[jjk]

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.

[pag]

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

[jjk]

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

[ejuscamaytal]

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!

[maubp]

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...

[ejuscamaytal]

Sorry, It's the error: I'm using glimmer 3.02 and ubuntu 12.10


edu@wall-e:~/Downloads/glimmer3.02/src$ make
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [delcher.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [icm.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [anomaly.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [entropy-profile.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [delcher.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [icm.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [anomaly.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [entropy-profile.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [delcher.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [icm.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [anomaly.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [entropy-profile.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'
edu@wall-e:~/Downloads/glimmer3.02/src$


I want to help me, please!

[ejuscamaytal]

Glimmer 3.02

Sorry, It's the error: I'm using glimmer 3.02 and ubuntu 12.10


edu@wall-e:~/Downloads/glimmer3.02/src$ make
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [delcher.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [icm.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [anomaly.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [entropy-profile.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [delcher.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [icm.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [anomaly.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [entropy-profile.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [delcher.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [icm.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [anomaly.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-profile.cc @@@@@@@@@@@@@@@@@@@@@
/bin/sh: 2: g++: not found
make[1]: *** [entropy-profile.o] Error 127
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'
edu@wall-e:~/Downloads/glimmer3.02/src$


I want to help me, please!

[maubp]

The key information there is g++: not found, meaning you do not have the GNU C++ compiler installed. I think you just need to do this on Ubuntu:

sudo apt-get install g++

[ejuscamaytal]

Excuse me, I've tried again but I get this error:

