make test error during MEME install

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xuzihe

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Jan 31, 2015, 3:31:42 AM1/31/15

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$nan@zihe:~/motif/meme_4.10.0$ ./configure --prefix=/nan/motif/meme_4.10.0 --with-url=http://meme.nbcr.net/meme
The configuration seemed successful!
    ========================
        Configuration parameters
        ========================

Install path:               /home/nan
Install UID:
Version:                    4.10.0
C compiler:                 gcc
C compiler flags:           -Wall -Wno-unused -DUNIX -D__USE_FIXED_PROTOTYPES__ -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O3
Linker:                     /usr/bin/ld
Special Libs:               -lmpi -lz -lm
MPICC                       /usr/bin/mpicc
MPIRUN                      /usr/bin/mpirun
MPI_CMD                     /usr/bin/mpirun -np
MPIINC                      -DMPI -I/usr/include
MPILIBDIR                   /usr/lib
MPIFLAGS                    -DPARALLEL
MEME URL:
PREVIOUS VERSION URL:
SERVER CONTACT:
DEVELOPER CONTACT:          me...@sdsc.edu
GO-SERVER URL:              http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID
PERL:                       /usr/bin/perl
PYTHON:                     /usr/local/bin/python
CONVERT:
GHOSTSCRIPT:                /usr/bin/gs
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:

Run the following commands to compile, test and install meme:
        make
        make test
        make install

