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**maubp** · 10-09-2009, 12:28 AM

Things like strcmp and strlen are core C/C++ functions - if the compiler can't find their definitions it suggests there is something seriously wrong with your setup (e.g. missing the core development libraries, or something with the path configuration).

Can you compile anything? e.g. a simple "hello world" style C or C++ program?

**anyone1985** · 10-09-2009, 04:40 AM

Yes, I had compile the maq, velvet successful. I guess missing the core development libraries is not the problem.

Originally posted by maubp View Post

Things like strcmp and strlen are core C/C++ functions - if the compiler can't find their definitions it suggests there is something seriously wrong with your setup (e.g. missing the core development libraries, or something with the path configuration).

Can you compile anything? e.g. a simple "hello world" style C or C++ program?

**nilshomer** · 10-09-2009, 09:30 AM

Originally posted by anyone1985 View Post

When I installed the glimmer3, I came across fatal compile error. Please help me!

bioinfo@bioinfo-desktop:~/software/glimmer3.02/src$ make
* Make Target is all
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
delcher.cc: In function ‘void Reverse_String(char*)’:
delcher.cc:284: error: ‘strlen’ was not declared in this scope
delcher.cc: In function ‘char* Strip_Trailing(char*, char)’:
delcher.cc:404: error: ‘strlen’ was not declared in this scope
make[1]: *** [delcher.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Common'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
icm.cc: In member function ‘void ICM_t::Full_Window_Distrib(char*, int, float*)’:
icm.cc:525: error: ‘memcpy’ was not declared in this scope
icm.cc: In member function ‘void ICM_t::Write_Header(FILE*, bool)’:
icm.cc:961: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘void ICM_Training_t::Count_Char_Pairs_Restricted(const char*, int)’:
icm.cc:1175: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::Score_Window(char*)’:
icm.cc:1551: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::subrange_score(char*, int, int)’:
icm.cc:1599: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Train_Model(std::vector<char*, std::allocator<char*> >&)’:
icm.cc:1714: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Write_Header(FILE*, bool)’:
icm.cc:1775: error: ‘strcat’ was not declared in this scope
icm.cc:1777: error: ‘strcat’ was not declared in this scope
icm.cc:1779: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Char_Pairs(int (*)[16], char*, int, int)’:
icm.cc:1825: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Single_Chars(int*, char*, int, int)’:
icm.cc:1856: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_Data(std::vector<char*, std::allocator<char*> >&, int*)’:
icm.cc:1941: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_String(char*, int*, int)’:
icm.cc:1970: error: ‘strncpy’ was not declared in this scope
icm.cc: In function ‘int Subscript(char)’:
icm.cc:1986: error: ‘strchr’ was not declared in this scope
make[1]: *** [icm.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/ICM'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
anomaly.cc: In function ‘int main(int, char**)’:
anomaly.cc:82: warning: suggest parentheses around && within ||
anomaly.cc: In function ‘bool Is_Start_Codon(const char*)’:
anomaly.cc:264: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘bool Is_Stop_Codon(const char*)’:
anomaly.cc:282: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘void Parse_Command_Line(int, char**)’:
anomaly.cc:308: error: ‘strtok’ was not declared in this scope
anomaly.cc:310: error: ‘strdup’ was not declared in this scope
anomaly.cc:328: error: ‘strdup’ was not declared in this scope
make[1]: *** [anomaly.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Glimmer'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@
entropy-score.cc: In function ‘int main(int, char**)’:
entropy-score.cc:76: error: ‘strcmp’ was not declared in this scope
entropy-score.cc:156: error: ‘strlen’ was not declared in this scope
make[1]: *** [entropy-score.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
delcher.cc: In function ‘void Reverse_String(char*)’:
delcher.cc:284: error: ‘strlen’ was not declared in this scope
delcher.cc: In function ‘char* Strip_Trailing(char*, char)’:
delcher.cc:404: error: ‘strlen’ was not declared in this scope
make[1]: *** [delcher.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Common'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
icm.cc: In member function ‘void ICM_t::Full_Window_Distrib(char*, int, float*)’:
icm.cc:525: error: ‘memcpy’ was not declared in this scope
icm.cc: In member function ‘void ICM_t::Write_Header(FILE*, bool)’:
icm.cc:961: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘void ICM_Training_t::Count_Char_Pairs_Restricted(const char*, int)’:
icm.cc:1175: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::Score_Window(char*)’:
icm.cc:1551: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::subrange_score(char*, int, int)’:
icm.cc:1599: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Train_Model(std::vector<char*, std::allocator<char*> >&)’:
icm.cc:1714: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Write_Header(FILE*, bool)’:
icm.cc:1775: error: ‘strcat’ was not declared in this scope