edu@wall-e:~/Downloads/glimmer3.02/src$ make
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
delcher.cc:1:0: note: this is the location of the previous definition
delcher.cc: In function ‘void Reverse_String(char*)’:
delcher.cc:284:17: error: ‘strlen’ was not declared in this scope
delcher.cc: In function ‘char* Strip_Trailing(char*, char)’:
delcher.cc:404:19: error: ‘strlen’ was not declared in this scope
make[1]: *** [delcher.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
icm.cc:1:0: note: this is the location of the previous definition
icm.cc: In member function ‘void ICM_t::Full_Window_Distrib(char*, int, float*)’:
icm.cc:525:81: error: ‘memcpy’ was not declared in this scope
icm.cc: In member function ‘void ICM_t::Write_Header(FILE*, bool)’:
icm.cc:961:9: 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:1175:29: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::Score_Window(char*)’:
icm.cc:1551:28: 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:1599:28: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Train_Model(std::vector<char*>&)’:
icm.cc:1714:44: 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:1775:30: error: ‘strcat’ was not declared in this scope
icm.cc:1777:27: error: ‘strcat’ was not declared in this scope
icm.cc:1779:9: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Char_Pairs(int (*)[16], char*, int, int)’:
icm.cc:1825:29: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Single_Chars(int*, char*, int, int)’:
icm.cc:1856:29: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_Data(std::vector<char*>&, int*)’:
icm.cc:1941:26: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_String(char*, int*, int)’:
icm.cc:1970:23: error: ‘strncpy’ was not declared in this scope
icm.cc: In function ‘int Subscript(char)’:
icm.cc:1986:51: error: ‘strchr’ was not declared in this scope
make[1]: *** [icm.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
anomaly.cc:1:0: note: this is the location of the previous definition
anomaly.cc: In function ‘int main(int, char**)’:
anomaly.cc:82:76: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
anomaly.cc: In function ‘bool Is_Start_Codon(const char*)’:
anomaly.cc:264:41: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘bool Is_Stop_Codon(const char*)’:
anomaly.cc:282:40: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘void Parse_Command_Line(int, char**)’:
anomaly.cc:308:40: error: ‘strtok’ was not declared in this scope
anomaly.cc:310:27: error: ‘strdup’ was not declared in this scope
anomaly.cc:328:27: error: ‘strdup’ was not declared in this scope
make[1]: *** [anomaly.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
entropy-score.cc:1:0: note: this is the location of the previous definition
entropy-score.cc: In function ‘int main(int, char**)’:
entropy-score.cc:76:32: error: ‘strcmp’ was not declared in this scope
entropy-score.cc:156:23: error: ‘strlen’ was not declared in this scope
make[1]: *** [entropy-score.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
delcher.cc:1:0: note: this is the location of the previous definition
delcher.cc: In function ‘void Reverse_String(char*)’:
delcher.cc:284:17: error: ‘strlen’ was not declared in this scope
delcher.cc: In function ‘char* Strip_Trailing(char*, char)’:
delcher.cc:404:19: error: ‘strlen’ was not declared in this scope
make[1]: *** [delcher.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
icm.cc:1:0: note: this is the location of the previous definition
icm.cc: In member function ‘void ICM_t::Full_Window_Distrib(char*, int, float*)’:
icm.cc:525:81: error: ‘memcpy’ was not declared in this scope
icm.cc: In member function ‘void ICM_t::Write_Header(FILE*, bool)’:
icm.cc:961:9: 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:1175:29: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::Score_Window(char*)’:
icm.cc:1551:28: 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:1599:28: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Train_Model(std::vector<char*>&)’:
icm.cc:1714:44: 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:1775:30: error: ‘strcat’ was not declared in this scope
icm.cc:1777:27: error: ‘strcat’ was not declared in this scope
icm.cc:1779:9: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Char_Pairs(int (*)[16], char*, int, int)’:
icm.cc:1825:29: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Single_Chars(int*, char*, int, int)’:
icm.cc:1856:29: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_Data(std::vector<char*>&, int*)’:
icm.cc:1941:26: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_String(char*, int*, int)’:
icm.cc:1970:23: error: ‘strncpy’ was not declared in this scope
icm.cc: In function ‘int Subscript(char)’:
icm.cc:1986:51: error: ‘strchr’ was not declared in this scope
make[1]: *** [icm.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
anomaly.cc:1:0: note: this is the location of the previous definition
anomaly.cc: In function ‘int main(int, char**)’:
anomaly.cc:82:76: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
anomaly.cc: In function ‘bool Is_Start_Codon(const char*)’:
anomaly.cc:264:41: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘bool Is_Stop_Codon(const char*)’:
anomaly.cc:282:40: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘void Parse_Command_Line(int, char**)’:
anomaly.cc:308:40: error: ‘strtok’ was not declared in this scope
anomaly.cc:310:27: error: ‘strdup’ was not declared in this scope
anomaly.cc:328:27: error: ‘strdup’ was not declared in this scope
make[1]: *** [anomaly.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
entropy-score.cc:1:0: note: this is the location of the previous definition
entropy-score.cc: In function ‘int main(int, char**)’:
entropy-score.cc:76:32: error: ‘strcmp’ was not declared in this scope
entropy-score.cc:156:23: error: ‘strlen’ was not declared in this scope
make[1]: *** [entropy-score.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'
* Make Target is all
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Common all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Common'
@@@@@@@@@@@@@@@@@@@ delcher.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
delcher.cc:1:0: note: this is the location of the previous definition
delcher.cc: In function ‘void Reverse_String(char*)’:
delcher.cc:284:17: error: ‘strlen’ was not declared in this scope
delcher.cc: In function ‘char* Strip_Trailing(char*, char)’:
delcher.cc:404:19: error: ‘strlen’ was not declared in this scope
make[1]: *** [delcher.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Common'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/ICM all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/ICM'
@@@@@@@@@@@@@@@@@@@ icm.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
icm.cc:1:0: note: this is the location of the previous definition
icm.cc: In member function ‘void ICM_t::Full_Window_Distrib(char*, int, float*)’:
icm.cc:525:81: error: ‘memcpy’ was not declared in this scope
icm.cc: In member function ‘void ICM_t::Write_Header(FILE*, bool)’:
icm.cc:961:9: 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:1175:29: error: ‘strlen’ was not declared in this scope
icm.cc: In member function ‘double Fixed_Length_ICM_t::Score_Window(char*)’:
icm.cc:1551:28: 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:1599:28: error: ‘strncpy’ was not declared in this scope
icm.cc: In member function ‘void Fixed_Length_ICM_Training_t::Train_Model(std::vector<char*>&)’:
icm.cc:1714:44: 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:1775:30: error: ‘strcat’ was not declared in this scope
icm.cc:1777:27: error: ‘strcat’ was not declared in this scope
icm.cc:1779:9: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Char_Pairs(int (*)[16], char*, int, int)’:
icm.cc:1825:29: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Count_Single_Chars(int*, char*, int, int)’:
icm.cc:1856:29: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_Data(std::vector<char*>&, int*)’:
icm.cc:1941:26: error: ‘strlen’ was not declared in this scope
icm.cc: In function ‘void Permute_String(char*, int*, int)’:
icm.cc:1970:23: error: ‘strncpy’ was not declared in this scope
icm.cc: In function ‘int Subscript(char)’:
icm.cc:1986:51: error: ‘strchr’ was not declared in this scope
make[1]: *** [icm.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/ICM'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Glimmer all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
@@@@@@@@@@@@@@@@@@@ anomaly.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
anomaly.cc:1:0: note: this is the location of the previous definition
anomaly.cc: In function ‘int main(int, char**)’:
anomaly.cc:82:76: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
anomaly.cc: In function ‘bool Is_Start_Codon(const char*)’:
anomaly.cc:264:41: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘bool Is_Stop_Codon(const char*)’:
anomaly.cc:282:40: error: ‘strncmp’ was not declared in this scope
anomaly.cc: In function ‘void Parse_Command_Line(int, char**)’:
anomaly.cc:308:40: error: ‘strtok’ was not declared in this scope
anomaly.cc:310:27: error: ‘strdup’ was not declared in this scope
anomaly.cc:328:27: error: ‘strdup’ was not declared in this scope
make[1]: *** [anomaly.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Glimmer'
##### Making Directory /home/edu/Downloads/glimmer3.02/src/Util all #####
make[1]: Entering directory `/home/edu/Downloads/glimmer3.02/src/Util'
@@@@@@@@@@@@@@@@@@@ entropy-score.cc @@@@@@@@@@@@@@@@@@@@@
<command-line>:0:0: warning: "__cplusplus" redefined [enabled by default]
entropy-score.cc:1:0: note: this is the location of the previous definition
entropy-score.cc: In function ‘int main(int, char**)’:
entropy-score.cc:76:32: error: ‘strcmp’ was not declared in this scope
entropy-score.cc:156:23: error: ‘strlen’ was not declared in this scope
make[1]: *** [entropy-score.o] Error 1
make[1]: Leaving directory `/home/edu/Downloads/glimmer3.02/src/Util'

[maubp]

Try doing "make clean" (which should reset any partial compile) and then repeat "make" just in case this is something simple from the previous failed attempts.

[ejuscamaytal]

I understand, but I already did it and the same error keeps coming.

[maubp]

I wasn't confident 'make clean' would work, but it was worth trying. Unless anyone else has a suggestion, email the tool authors - and then please post any solution here.