problam with installing MEME on linux

[wuj...@genomics.cn]

I used this command to install MEME on linux system:

     ./configure --prefix=/ifs1/ATAC/meme_4.10.1-test1221 --with-url="http://meme.nbcr.net/meme" --enable-build-libxml2 --enable-build-libxslt

     make > build.log

     make clean

     make install > build_install.log

The error in the build.log:

    $ make > build.log

json-reader.c: In function 'read_var':

json-reader.c:232:7: warning: implicit declaration of function 'isblank' [-Wimplicit-function-declaration]

       if (!isblank(chunk[i])) break;

       ^

json-reader.c: In function 'process_number_token':

json-reader.c:318:11: warning: implicit declaration of function 'strtold' [-Wimplicit-function-declaration]

           jsonrd->token.value_number = strtold(str_internal(jsonrd->buf), NULL);

           ^

centrimo.c: In function 'output_centrimo_text':

centrimo.c:1136:7: warning: implicit declaration of function 'round' [-Wimplicit-function-declaration]

       round(window->sites), stats->sites, window_prob);

       ^

centrimo.c:1136:7: warning: incompatible implicit declaration of built-in function 'round'

spamo.c: In function 'process_arguments':

spamo.c:461:9: warning: implicit declaration of function 'strtof' [-Wimplicit-function-declaration]

         options->odds = strtof(optarg, NULL);

         ^

The error in the build_install.log:

make[6]: *** [install-exDATA] Error 1

make[6]: Leaving directory `/ifs1/ATAC/meme_4.10.1-test1221/doc/examples/compute_prior_dist_example_output_files'

make[5]: *** [install-am] Error 2

make[5]: Leaving directory `/ifs1/ATAC/meme_4.10.1-test1221/doc/examples/compute_prior_dist_example_output_files'

make[4]: *** [install-recursive] Error 1

make[4]: Leaving directory `/ifs1/ATAC/meme_4.10.1-test1221/doc/examples'

make[3]: *** [install-recursive] Error 1

make[3]: Leaving directory `/ifs1/ATAC/meme_4.10.1-test1221/doc'

make[2]: *** [install] Error 2

make[2]: Leaving directory `/ifs1/ATAC/meme_4.10.1-test1221/doc'

make[1]: *** [install-recursive] Error 1

make[1]: Leaving directory `/ifs1/ATAC/meme_4.10.1-test1221'

make: *** [install] Error 2

Hope you could help me.

For further information in the build.log and build_install.log, you could leave your e-mail and I would sent it to you.

By the way, actually I've already installed meme v4.8.1, but I couldn't find the matrix2meme function. If you could give me some suggestions about how to use matrix2meme without v4.10.0, I may not be so frustrated with this installation.: (

[CharlesEGrant]

Hi Wujiaqi,

./configure --prefix=/ifs1/ATAC/meme_4.10.1-test1221

It looks like you are configuring the MEME Suite to install into its distribution directory. This won't work. The installation directory has to be distinct from the distribution directory or it would end up clobbering the documentation source. If you like, you can install to a subdirectory of the distribution directory. For example

./configure --prefix=/ifs1/ATAC/meme_4.10.1-test1221/build

 

$ make > build.log
json-reader.c: In function 'read_var':
json-reader.c:232:7: warning: implicit declaration of function 'isblank' [-Wimplicit-function-declaration]
       if (!isblank(chunk[i])) break;
       ^

This is a warning rather than an error and you can ignore it.

[wuj...@genomics.cn]

Thank you.

It works.

Like you said, I could ignore the warning and use this tool.