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Thread Tools |
10-08-2009, 09:56 PM
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#1 |
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Member
Location: shanghai, chia Join Date: Mar 2009
Posts: 67
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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$ |
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10-09-2009, 01:28 AM
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#2 |
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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? |
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10-09-2009, 05:40 AM
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#3 | |
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Member
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:
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10-09-2009, 10:30 AM
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#4 | |
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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Quote:
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10-09-2009, 07:49 PM
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#5 |
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Member
Location: shanghai, chia Join Date: Mar 2009
Posts: 67
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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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10-11-2009, 07:57 AM
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#6 | |
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Senior Member
Location: 45°30'25.22"N / 9°15'53.00"E Join Date: Apr 2009
Posts: 258
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Quote:
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10-11-2009, 10:09 AM
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#7 | |
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Member
Location: shanghai, chia Join Date: Mar 2009
Posts: 67
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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:
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10-12-2009, 02:46 AM
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#8 |
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Senior Member
Location: 45°30'25.22"N / 9°15'53.00"E Join Date: Apr 2009
Posts: 258
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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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10-12-2009, 06:15 PM
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#9 |
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Member
Location: shanghai, chia Join Date: Mar 2009
Posts: 67
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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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06-23-2010, 01:03 AM
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#10 |
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Member
Location: Germany Join Date: Jun 2009
Posts: 36
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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",
Best -Jonathan |
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09-30-2010, 08:05 PM
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#11 |
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Junior Member
Location: Penang Join Date: Sep 2010
Posts: 1
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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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09-30-2010, 11:55 PM
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#12 |
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Member
Location: Germany Join Date: Jun 2009
Posts: 36
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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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08-24-2011, 08:46 AM
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#13 |
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Member
Location: New York Join Date: Mar 2011
Posts: 27
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Thanks a lot, Jonathan. Was a big help!
-Surya |
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03-30-2012, 06:39 AM
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#14 |
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Member
Location: Alps Join Date: Jan 2011
Posts: 27
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Thank you Jonathan for thinking about the "people of the future"
 Works like a charm !! Antoine |
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07-16-2012, 08:09 AM
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#15 | |
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Member
Location: CA, USA Join Date: May 2012
Posts: 72
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Quote:
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11-15-2012, 08:43 AM
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#16 |
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Member
Location: Brisbane Join Date: Nov 2009
Posts: 21
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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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11-15-2012, 09:42 AM
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#17 |
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Member
Location: CA, USA Join Date: May 2012
Posts: 72
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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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11-15-2012, 10:35 PM
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#18 |
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Member
Location: Brisbane Join Date: Nov 2009
Posts: 21
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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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11-29-2012, 06:16 AM
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#19 |
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Junior Member
Location: yes Join Date: Apr 2012
Posts: 5
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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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11-29-2012, 06:37 AM
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#20 | |
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Peter (Biopython etc)
Location: Dundee, Scotland, UK Join Date: Jul 2009
Posts: 1,543
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Quote:
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 06:50 AM. |
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