make problem on ubuntu 15.04 Wily

[Mandar Ankolkar]

Hello all,
Trying to install the MEME (binary version) on a fresh ubuntu. I manually installed the libxml2, libxslt, openjdk-jre-8, installed tomcat9. Ran ./configure using the following command:
./configure --prefix=$HOME/mandar/meme/ --with-url=http://meme-suite.org --enable-web="http://meme-suite.org/opal2/services"

The make command gives following errors. PLease suggest, where could I be going wrong. Following is the error:


make  all-recursive
make[1]: Entering directory '/home/mandar/Downloads/meme_4.11.0'
Making all in src
make[2]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src'
make  all-recursive
make[3]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src'
Making all in filters
make[4]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/filters'
Making all in purge
make[5]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/filters/purge'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/filters/purge'
Making all in dust
make[5]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/filters/dust'
make[5]: Nothing to be done for 'all'.
make[5]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/filters/dust'
make[5]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/filters'
make[5]: Nothing to be done for 'all-am'.
make[5]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/filters'
make[4]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/filters'
Making all in libxml2
make[4]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2'
Making all in include
make[5]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2/include'
Making all in .
make[6]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2/include'
make[6]: Nothing to be done for 'all-am'.
make[6]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2/include'
Making all in libxml
make[6]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2/include/libxml'
make[6]: Nothing to be done for 'all'.
make[6]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2/include/libxml'
make[5]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2/include'
Making all in .
make[5]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2'
make[5]: Nothing to be done for 'all-am'.
make[5]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2'
make[4]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/libxml2'
Making all in libxslt
make[4]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/libxslt'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/libxslt'
Making all in libexslt
make[4]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/libexslt'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/libexslt'
Making all in wiggle
make[4]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src/wiggle'
make[4]: Nothing to be done for 'all'.
make[4]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src/wiggle'
Making all in .
make[4]: Entering directory '/home/mandar/Downloads/meme_4.11.0/src'
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__   -O3   -o alphtype alphtype-alphtype.o libcommon.la -lz -lm
libtool: link: gcc -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -O3 -o alphtype alphtype-alphtype.o  ./.libs/libcommon.a -lz -lm
Makefile:1620: recipe for target 'alphtype' failed
make[4]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src'
Makefile:4196: recipe for target 'all-recursive' failed
make[3]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src'
Makefile:1518: recipe for target 'all' failed
make[2]: Leaving directory '/home/mandar/Downloads/meme_4.11.0/src'
Makefile:713: recipe for target 'all-recursive' failed
make[1]: Leaving directory '/home/mandar/Downloads/meme_4.11.0'
Makefile:644: recipe for target 'all' failed

[CharlesEGrant]

Hi Mandar,

You don't need to worry about Java and Tomcat unless you are intending to set up a local version of the web server. It isn't needed to support the command line version of the MEME Suite.

Did the 'configure' command report any errors or warnings? Could you forward us the file 'config.log' which you should find in the top directory of the source distribution? It would also be helpful to capture more information from the 'make' step. Could you try running the following commands:

make clean
make &> make.log

and then forward us copies of 'config.log' and 'make.log'?

[Kyle Hernandez]

Has anything come of this? I am having the same issues with alphtype compilation.

Kyle

[cegrant]

It looks like both of you are running into the same issue reported here: Make problem. The problem is that newer versions of Ubuntu are distributed with version 5.1 of GCC, which changes the default C standard used by the compiler. We'll have a new release in the next couple of weeks that fixes this. In the meantime there are a couple of ways of working around the problem. The first is to override the C compiler flags built into the MEME Suite make file. Try running the commands 

make clean
make AM_CFLAGS="-std=gnu89"

This seems to work for some users, but not all. Alternatively you could install a version of GCC older then 5.0, and rerun 

make clean
./configure [options]
make

[Kyle Hernandez]

I just figured out what worked for me. I tried the AM_FLAGS approach, but it failed. I had to completely remove the decompressed directory form the tar.gz archive and then re-extract the files. Then, I was able to use my configure command (including the making libxml flags). Next, I had to actually set the CXX and CC flags to a different version of gcc that I had on my system (I had 4.9 also, but the user posting on that thread also tried with 4.7) as discussed in that other post:

make CXX=g++-4.9 CC=gcc-4.9

and it worked

[Chris]

I'm having problems with Ubuntu 14.04 and gcc-4.9.
I've tried

make clean
make CXX=g++-4.9 CC=gcc-4.9

and this isn't working.
I have the error:
libtool: link: gcc-4.9 -std=gnu89 -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -O3 -o create-priors create_priors-create-priors.o  ./.libs/libcommon.a -lz -lm
/usr/bin/ld: cannot find -lz
I'm a novice to Ubuntu, any advice would be appreciated.

[CharlesEGrant]

Hi Chris,

The error message:

/usr/bin/ld: cannot find -lz

indicates that you don't the libz file compression library installed on your system. This is one of the prerequisites for running the MEME Suite. It's a pretty common library, but for some reason is not included in some Ubuntu distributions. To install it, 'su' to root and run

apt-get install zlib1g-dev

Charles

[Chris]

Hi Charles,
Many thanks, I missed that point in the installation notes. This solution got me successfully through the "make" command but MEME crashed on "make test"...I found that I had to install libxml-parser-perl as well. Perhaps this is another Ubuntu omission.
Chris