MEME suit installtion on Ubuntu 15.04 giving error

[Ashwin Kelkar]

Hello everyone
I have been trying to install the 2015 versions of MEME (I tried all three in order or most recent to older versions) on an ubuntu 15.04 distribution.

I use the commands given in the INSTALL file as follows :
./configure --prefix=$HOME/meme --with-url="http://meme.nbcr.net/meme"

followed by :
make

For all three versions I get the same error at the same stage during the make stage -

libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/libxml2 -I../../src -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -O3 -MT libxslt_la-xsltutils.lo -MD -MP -MF .deps/libxslt_la-xsltutils.Tpo -c xsltutils.c  -fPIC -DPIC -o .libs/libxslt_la-xsltutils.o
xsltutils.c: In function ‘xsltSaveResultTo’:
xsltutils.c:1541:30: warning: passing argument 1 of ‘xmlBufferWriteQuotedString’ from incompatible pointer type
   xmlBufferWriteQuotedString(buf->buffer, result->version);
                              ^
In file included from /usr/include/libxml2/libxml/parser.h:16:0,
                 from /usr/include/libxml2/libxml/globals.h:18,
                 from /usr/include/libxml2/libxml/threads.h:35,
                 from /usr/include/libxml2/libxml/xmlmemory.h:218,
                 from xsltutils.c:33:
/usr/include/libxml2/libxml/tree.h:1130:3: note: expected ‘xmlBufferPtr’ but argument is of type ‘xmlBufPtr’
   xmlBufferWriteQuotedString(xmlBufferPtr buf,
   ^
xsltutils.c:1554:30: warning: passing argument 1 of ‘xmlBufferWriteQuotedString’ from incompatible pointer type
   xmlBufferWriteQuotedString(buf->buffer, (xmlChar *) encoding);
                              ^
In file included from /usr/include/libxml2/libxml/parser.h:16:0,
                 from /usr/include/libxml2/libxml/globals.h:18,
                 from /usr/include/libxml2/libxml/threads.h:35,
                 from /usr/include/libxml2/libxml/xmlmemory.h:218,
                 from xsltutils.c:33:
/usr/include/libxml2/libxml/tree.h:1130:3: note: expected ‘xmlBufferPtr’ but argument is of type ‘xmlBufPtr’
   xmlBufferWriteQuotedString(xmlBufferPtr buf,
   ^
xsltutils.c: In function ‘xsltSaveResultToString’:
xsltutils.c:1758:26: error: dereferencing pointer to incomplete type
  *doc_txt_len = buf->conv->use;
                          ^
xsltutils.c:1759:37: error: dereferencing pointer to incomplete type
  *doc_txt_ptr = xmlStrndup(buf->conv->content, *doc_txt_len);
                                     ^
xsltutils.c:1761:28: error: dereferencing pointer to incomplete type
  *doc_txt_len = buf->buffer->use;
                            ^
xsltutils.c:1762:39: error: dereferencing pointer to incomplete type
  *doc_txt_ptr = xmlStrndup(buf->buffer->content, *doc_txt_len);
                                       ^
Makefile:629: recipe for target 'libxslt_la-xsltutils.lo' failed
make[4]: *** [libxslt_la-xsltutils.lo] Error 1
make[4]: Leaving directory '/home/ashwin/tools/meme_4.10.0/src/libxslt'
Makefile:4003: recipe for target 'all-recursive' failed
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory '/home/ashwin/tools/meme_4.10.0/src'
Makefile:1425: recipe for target 'all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory '/home/ashwin/tools/meme_4.10.0/src'
Makefile:681: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/home/ashwin/tools/meme_4.10.0'
Makefile:611: recipe for target 'all' failed
make: *** [all] Error 2


Could anyone let me know what is the workaround to this ? Or how do I fix this problem ?

Cheers
Ashwin

[Paulo Oliveira]

Hi Ashwin

I got to compile using libxml and libxsl included in meme_4.10.2 tardist. Just use the following keys in configure:
./configure  --enable-build-libxml2  --enable-build-libxslt

Do not forget to run make clean to remove the garbage of previous compilation.

Regards

Paulo

[CharlesEGrant]

Hi Ashwin,

and --enable-build-libxslt flags for configure.The MEME Suite depends on two open source libraries, libxml2 and libxslt. These are widely distributed and already installed on many systems. However, as a convenience if they are not already installed, the MEME Suite includes the source for these libraries. During configuration if a locally installed library copy is detected MEME Suite will use that. Sometimes though a system will have a version of libxml2 installed, but not libxslt. Furthermore it may be that the locally installed version of libxml2 is incompatible with the version of libxslt distributed with the MEME Source. As pointed out by Paulo Oiveira the solution is to direct the 'configure' command to build both libraries from the source distributed with the MEME Suite. This is done with the --enable-build-libxml2 and --enable-build-libxslt flags for configure. Try using the commands

./configure --prefix=$HOME/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt

make clean
make