icm.cc:1777: error: ‘strcat’ was not declared in this scope
icm.cc:1779: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Char_Pairs(int (*)[16], char*, int, int)’:
icm.cc:1825: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Single_Chars(int*, char*, int, int)’:
icm.cc:1856: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_Data(std::vector<char*, std::allocator<char*> >&, int*)’:
icm.cc:1941: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_String(char*, int*, int)’:
icm.cc:1970: error: ‘strncpy’ was not declared in this scope
icm.cc: In function ‘int Subscript(char)’:
icm.cc:1986: error: ‘strchr’ was not declared in this scope
make[1]: *** [icm.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/ICM'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
anomaly.cc: In function ‘int main(int, char**)’:
anomaly.cc:82: warning: suggest parentheses around && within ||
anomaly.cc: In function ‘bool Is_Start_Codon(const char*)’:
anomaly.cc:264: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘bool Is_Stop_Codon(const char*)’:
anomaly.cc:282: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘void Parse_Command_Line(int, char**)’:
anomaly.cc:308: error: ‘strtok’ was not declared in this scope
anomaly.cc:310: error: ‘strdup’ was not declared in this scope
anomaly.cc:328: error: ‘strdup’ was not declared in this scope
make[1]: *** [anomaly.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Glimmer'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@
entropy-score.cc: In function ‘int main(int, char**)’:
entropy-score.cc:76: error: ‘strcmp’ was not declared in this scope
entropy-score.cc:156: error: ‘strlen’ was not declared in this scope
make[1]: *** [entropy-score.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
delcher.cc: In function ‘void Reverse_String(char*)’:
delcher.cc:284: error: ‘strlen’ was not declared in this scope
delcher.cc: In function ‘char* Strip_Trailing(char*, char)’:
delcher.cc:404: error: ‘strlen’ was not declared in this scope
make[1]: *** [delcher.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Common'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
icm.cc: In member function ‘void ICM_t::Full_Window_Distrib(char*, int, float*)’:
icm.cc:525: error: ‘memcpy’ was not declared in this scope
icm.cc: In member function ‘void ICM_t::Write_Header(FILE*, bool)’:
icm.cc:961: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘void ICM_Training_t::Count_Char_Pairs_Restricted(const char*, int)’:
icm.cc:1175: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::Score_Window(char*)’:
icm.cc:1551: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::subrange_score(char*, int, int)’:
icm.cc:1599: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Train_Model(std::vector<char*, std::allocator<char*> >&)’:
icm.cc:1714: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Write_Header(FILE*, bool)’:
icm.cc:1775: error: ‘strcat’ was not declared in this scope
icm.cc:1777: error: ‘strcat’ was not declared in this scope
icm.cc:1779: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Char_Pairs(int (*)[16], char*, int, int)’:
icm.cc:1825: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Single_Chars(int*, char*, int, int)’:
icm.cc:1856: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_Data(std::vector<char*, std::allocator<char*> >&, int*)’:
icm.cc:1941: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_String(char*, int*, int)’:
icm.cc:1970: error: ‘strncpy’ was not declared in this scope
icm.cc: In function ‘int Subscript(char)’:
icm.cc:1986: error: ‘strchr’ was not declared in this scope
make[1]: *** [icm.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/ICM'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
anomaly.cc: In function ‘int main(int, char**)’:
anomaly.cc:82: warning: suggest parentheses around && within ||
anomaly.cc: In function ‘bool Is_Start_Codon(const char*)’:
anomaly.cc:264: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘bool Is_Stop_Codon(const char*)’:
anomaly.cc:282: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘void Parse_Command_Line(int, char**)’:
anomaly.cc:308: error: ‘strtok’ was not declared in this scope
anomaly.cc:310: error: ‘strdup’ was not declared in this scope
anomaly.cc:328: error: ‘strdup’ was not declared in this scope
make[1]: *** [anomaly.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Glimmer'
##### Making Directory /home/bioinfo/software/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/bioinfo/software/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@
entropy-score.cc: In function ‘int main(int, char**)’:
entropy-score.cc:76: error: ‘strcmp’ was not declared in this scope
entropy-score.cc:156: error: ‘strlen’ was not declared in this scope
make[1]: *** [entropy-score.o] Error 1
make[1]: Leaving directory `/home/bioinfo/software/glimmer3.02/src/Util'
bioinfo@bioinfo-desktop:~/software/glimmer3.02/src$

Is there a configure script? If so, what is the output?

**anyone1985** · 10-09-2009, 06:49 PM

No, there is no aconfigure script. As the manual, I have changed the src/common/delcher.hh, or compile in the SimpleMake directory. However, the fatal error always happened.

**dawe** · 10-11-2009, 06:57 AM

Originally posted by anyone1985 View Post

No, there is no aconfigure script. As the manual, I have changed the src/common/delcher.hh, or compile in the SimpleMake directory. However, the fatal error always happened.

