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  • #16
    Why don't you install the library either by using Ubuntu software center/method below?

    Code:
    $sudo apt-get install libgtextutils0
    Since you got the precompiled binaries for fastx-toolkit you should not need to install this separately.

    Comment


    • #17
      Thanks GenoMax.

      Comment


      • #18
        make errors

        I have met the same problem. How to solve it? Anybody helps?
        Originally posted by jazz View Post
        I am trying to install libgtextutils for running the FASTX toolkit on my Ubuntu, but I am getting the following error after 'sudo make install' command

        Making install in m4
        make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
        make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
        make[2]: Nothing to be done for `install-exec-am'.
        test -z "/usr/share/aclocal" || /bin/mkdir -p "/usr/share/aclocal"
        make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
        make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/m4'
        Making install in src
        make[1]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
        Making install in gtextutils
        make[2]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
        make[3]: Entering directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
        test -z "/usr/lib" || /bin/mkdir -p "/usr/lib"
        /bin/bash ../../libtool --mode=install /usr/bin/install -c 'libgtextutils.la' '/usr/lib/libgtextutils.la'
        libtool: install: /usr/bin/install -c .libs/libgtextutils-0.6.1.so.0.0.0 /usr/lib/libgtextutils-0.6.1.so.0.0.0
        /usr/bin/install: cannot stat `.libs/libgtextutils-0.6.1.so.0.0.0': No such file or directory
        make[3]: *** [install-libLTLIBRARIES] Error 1
        make[3]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
        make[2]: *** [install-am] Error 2
        make[2]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src/gtextutils'
        make[1]: *** [install-recursive] Error 1
        make[1]: Leaving directory `/home/jkhurana/Downloads/libgtextutils-0.6.1/src'
        make: *** [install-recursive] Error 1

        Can anyone help me in this, since this tool is crucial for running FASTX.

        thanks

        Comment


        • #19
          Originally posted by Zhang Siting View Post
          I have met the same problem. How to solve it? Anybody helps?
          Install the library either by using Ubuntu software center/method below:

          Code:
          $sudo apt-get install libgtextutils0

          Best,
          Naresh

          Comment


          • #20
            Problem solved

            , thanks for your quick reply.
            This method doesn't work for me anyway. But I solve the problem just using the latest version of libgtextutils and fastx-toolkit. Hope this info helps.

            Originally posted by nareshvasani View Post
            Install the library either by using Ubuntu software center/method below:

            Code:
            $sudo apt-get install libgtextutils0

            Best,
            Naresh

            Comment


            • #21
              After make coomand
              below message pop up

              make all-recursive
              make[1]: Entering directory `/root/libgtextutils-0.6'
              Making all in m4
              make[2]: Entering directory `/root/libgtextutils-0.6/m4'
              make[2]: Nothing to be done for `all'.
              make[2]: Leaving directory `/root/libgtextutils-0.6/m4'
              Making all in src
              make[2]: Entering directory `/root/libgtextutils-0.6/src'
              Making all in gtextutils
              make[3]: Entering directory `/root/libgtextutils-0.6/src/gtextutils'
              /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT pipe_fitter.lo -MD -MP -MF .deps/pipe_fitter.Tpo -c -o pipe_fitter.lo pipe_fitter.c
              libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT pipe_fitter.lo -MD -MP -MF .deps/pipe_fitter.Tpo -c pipe_fitter.c -fPIC -DPIC -o .libs/pipe_fitter.o
              pipe_fitter.c: In function ‘pipe_close’:
              pipe_fitter.c:30:6: error: variable ‘i’ set but not used [-Werror=unused-but-set-variable]
              cc1: all warnings being treated as errors
              make[3]: *** [pipe_fitter.lo] Error 1
              make[3]: Leaving directory `/root/libgtextutils-0.6/src/gtextutils'
              make[2]: *** [all-recursive] Error 1
              make[2]: Leaving directory `/root/libgtextutils-0.6/src'
              make[1]: *** [all-recursive] Error 1
              make[1]: Leaving directory `/root/libgtextutils-0.6'
              make: *** [all] Error 2

              Can you please help me out to solve this issue

              I ran the command
              sudo apt-get install libtextutils0

              it shows the popup:

              Reading package lists... Done
              Building dependency tree
              Reading state information... Done
              libgtextutils0 is already the newest version.
              0 upgraded, 0 newly installed, 0 to remove and 330 not upgraded.

