[GenoMax]

My question was about the version of unix/linux you are using. Are you the "administrator" or is there someone you can ask help from?

What program from the fastx_toolkit are you most interested in? There are other options that may allow you to move on with your analysis. We can offer suggestions once we know what you are trying to do.

[Nanu]

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.

[GenoMax]

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?

[Nanu]

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

[GenoMax]

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

[Nanu]

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.

[GenoMax]

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

[Nanu]

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 ????

[GenoMax]

You need to install

$ sudo apt-get install libgtexutils-dev

[Nanu]

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

[Nanu]

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

[Zhang Siting]

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.

Install the library either by using Ubuntu software center/method below:

Code:
$sudo apt-get install libgtextutils0

Best,
Naresh

[nareshvasani]

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

[Zhang Siting]

make errors

I have met the same problem. How to solve it? Anybody helps?

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

[nareshvasani]

Thanks GenoMax.