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  • #16
    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.

    Comment


    • #17
      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

      Comment


      • #18
        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

        Comment


        • #19
          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!

          Comment


          • #20
            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, 06:50 AM.

            Comment


            • #21
              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!

              Comment


              • #22
                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!

                Comment


                • #23
                  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:

                  Code:
                  sudo apt-get install g++

                  Comment


                  • #24
                    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'

                    Comment


                    • #25
                      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.

                      Comment


                      • #26
                        I understand, but I already did it and the same error keeps coming.

                        Comment


                        • #27
                          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.

                          Comment

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