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Old 10-08-2009, 08:56 PM   #1
anyone1985
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Location: shanghai, chia

Join Date: Mar 2009
Posts: 67
Default glimmer compile error

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$
anyone1985 is offline   Reply With Quote
Old 10-09-2009, 12:28 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
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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?
maubp is offline   Reply With Quote
Old 10-09-2009, 04:40 AM   #3
anyone1985
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Location: shanghai, chia

Join Date: Mar 2009
Posts: 67
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Yes, I had compile the maq, velvet successful. I guess missing the core development libraries is not the problem.


Quote:
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?
anyone1985 is offline   Reply With Quote
Old 10-09-2009, 09:30 AM   #4
nilshomer
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Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
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Quote:
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?
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Old 10-09-2009, 06:49 PM   #5
anyone1985
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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.
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Old 10-11-2009, 06:57 AM   #6
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Quote:
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
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Old 10-11-2009, 09:09 AM   #7
anyone1985
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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.



Quote:
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
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Old 10-12-2009, 01:46 AM   #8
dawe
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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
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Old 10-12-2009, 05:15 PM   #9
anyone1985
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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>.
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Old 06-23-2010, 12:03 AM   #10
Jonathan
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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
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Old 09-30-2010, 07:05 PM   #11
rizal
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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 ?
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Old 09-30-2010, 10:55 PM   #12
Jonathan
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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
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Old 08-24-2011, 07:46 AM   #13
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Thanks a lot, Jonathan. Was a big help!

-Surya
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Old 03-30-2012, 05:39 AM   #14
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Thank you Jonathan for thinking about the "people of the future"
Works like a charm !!

Antoine
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Old 07-16-2012, 07:09 AM   #15
pag
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Quote:
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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Old 11-15-2012, 07:43 AM   #16
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Unfortunately I wasn't so lucky. I am running ubuntu 12.10 but cant compile it whatsoever. I found out that there is a package called tigr-glimmer3. As I havent been able to run it yet, still looking at all the parameters... I was wondering if this is the same application as I tried to compile.
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Old 11-15-2012, 08:42 AM   #17
pag
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I appear to have both tigr-glimmer(3) related files in /usr/bin and /usr/lib as well as a glimmer installation within AGeS.

what compilation error did you get? do you have gcc?

here's my output of gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.6/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.6.3-1ubuntu5' --with-bugurl=file:///usr/share/doc/gcc-4.6/README.Bugs --enable-languages=c,c++,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.6 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.6 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)

uname -a :
Linux blah 3.2.0-32-generic-tuxonice #51~ppa1-Ubuntu SMP Sat Oct 13 07:58:37 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

lsb_release -a :
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 12.04.1 LTS
Release: 12.04
Codename: precise


I wouldn't think 12.10 would be much different from .04, but one never knows with these things:P
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Old 11-15-2012, 09:35 PM   #18
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gcc -v
Using built-in specs.
COLLECT_GCC=/usr/bin/gcc-4.7.real
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.7/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu/Linaro 4.7.2-2ubuntu1' --with-bugurl=file:///usr/share/doc/gcc-4.7/README.Bugs --enable-languages=c,c++,go,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.7 --enable-shared --enable-linker-build-id --with-system-zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.7 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --enable-plugin --enable-objc-gc --disable-werror --with-arch-32=i686 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.7.2 (Ubuntu/Linaro 4.7.2-2ubuntu1)

As far as I can see there is a version difference within gcc.

Linux me 3.5.0-18-generic #29-Ubuntu SMP Fri Oct 19 10:26:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 12.10
Release: 12.10
Codename: quantal
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Old 11-29-2012, 05:16 AM   #19
ejuscamaytal
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Default Installing glimmer 3

Excuse me, I am installing glimmer, in ubuntu, but it fails when I type make. I would like somebody help me, please!
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Old 11-29-2012, 05:37 AM   #20
maubp
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Quote:
Originally Posted by ejuscamaytal View Post
Excuse me, I am installing glimmer, in ubuntu, but it fails when I type make. I would like somebody help me, please!
If you want some help, you must make more effort to make it possible for people to help you without guessing or reading your mind. What was your error? What exactly did you type? Which version of Ubuntu and glimmer? etc

There was a really good paper on how to ask good questions I wanted to cite but I can't remember the reference...

Last edited by maubp; 11-29-2012 at 05:50 AM.
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