MEME (meme_4.10.0_1.tar.gz) install failing on Ubuntu 14.04.1 LTS

[atisou]

Hello,

I am trying to install MEME de novo on my linux, with no success so far.
After downloading the most recent pre-patched file (meme_4.10.0_1.tar.gz), decompressing it, cd in it, running:

./configure prefix=/home/username/Downloads/myprograms/meme_4.10.0_1/meme --with-url=http://meme.nbcr.net/meme

I do a

make

and here is the error I get:

/bin/sed -e 's%@catalina.home@%%' -e 's%@version@%4.10.0%' -e 's%@site.url@%http://meme.nbcr.net/meme%' -e 's%@site.services@%no%' -e 's%@site.DN@%%' -e 's%@site.contact@%%' -e 's%@developer.contact@%me...@sdsc.edu%' -e 's%@expiry@%4%' -e 's%@bin.dir@%/home/username/Downloads/myprograms/meme_4.10.0_1/meme/bin%' -e 's%@etc.dir@%/home/username/Downloads/myprograms/meme_4.10.0_1/meme/etc%' -e 's%@lib.dir@%/home/username/Downloads/myprograms/meme_4.10.0_1/meme/lib%' -e 's%@db.dir@%/home/username/Downloads/myprograms/meme_4.10.0_1/meme/db%' -e 's%@sendmail@%/usr/lib/sendmail%' MemeSuite.properties.in > MemeSuite.properties
make  all-recursive
make[1]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1'
Making all in src
make[2]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src'
echo '#define MEME_DIR "/home/username/Downloads/myprograms/meme_4.10.0_1/meme"' >dir.h
echo '#define ETC_DIR "/home/username/Downloads/myprograms/meme_4.10.0_1/meme/etc" ' >> dir.h  
echo '#define BIN_DIR "/home/username/Downloads/myprograms/meme_4.10.0_1/meme/bin" ' >> dir.h
echo '#define TEMP_DIR "" ' >> dir.h
make  all-recursive
make[3]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src'
Making all in filters
make[4]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/filters'
Making all in purge
make[5]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/filters/purge'
make[5]: Nothing to be done for `all'.
make[5]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/filters/purge'
Making all in dust
make[5]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/filters/dust'
make[5]: Nothing to be done for `all'.
make[5]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/filters/dust'
make[5]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/filters'
make[5]: Nothing to be done for `all-am'.
make[5]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/filters'
make[4]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/filters'
Making all in libxml2
make[4]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/libxml2'
make[5]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/libxml2'
make[5]: Nothing to be done for `all-am'.
make[5]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/libxml2'
make[4]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/libxml2'
Making all in libxslt
make[4]: Entering directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/libxslt'
/bin/bash ../../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I../..     -I/usr/include/libxml2 -I../../src -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__    -MT libxslt_la-xsltutils.lo -MD -MP -MF .deps/libxslt_la-xsltutils.Tpo -c -o libxslt_la-xsltutils.lo `test -f 'xsltutils.c' || echo './'`xsltutils.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/libxml2 -I../../src -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -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:1541:3: warning: passing argument 1 of 'xmlBufferWriteQuotedString' from incompatible pointer type [enabled by default]
   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:1123:3: note: expected 'xmlBufferPtr' but argument is of type 'xmlBufPtr'
   xmlBufferWriteQuotedString(xmlBufferPtr buf,
   ^
xsltutils.c:1554:3: warning: passing argument 1 of 'xmlBufferWriteQuotedString' from incompatible pointer type [enabled by default]
   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:1123:3: 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);
                                       ^
make[4]: *** [libxslt_la-xsltutils.lo] Error 1
make[4]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src/libxslt'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/home/username/Downloads/myprograms/meme_4.10.0_1'
make: *** [all] Error 2

After googling around about this particular error:

/usr/include/libxml2/libxml/tree.h:1123:3: note: expected 'xmlBufferPtr' but argument is of type 'xmlBufPtr'
   xmlBufferWriteQuotedString(xmlBufferPtr buf,

it seems to be a compatibility issue between my local libxml2 (more preciesely the function xmlBufferWriteQuotedString() in /usr/include/libxml2/libxml/tree.h) and the src/libxslt from MEME (more precisely the function xsltSaveResultTo() in src/libxslt/xsltutils.c).
One seems to be using an argument 'xmlBufferPtr' while the other 'xmlBufPtr'.


I have a recent version of libxml2:

username@username:~/Downloads/myprograms/meme_4.10.0_1$ apt-show-versions libxml2
libxml2:amd64/trusty-security 2.9.1+dfsg1-3ubuntu4.3 uptodate

Does anyone have experienced this same issue and could help me to fix it please?


Thanks.

[James Johnson]

This happens because you have libxml installed on your system but you do not have libxslt. The libxslt library depends on the libxml library and requires a matching version. When libxslt is not available the MEME suite will attempt to build it from included source however this frequently fails due to incompatible versions.

There is a very simple fix, either install libxslt-devel or configure the MEME suite with the additional options "--enable-build-libxml2 --enable-build-libxslt" which will cause the included source to be compiled and used.

Since you're using 4.10.0 I also recommend you point the URL at the EBI server as NBCR have chosen not to upgrade their server.

So the commands you should run are:

./configure prefix=/home/username/Downloads/myprograms/meme_4.10.0_1/meme --with-url=http://meme.ebi.edu.au/meme/ --enable-build-libxml2 --enable-build-libxslt
make clean
make
make install