$nan@zihe:~/motif/meme_4.10.0$ make

It did not show errors.
...
chmod +x jaspar2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' hart2meme-bkg.pl.in > hart2meme-bkg; \
chmod +x hart2meme-bkg
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' hartemink2psp.pl.in > hartemink2psp; \
chmod +x hartemink2psp
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' iupac2meme.pl.in > iupac2meme; \
chmod +x iupac2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' matrix2meme.pl.in > matrix2meme; \
chmod +x matrix2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' meme-chip.pl.in > meme-chip; \
chmod +x meme-chip
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' meme-get-motif.pl.in > meme-get-motif; \
chmod +x meme-get-motif
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' meme-rename.pl.in > meme-rename; \
chmod +x meme-rename
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' meme_xml_to_html.pl.in > meme_xml_to_html; \
chmod +x meme_xml_to_html
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' meme2meme.pl.in > meme2meme; \
chmod +x meme2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' nmica2meme.pl.in > nmica2meme; \
chmod +x nmica2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' priority2meme.pl.in > priority2meme; \
chmod +x priority2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' psp-gen.pl.in > psp-gen; \
chmod +x psp-gen
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' rna2meme.pl.in > rna2meme; \
chmod +x rna2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' scpd2meme.pl.in > scpd2meme; \
chmod +x scpd2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' sites2meme.pl.in > sites2meme; \
chmod +x sites2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' taipale2meme.pl.in > taipale2meme; \
chmod +x taipale2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' tamo2meme.pl.in > tamo2meme; \
chmod +x tamo2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' transfac2meme.pl.in > transfac2meme; \
chmod +x transfac2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' uniprobe2meme.pl.in > uniprobe2meme; \
chmod +x uniprobe2meme
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' Globals.pm.in > Globals.pm
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/nan/motif/meme_4.10.0/lib/perl%' -e 's%@PYTHONLIBDIR@%/nan/motif/meme_4.10.0/lib/python%' -e 's%@JAVALIBDIR@%/nan/motif/meme_4.10.0/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/nan/motif/meme_4.10.0/etc%' -e 's%@BINDIR@%/nan/motif/meme_4.10.0/bin%' -e 's%@MEMELOGS@%/nan/motif/meme_4.10.0/LOGS%' -e 's%@MEMEDB@%/nan/motif/meme_4.10.0/db%' -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/nan/motif/meme_4.10.0/doc/%' MemeWebUtils.pm.in > MemeWebUtils.pm
cp fasta-dinucleotide-shuffle fasta-dinucleotide-shuffle.py
cp fasta-hamming-enrich fasta-hamming-enrich.py
make[2]:Leaving directory `/home/nan/motif/meme_4.10.0/scripts'
Making all in tests
make[2]: Entering directory `/home/nan/motif/meme_4.10.0/tests'
make[3]: Entering directory `/home/nan/motif/meme_4.10.0'
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0'
Making all in ame
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/ame'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/ame'
Making all in clustalw2fasta
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/clustalw2fasta'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/clustalw2fasta'
Making all in centrimo
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/centrimo'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/centrimo'
Making all in common
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/common'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/common'
Making all in create-priors
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/create-priors'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/create-priors'
Making all in draw-mhmm
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/draw-mhmm'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/draw-mhmm'
Making all in dreme
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/dreme'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/dreme'
Making all in fasta-center
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/fasta-center'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/fasta-center'
Making all in fimo
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/fimo'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/fimo'
Making all in gomo
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/gomo'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/gomo'
Making all in mast
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/mast'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/mast'
Making all in mcast
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/mcast'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/mcast'
Making all in meme
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/meme'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/meme'
Making all in mhmm
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/mhmm'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/mhmm'
Making all in mhmms
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/mhmms'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/mhmms'
Making all in mhmmscan
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/mhmmscan'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/mhmmscan'
Making all in motiph
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/motiph'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/motiph'
Making all in psp-gen
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/psp-gen'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/psp-gen'
Making all in qvalue
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/qvalue'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/qvalue'
Making all in scaffold
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/scaffold'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/scaffold'
Making all in spamo
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/spamo'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/spamo'
Making all in tomtom
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/tomtom'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/tomtom'
Making all in web
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests/web'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all'.
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests/web'
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/tests'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Nothing to be done for `all-am'。
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/tests'
make[2]:Leaving directory `/home/nan/motif/meme_4.10.0/tests'
Making all in doc
make[2]: Entering directory `/home/nan/motif/meme_4.10.0/doc'
make[3]: Entering directory `/home/nan/motif/meme_4.10.0'
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0'
/bin/sed -e "/INSERT_COPYING_FILE/r ../COPYING" -e "/INSERT_COPYING_FILE/d" copyright.html.in > copyright.html
make all-recursive
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/doc'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
Making all in examples
make[4]: Entering directory `/home/nan/motif/meme_4.10.0/doc/examples'
Making all in compute_prior_dist_example_output_files
make[5]: Entering directory `/home/nan/motif/meme_4.10.0/doc/examples/compute_prior_dist_example_output_files'
make[6]: Entering directory `/home/nan/motif/meme_4.10.0'
make[6]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[5]: Nothing to be done for `all'.
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0/doc/examples/compute_prior_dist_example_output_files'
Making all in sample_opal_scripts
make[5]: Entering directory `/home/nan/motif/meme_4.10.0/doc/examples/sample_opal_scripts'
make[6]: Entering directory `/home/nan/motif/meme_4.10.0'
make[6]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[5]: Nothing to be done for `all'.
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0/doc/examples/sample_opal_scripts'
make[5]: Entering directory `/home/nan/motif/meme_4.10.0/doc/examples'
make[5]: Nothing to be done for `all-am'。
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0/doc/examples'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0/doc/examples'
Making all in images
make[4]: Entering directory `/home/nan/motif/meme_4.10.0/doc/images'
make[5]: Entering directory `/home/nan/motif/meme_4.10.0'
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[4]: Nothing to be done for `all'.
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0/doc/images'
Making all in css
make[4]: Entering directory `/home/nan/motif/meme_4.10.0/doc/css'
make[5]: Entering directory `/home/nan/motif/meme_4.10.0'
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[4]: Nothing to be done for `all'.
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0/doc/css'
Making all in js
make[4]: Entering directory `/home/nan/motif/meme_4.10.0/doc/js'
make[5]: Entering directory `/home/nan/motif/meme_4.10.0'
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0'
/bin/sed -e 's%\@VERSION\@%4.10.0%g' -e 's%\@CONTACT\@%%g' -e 's%\@DEV_CONTACT\@%me...@sdsc.edu%g' -e 's%\@URL\@%http://meme.nbcr.net/meme%g' -e 's%\@PREV_URL\@%%g' -e 's%\@PREV_VER\@%%g' -e 's%\@NOTICES_URL\@%./notices.txt%g' -e 's%\@NEWS_URL\@%./news.txt%g' menu-configure.js.in > menu-configure.js
make all-am
make[5]: Entering directory `/home/nan/motif/meme_4.10.0/doc/js'
make[6]: Entering directory `/home/nan/motif/meme_4.10.0'
make[6]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[5]: Nothing to be done for `all-am'。
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0/doc/js'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0/doc/js'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0/doc'
make[5]: Entering directory `/home/nan/motif/meme_4.10.0'
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[4]: Nothing to be done for `all-am'。
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0/doc'
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/doc'
make[2]:Leaving directory `/home/nan/motif/meme_4.10.0/doc'
Making all in etc
make[2]: Entering directory `/home/nan/motif/meme_4.10.0/etc'
make[3]: Entering directory `/home/nan/motif/meme_4.10.0'
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0'
/bin/sed -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@AMIGO_URL@%http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID%' constants.js.in > constants.js
/bin/sed -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@AMIGO_URL@%http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID%' constants.xsl.in > constants.xsl
/bin/sed 's/tname/delay_draw.js/' xsl-wrapper.in | /bin/sed '5r delay_draw.js' > delay_draw.js.xsl
/bin/sed 's/tname/dreme-to-html.css/' xsl-wrapper.in | /bin/sed '5r dreme-to-html.css' > dreme-to-html.css.xsl
/bin/sed 's/tname/dreme-to-html.js/' xsl-wrapper.in | /bin/sed '5r dreme-to-html.js' > dreme-to-html.js.xsl
/bin/sed -e 's%@SITE_URL@%http://meme.nbcr.net/meme%' -e 's%@AMIGO_URL@%http://amigo.geneontology.org/cgi-bin/amigo/term_details?term=GO_TERM_ID%' logging.conf.in > logging.conf
/bin/sed 's/tname/mast-to-html.css/' xsl-wrapper.in | /bin/sed '5r mast-to-html.css' > mast-to-html.css.xsl
/bin/sed 's/tname/mast-to-html.js/' xsl-wrapper.in | /bin/sed '5r mast-to-html.js' > mast-to-html.js.xsl
/bin/sed 's/tname/meme.css/' xsl-wrapper.in | /bin/sed '5r meme.css' > meme.css.xsl
/bin/sed 's/tname/motif_logo.js/' xsl-wrapper.in | /bin/sed '5r motif_logo.js' > motif_logo.js.xsl
/bin/sed 's/tname/spamo-to-html.css/' xsl-wrapper.in | /bin/sed '5r spamo-to-html.css' > spamo-to-html.css.xsl
/bin/sed 's/tname/spamo-to-html.js/' xsl-wrapper.in | /bin/sed '5r spamo-to-html.js' > spamo-to-html.js.xsl
/bin/sed 's/tname/spamo_graph.js/' xsl-wrapper.in | /bin/sed '5r spamo_graph.js' > spamo_graph.js.xsl
/bin/sed 's/tname/tomtom-to-html.css/' xsl-wrapper.in | /bin/sed '5r tomtom-to-html.css' > tomtom-to-html.css.xsl
/bin/sed 's/tname/tomtom-to-html.js/' xsl-wrapper.in | /bin/sed '5r tomtom-to-html.js' > tomtom-to-html.js.xsl
/bin/sed 's/tname/utilities.js/' xsl-wrapper.in | /bin/sed '5r utilities.js' > utilities.js.xsl
make[2]:Leaving directory `/home/nan/motif/meme_4.10.0/etc'
make[2]: Entering directory `/home/nan/motif/meme_4.10.0'
make[2]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[1]:Leaving directory `/home/nan/motif/meme_4.10.0'

