus, I was wondering if anyone had sucess compiling peakseq without modifying the files.

I am using gcc version 4.5.2 on ubuntu 11.04

[epi]

Same thing here.

Any suggestions folks

[Mirrian]

You have to add "#include <string.h>" in the beginning of following two files and make again.

src/genomics/chip_seq/peak_selector/peakseq.cpp and
src/lib/utils/ansi_string/ansi_string.cpp

Mirrian

[AL_B]

compilation of PeakSeq

I added to ansi_string.cpp and peakseq.cpp
#include<cstring>
and it worked (fixed the problem of strcpy and memset)

[maxUlysse]

I think it's better to add
#include<cstring>
than
#include <string.h>
in src/genomics/chip_seq/peak_selector/peakseq.cpp and
src/lib/utils/ansi_string/ansi_string.cpp
Because, it's says clearly in ansi_string.cpp that string.h should do not be added.