It would be helpful to know which system/OS are your running. I guess it's a standard linux install, and you are missing libstdc++-devel or something like that. Also, maq is written in C

**anyone1985** · 10-11-2009, 09:09 AM

I think i have install the libstdc++6, however, the compile still failed. My system is ubuntu, the kernel is
Linux 2.6.27-14-server #1 SMP Tue Jul 7 22:58:31 UTC 2009 x86_64 GNU/Linux, my gcc compiler is gcc (Ubuntu 4.3.2-1ubuntu12) 4.3.2.

Originally posted by dawe View Post

It would be helpful to know which system/OS are your running. I guess it's a standard linux install, and you are missing libstdc++-devel or something like that. Also, maq is written in C

**dawe** · 10-12-2009, 01:46 AM

Hi again. You are using gcc 4.3 and it requires some headers not needed before. You can either apply this patch:

diff -Naur glimmer3.02/src/Common/delcher.hh glimmer3.02.gcc-4.3/src/Common/delcher.hh
--- glimmer3.02/src/Common/delcher.hh 2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02.gcc-4.3/src/Common/delcher.hh 2009-10-12 11:42:58.000000000 +0200
@@ -31,7 +31,9 @@
#include <fstream>
#include <vector>
#include <string>
-
+#include <climits>
+#include <cstring>
+#include <memory>
#include "exceptions.hh"

or install gcc-4.2.
HTH

d

**anyone1985** · 10-12-2009, 05:15 PM

Thanks for your help. The author of glimmer has provided me the simplest to compile successful. Chane the line 26 of file delcher.hh in the src/Common directory from
#include <sting> to #include <cstring>.

**Jonathan** · 06-23-2010, 12:03 AM

Hi all, sorry to raise this thread from the dead, but I'd like to share the following with you - or whoever might come across this issues:

Compiling Glimmer3 on the latest Fedora linux (FC13, 2.6.33.5-124.fc13.x86_64) caused some problems using the gcc 4.4.4 20100503 (Red Hat 4.4.4-2).

So these are the patches to the original source to make it compile:

Code:

diff -Naur glimmer3.02/src/Common/delcher.hh glimmer3.02-fc13/src/Common/delcher.hh
--- glimmer3.02/src/Common/delcher.hh	2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02-fc13/src/Common/delcher.hh	2010-06-23 09:45:17.351561806 +0200
@@ -30,7 +30,9 @@
 #include  <iomanip>
 #include  <fstream>
 #include  <vector>
-#include  <string>
+#include <cstring>
+#include <climits>
+#include <memory>
 
 #include  "exceptions.hh"
 
diff -Naur glimmer3.02/src/Common/gene.cc glimmer3.02-fc13/src/Common/gene.cc
--- glimmer3.02/src/Common/gene.cc	2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02-fc13/src/Common/gene.cc	2010-06-23 09:53:43.823498072 +0200
@@ -260,7 +260,7 @@
 //  Print the contents of this PWM to  fp .
 
   {
-   char  * tag = "acgt";
+   char  * tag = (char*)"acgt";
    int  width;
    int  i, j;
 
@@ -445,7 +445,7 @@
   {
    char  * p;
 
-   p = strchr (CONVERSION_STRING, tolower (ch));
+   p = (char*)strchr (CONVERSION_STRING, tolower (ch));
    if  (p == NULL)
        return  4;
 
diff -Naur glimmer3.02/src/ICM/icm.cc glimmer3.02-fc13/src/ICM/icm.cc
--- glimmer3.02/src/ICM/icm.cc	2006-06-12 21:40:14.000000000 +0200
+++ glimmer3.02-fc13/src/ICM/icm.cc	2010-06-23 09:51:21.305436344 +0200
@@ -1983,7 +1983,7 @@
   {
    char  * p;
 
-   p = strchr (ALPHA_STRING, tolower (Filter (ch)));
+   p = (char*) strchr (ALPHA_STRING, tolower (Filter (ch)));
    if  (p == NULL)
        {
         fprintf (stderr, "ERROR:  Bad character %c in subscript conversion",

Hope this helps someone,
Best
-Jonathan

**rizal** · 09-30-2010, 07:05 PM

Hi,

I am a beginner to Linux. Recently i have installed glimmer on fedora core 13 and have the same error.

My question is how to apply the patches code given above? Can i just insert the codes after the last line in the file delcher.hh ?

**Jonathan** · 09-30-2010, 10:55 PM

Nope.

Do you see the lines with
"@@ [some numbers] @@"
??

The numbers in between are the line-numbers,
so go there, find the lines that have a "-" or nothing before them,
Check if these lines actually match, then remove the lines with "-" and add the lines with "+" where listed.

PM me for more q&a.
-Jonathan

**suryasaha** · 08-24-2011, 07:46 AM

Thanks a lot, Jonathan. Was a big help!

-Surya

**pasta** · 03-30-2012, 05:39 AM

Thank you Jonathan for thinking about the "people of the future"

Works like a charm !!

Antoine

**pag** · 07-16-2012, 07:09 AM

Originally posted by suryasaha View Post

Thanks a lot, Jonathan. Was a big help!

-Surya

I'd like to add my thanks in this thread!

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