Make test fail- HTML+JSON error

[GV]

Trying to build MEME from source with open-mpi but make test fails

 

OS: Red Hat Enterprise Linux Server release 5.6 (Tikanga)

steps followed:

/configure --with-mpidir=/home/group2/nandan/apps/openmpi/ --with-python="/opt/python2.7/python" --with-python3="/opt/python/bin/python3.6" --prefix=/home/group2/nandan/apps/meme/ --enable-build-libxml2 --enable-build-libxslt --with-gs=/home/group2/nandan/apps/ghostscript-9.22/bin/gs
 
make AM_CFLAGS='-DNAN="(0.0/0.0)" -DINFINITY="(1.0/0.0)"'

make test
cp -f src/parallel/meme src/meme; \
    cp -f src/parallel/momo src/momo; \
    cd tests/scripts; make check
make[1]: Entering directory `/home/group2/nandan/apps/meme_4.12.0/tests/scripts'
make  test_driver
make[2]: Entering directory `/home/group2/nandan/apps/meme_4.12.0/tests/scripts'
/bin/sed -e 's%@WHICHPERL@%/usr/local/bin/perl%' test_driver.pl.in > test_driver
chmod +x test_driver
make[2]: Leaving directory `/home/group2/nandan/apps/meme_4.12.0/tests/scripts'
make  check-TESTS
make[2]: Entering directory `/home/group2/nandan/apps/meme_4.12.0/tests/scripts'
make[3]: Entering directory `/home/group2/nandan/apps/meme_4.12.0/tests/scripts'
PASS: ama1
PASS: ama2
PASS: ame1
PASS: centrimo1
PASS: create-priors1
PASS: create-priors2
PASS: dreme1
PASS: dreme2
PASS: fasta-center1
PASS: fasta-dinucleotide-shuffle1
FAIL: fimo1 (CRASH!)
PASS: fimo2
PASS: fimo3
PASS: fimo4
PASS: glam2_1
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
PASS: meme1
PASS: meme2
PASS: meme3
PASS: meme4
PASS: meme5
PASS: meme6
PASS: meme_psp
FAIL: meme-chip1 (differences in meme-chip.html)
PASS: momo1
PASS: momo2
PASS: momo3
PASS: momo4
PASS: momo5
PASS: momo6
PASS: momo7
PASS: momo8
PASS: momo9
PASS: momo10
PASS: momo11
PASS: momo12
PASS: momo13
PASS: momo14
PASS: momo15
PASS: momo16
PASS: momo17
PASS: motif-in.meme.crp0.text
PASS: motif-in.meme.crp0.xml
FAIL: motif-in.meme.crp0.html
PASS: motif-in.meme.lipocalin.text
PASS: motif-in.meme.lipocalin.xml
FAIL: motif-in.meme.lipocalin.html
PASS: motif-in.meme.puf3p.text
PASS: motif-in.meme.puf3p.xml
FAIL: motif-in.meme.puf3p.html
PASS: motif-in.meme.crp0.extdna.text
PASS: motif-in.meme.crp0.extdna.xml
FAIL: motif-in.meme.crp0.extdna.html
PASS: motif-in.dreme.klf1.text
PASS: motif-in.dreme.klf1.xml
FAIL: motif-in.dreme.klf1.html
PASS: motif-in.dreme.klf1.extdna.text
PASS: motif-in.dreme.klf1.extdna.xml
FAIL: motif-in.dreme.klf1.extdna.html
PASS: motif-in.dreme.puf3p.text
PASS: motif-in.dreme.puf3p.xml
FAIL: motif-in.dreme.puf3p.html
PASS: motiph1
FAIL: motiph2 (CRASH!)
PASS: psp-gen1
PASS: psp-gen2
PASS: psp-gen3
PASS: qvalue1
PASS: qvalue2
PASS: spamo1
PASS: spamo2
PASS: tomtom_allr
PASS: tomtom_ed
PASS: tomtom_kullback
PASS: tomtom_pearson
PASS: tomtom_sandelin
PASS: tomtom_blic1
PASS: tomtom_blic5
PASS: tomtom_allr_cs
PASS: tomtom_ed_cs
PASS: tomtom_kullback_cs
PASS: tomtom_pearson_cs
PASS: tomtom_sandelin_cs
PASS: tomtom_blic1_cs
PASS: tomtom_blic5_cs
============================================================================
Testsuite summary for meme 4.12.0
============================================================================
# TOTAL: 106
# PASS:  96
# SKIP:  0
# XFAIL: 0
# FAIL:  10
# XPASS: 0
# ERROR: 0
============================================================================
See tests/scripts/test-suite.log
============================================================================
make[3]: *** [test-suite.log] Error 1
make[3]: Leaving directory `/home/group2/nandan/apps/meme_4.12.0/tests/scripts'
make[2]: *** [check-TESTS] Error 2
make[2]: Leaving directory `/home/group2/nandan/apps/meme_4.12.0/tests/scripts'
make[1]: *** [check-am] Error 2
make[1]: Leaving directory `/home/group2/nandan/apps/meme_4.12.0/tests/scripts'
make: *** [test] Error 2

contents of test-suite.log

RUN: fimo
=========

*******************************************************************************
Test fimo1 ...
fimo --oc results/fimo1 --motif-pseudo 0.01 fimo/MCM1.meme.html fimo/spiked.fasta &> log
Errors from MEME HTML+JSON parser:
Alphabet ambiguous symbol A requires attribute "equals".
FATAL: No motifs could be read.

-------------------------------------------------------------------------------
fimo exited with value 1 indicating failure.
FAILED!
*******************************************************************************
Test fimo2 ...
fimo --oc results/fimo2 --motif CGGYGGGG --motif GCATCRGRBSAGA --no-qvalue --thresh 0.01 common/crp0.meme.xml motiph/spiked.fasta &> log
Skipping motif +TKTGANCNABNTCACAHWT.
Skipping motif -TKTGANCNABNTCACAHWT.
Using motif +CGGYGGGG of width 8.
Using motif -CGGYGGGG of width 8.
Using motif +GCATCRGRBSAGA of width 13.
Using motif -GCATCRGRBSAGA of width 13.
PASSED!
*******************************************************************************

[CharlesEGrant]

It's probably not related to the problem, but why are you using

AM_CFLAGS='-DNAN="(0.0/0.0)" -DINFINITY="(1.0/0.0)"'

? Those constants are defined in <math.h>, which we include from our source.

The test is failing when FIMO tries to read the motif file tests/fimo/MCM1.meme.html. Either your copy of that file has been corrupted, or there is some problem with the build of the software on your machine. Were there any errors or warning messages during the build? Could you attach copies of tests/script/fimo.log and motif-in.log? That would help us troubleshoot the problem.