problem in installing glimmer3.02
msc2
msc2 at bioinfo.ernet.in
Sun Nov 2 10:51:14 UTC 2008
Dear sir,
I have downloaded glimmer3.02 package and when i typed make, the
following error is showing..
[root at llocalhost src]# make
* Make Target is all
##### Making Directory /bioinfo/glimmer3.02/src/Common all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Common'
##### Making Directory /bioinfo/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/ICM'
##### Making Directory /bioinfo/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Glimmer'
##### Making Directory /bioinfo/glimmer3.02/src/Util all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /bioinfo/glimmer3.02/src/Common all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Common'
##### Making Directory /bioinfo/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/ICM'
##### Making Directory /bioinfo/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Glimmer'
##### Making Directory /bioinfo/glimmer3.02/src/Util all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /bioinfo/glimmer3.02/src/Common all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Common'
##### Making Directory /bioinfo/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/ICM'
##### Making Directory /bioinfo/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Glimmer'
##### Making Directory /bioinfo/glimmer3.02/src/Util all #####
make[1]: Entering directory `/bioinfo/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 `/bioinfo/glimmer3.02/src/Util'
so i am not able to solve this problem.i will be very happy if you can
provide me steps in solving this problem.
my system information
redhat linux 2.6.25-14.fcq.i686
fedora 9
gcc compiler:version 4.3.0 20080428(Red Hat 4.3.0-8)(GCC)
Thank you sir
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