[GenoMax]

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

$sudo apt-get install libgtextutils0

Since you got the precompiled binaries for fastx-toolkit you should not need to install this separately.

[nareshvasani]

Thanks GenoMax.

[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]

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]

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

[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

[GenoMax]

You need to install

$ sudo apt-get install libgtexutils-dev

[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]

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

[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]

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]

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

[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]

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.