              Please help me to resolve the issue for installing libtextutils0.6

              Comment


              • #22
                After make coomand
                below message pop up

                make all-recursive
                make[1]: Entering directory `/root/libgtextutils-0.6'
                Making all in m4
                make[2]: Entering directory `/root/libgtextutils-0.6/m4'
                make[2]: Nothing to be done for `all'.
                make[2]: Leaving directory `/root/libgtextutils-0.6/m4'
                Making all in src
                make[2]: Entering directory `/root/libgtextutils-0.6/src'
                Making all in gtextutils
                make[3]: Entering directory `/root/libgtextutils-0.6/src/gtextutils'
                /bin/sh ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT pipe_fitter.lo -MD -MP -MF .deps/pipe_fitter.Tpo -c -o pipe_fitter.lo pipe_fitter.c
                libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT pipe_fitter.lo -MD -MP -MF .deps/pipe_fitter.Tpo -c pipe_fitter.c -fPIC -DPIC -o .libs/pipe_fitter.o
                pipe_fitter.c: In function ‘pipe_close’:
                pipe_fitter.c:30:6: error: variable ‘i’ set but not used [-Werror=unused-but-set-variable]
                cc1: all warnings being treated as errors
                make[3]: *** [pipe_fitter.lo] Error 1
                make[3]: Leaving directory `/root/libgtextutils-0.6/src/gtextutils'
                make[2]: *** [all-recursive] Error 1
                make[2]: Leaving directory `/root/libgtextutils-0.6/src'
                make[1]: *** [all-recursive] Error 1
                make[1]: Leaving directory `/root/libgtextutils-0.6'
                make: *** [all] Error 2

                Can you please help me out to solve this issue

                I ran the command
                sudo apt-get install libtextutils0

                it shows the popup:

                Reading package lists... Done
                Building dependency tree
                Reading state information... Done
                libgtextutils0 is already the newest version.
                0 upgraded, 0 newly installed, 0 to remove and 330 not upgraded.

                Please help me to resolve the issue for installing libtextutils0.6

                Comment


                • #23
                  You need to install
                  Code:
                  $ sudo apt-get install libgtexutils-dev

                  Comment


                  • #24
                    Thanks..Still I got the following error..
                    I already keep the pre-binaries of fastx.

                    make all-recursive
                    make[1]: Entering directory `/home/himanshu/Downloads/libgtextutils-0.6'
                    Making all in m4
                    make[2]: Entering directory `/home/himanshu/Downloads/libgtextutils-0.6/m4'
                    make[2]: Nothing to be done for `all'.
                    make[2]: Leaving directory `/home/himanshu/Downloads/libgtextutils-0.6/m4'
                    Making all in src
                    make[2]: Entering directory `/home/himanshu/Downloads/libgtextutils-0.6/src'
                    Making all in gtextutils
                    make[3]: Entering directory `/home/himanshu/Downloads/libgtextutils-0.6/src/gtextutils'
                    /bin/bash ../../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT pipe_fitter.lo -MD -MP -MF .deps/pipe_fitter.Tpo -c -o pipe_fitter.lo pipe_fitter.c
                    libtool: compile: gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT pipe_fitter.lo -MD -MP -MF .deps/pipe_fitter.Tpo -c pipe_fitter.c -fPIC -DPIC -o .libs/pipe_fitter.o
                    pipe_fitter.c: In function ‘pipe_close’:
                    pipe_fitter.c:30:6: error: variable ‘i’ set but not used [-Werror=unused-but-set-variable]
                    int i, status ;
                    ^
                    cc1: all warnings being treated as errors
                    make[3]: *** [pipe_fitter.lo] Error 1
                    make[3]: Leaving directory `/home/himanshu/Downloads/libgtextutils-0.6/src/gtextutils'
                    make[2]: *** [all-recursive] Error 1
                    make[2]: Leaving directory `/home/himanshu/Downloads/libgtextutils-0.6/src'
                    make[1]: *** [all-recursive] Error 1
                    make[1]: Leaving directory `/home/himanshu/Downloads/libgtextutils-0.6'
                    make: *** [all] Error 2

                    Please tell me what to do ????

