Problem installing MEME suite on OS 10.9.5

[scarlet...@gmail.com]

Hello,

I'm trying to install the command-line version of the meme suite but some of the tools get skipped and are not installed.

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

I got some errors towards the end like this:

configure: WARNING:     Neither Ghostscript or convert utilities were found. Png images won''t be generated from encapsulated postscript.  
configure: WARNING:    
Checking Required Perl Modules:
HTML::Template missing.
XML::Compile::SOAP11 missing. Used for downloading sequence databases from RSAT
XML::Compile::WSDL11 missing. Used for downloading sequence databases from RSAT
XML::Compile::Transport::SOAPHTTP missing. Used for downloading sequence databases from RSAT

Checking Optional Modules:
Log::Log4perl missing. Used for logging and debugging by developers.
Math::CDF missing. Only required for fasta-enriched-center script (which is not called by the web scripts).  

        ========================
        Configuration parameters
        ========================

  Install path:               /Users/sshell/meme
  Install UID:               
  Version:                    4.10.2
  C compiler:                 gcc
  C compiler flags:           -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__   -O3
  Linker:                     /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld
  Special Libs:               -lz -lm
  MPICC                       /usr/bin/mpicc
  MPIRUN                     
  MPI_CMD                      -np
  MPIINC                      -DMPI -I/usr/include
  MPILIBDIR                   /usr/lib
  MPIFLAGS                    -DPARALLEL
  MEME URL:                   http://meme-suite.org
  PREVIOUS VERSION URL:      
  SERVER CONTACT:            
  DEVELOPER CONTACT:          meme-...@uw.edu
  GO-SERVER URL:              http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID
  PERL:                       /usr/bin/perl
  PYTHON:                     /Users/sshell/Library/Enthought/Canopy_64bit/User/bin/python
  CONVERT:                   
  GHOSTSCRIPT:               
  BUILD LIBXML2:              yes
  LIBXML2 compiler flags:     -I${top_srcdir}/src/libxml2/include
  LIBXML2 libs:               ${top_builddir}/src/libxml2/libxml2.la
  BUILD LIBXSLT:              yes
  LIBXSLT compiler flags:     -I${top_srcdir}/src/
  LIBXSLT libs:               ${top_builddir}/src/libxslt/libxslt.la
  MEME DB:                    ${prefix}/db
  MEME LOGS:                  ${prefix}/LOGS
  MEME TEMP FILES:           
  OPAL URL:                   no
  OPAL DEPLOY DIRECTORY:     

Then after entering "make" and "make test" I get:

cd tests/scripts; make check
make  test_driver
/usr/bin/sed -e 's%@WHICHPERL@%/usr/bin/perl%' test_driver.pl.in > test_driver
chmod +x test_driver
make  check-TESTS
PASS: ama1
PASS: ama2
PASS: ame1
PASS: centrimo1
PASS: create-priors1
PASS: create-priors2
SKIP: dreme1
SKIP: dreme2
SKIP: fasta-center1
SKIP: fasta-dinucleotide-shuffle1
PASS: fimo1
PASS: fimo2
PASS: fimo3
PASS: fimo4
FAIL: glam2_1 (CRASH!)
PASS: glam2scan1
PASS: gomo1
PASS: gomo2
PASS: mast1
PASS: mast2
PASS: mast3
PASS: mast4
PASS: mast5
PASS: mast6
PASS: mast7
PASS: mast8
PASS: mast9
PASS: mast10
PASS: mast11
PASS: mast12
PASS: mast13
PASS: mast14
PASS: mast15
PASS: mast16
PASS: mast17
PASS: mast18
PASS: mcast1
SKIP: meme1
SKIP: meme2
SKIP: meme3
SKIP: meme4
SKIP: meme5
SKIP: meme6
SKIP: meme_psp
PASS: motiph1
PASS: motiph2
SKIP: psp-gen1
SKIP: psp-gen2
PASS: qvalue1
PASS: spamo1
PASS: spamo2
PASS: tomtom_allr
PASS: tomtom_ed
PASS: tomtom_kullback
PASS: tomtom_sandelin
PASS: tomtom_blic1
PASS: tomtom_blic5
PASS: tomtom_allr_cs
PASS: tomtom_ed_cs
PASS: tomtom_kullback_cs
PASS: tomtom_sandelin_cs
PASS: tomtom_blic1_cs
PASS: tomtom_blic5_cs
============================================================================
Testsuite summary for meme 4.10.2
============================================================================
# TOTAL: 63
# PASS:  49
# SKIP:  13
# XFAIL: 0
# FAIL:  1
# XPASS: 0
# ERROR: 0
============================================================================
See tests/scripts/test-suite.log
============================================================================
make[3]: *** [test-suite.log] Error 1
make[2]: *** [check-TESTS] Error 2
make[1]: *** [check-am] Error 2
make: *** [test] Error 2

And sure enough, no executable for "meme" has been created.

Any ideas what's going wrong? I tried "make clean" and then doing it again, but the output was the same.

Thanks so much for any help!

[CharlesEGrant]

Hi Scarlet, 

We'd need to see the details of the make step to trouble shoot the problem. Could you run

make clean

makle &> make.log

and forward us a copies of config.log and make.log?

[Skyler Hebdon]

I hope you figured it out already, but if you haven't here are some ways I got it to work recently. 

I am brand new to command line and scripts, but ran into some similar problems. Go to    http://meme-suite.org/doc/install.html?man_type=web    and follow their few lines of code to make sure that you have all the perl packages. It looks like you are missing HTML::Template, XML::Compile packages. Look for how the guide uses cpan to install those packages. I cycled through checking dependencies and using cpan to download. HTML::Template depends on (i think) CGI::Applications, so if it doesn't clear out of the dependencies try getting CGI. 

Also, be sure that you have the Xcode and command line tools compatible for 10.9.5. They can be found at https://developer.apple.com/downloads/   I used Xcode version 5.1.1 and the command line tools that work with that version. Some tutorials say to download from within Xcode preferences, but I had to go directly from this webpage because option wasn't available in Xcode. 

I hope this helps.