                    Comment


                    • #25
                      If you installed libgtexutils using apt-get then why are you trying to compile them from source?

                      Comment


                      • #26
                        When I am running the command make for fastx then it was showing the error
                        make all-recursive
                        make[1]: Entering directory `/home/himanshu/Downloads/fastx_toolkit-0.0.13'
                        Making all in m4
                        make[2]: Entering directory `/home/himanshu/Downloads/fastx_toolkit-0.0.13/m4'
                        make[2]: Nothing to be done for `all'.
                        make[2]: Leaving directory `/home/himanshu/Downloads/fastx_toolkit-0.0.13/m4'
                        Making all in src
                        make[2]: Entering directory `/home/himanshu/Downloads/fastx_toolkit-0.0.13/src'
                        Making all in libfastx
                        make[3]: Entering directory `/home/himanshu/Downloads/fastx_toolkit-0.0.13/src/libfastx'
                        gcc -DHAVE_CONFIG_H -I. -I../.. -g -O2 -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx.o -MD -MP -MF .deps/fastx.Tpo -c -o fastx.o fastx.c
                        In file included from /usr/include/stdio.h:937:0,
                        from fastx.c:18:
                        In function ‘fgets’,
                        inlined from ‘fastx_read_next_record’ at fastx.c:323:11:
                        /usr/include/x86_64-linux-gnu/bits/stdio2.h:261:2: error: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Werror]
                        return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
                        ^
                        In function ‘fgets’,
                        inlined from ‘fastx_read_next_record’ at fastx.c:365:12:
                        /usr/include/x86_64-linux-gnu/bits/stdio2.h:261:2: error: call to ‘__fgets_chk_warn’ declared with attribute warning: fgets called with bigger size than length of destination buffer [-Werror]
                        return __fgets_chk_warn (__s, __bos (__s), __n, __stream);
                        ^
                        cc1: all warnings being treated as errors
                        make[3]: *** [fastx.o] Error 1
                        make[3]: Leaving directory `/home/himanshu/Downloads/fastx_toolkit-0.0.13/src/libfastx'
                        make[2]: *** [all-recursive] Error 1
                        make[2]: Leaving directory `/home/himanshu/Downloads/fastx_toolkit-0.0.13/src'
                        make[1]: *** [all-recursive] Error 1
                        make[1]: Leaving directory `/home/himanshu/Downloads/fastx_toolkit-0.0.13'
                        make: *** [all] Error 2


                        So, I thought, this error is due to the libgrtextutils make command error. coz it was not showing the proper installation.

                        Comment


                        • #27
                          Are you compiling the latest fastx toolkit source (0.0.14)? You may need to get the latest libgtextutils that are available on the download page: http://hannonlab.cshl.edu/fastx_toolkit/download.html

                          Comment


                          • #28
                            I am compiling on 0.0.13 version of fastx...with the libgtextutils 0.6 version. Now what should I do ?

                            Comment


                            • #29
                              If you are compiling from source then may as well try the latest version. What flavor of *nix are you using?

                              BTW: Looking at another post on the forum you appear to be already running fastx using the pre-compiled binaries. Any specific reason to continue with compilation from source?

                              Comment


                              • #30
                                Genomax...
                                Firstly I was facing the error as i discussed with you. In this forum I understood about the binaries files when I checked for bin folder was there...Then i tried to execute it from there.. But I failed to continue it. From the binaries its showing error..so i tried for compiling through source.
                                I didnt know about *nix.

                                Comment

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