$nan@zihe:~/motif/meme_4.10.0$ sudo make test
Errors occured!!
[sudo] password for nan:
cd scripts; make check
make[1]: Entering directory `/home/nan/motif/meme_4.10.0/scripts'
make[2]: Entering directory `/home/nan/motif/meme_4.10.0'
make[2]:Leaving directory `/home/nan/motif/meme_4.10.0'
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/home/nan/lib/perl%' -e 's%@PYTHONLIBDIR@%/home/nan/lib/python%' -e 's%@JAVALIBDIR@%/home/nan/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/home/nan/etc%' -e 's%@BINDIR@%/home/nan/bin%' -e 's%@MEMELOGS@%/home/nan/LOGS%' -e 's%@MEMEDB@%/home/nan/db%' -e 's%@SITE_URL@%%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/home/nan/doc/%' Globals.pm.in > Globals.pm
/bin/sed -e 's%@ARCHIVE_REVISION@%994f5bf522b6536cb8e2324fa497ed91a1404a20%' -e 's%@ARCHIVE_DATE@%Wed May 21 10:35:36 2014 +1000%' -e 's%@ARCHIVE_VERSION@%4.10.0%' -e 's%@TMP_DIR@%%' -e 's%@WHICHPERL@%/usr/bin/perl%' -e 's%@WHICHPYTHON@%/usr/local/bin/python%' -e 's%@WHICHJAVA@%%' -e 's%@WHICHCONVERT@%%' -e 's%@WHICHGHOSTSCRIPT@%/usr/bin/gs%' -e 's%@PERLLIBDIR@%/home/nan/lib/perl%' -e 's%@PYTHONLIBDIR@%/home/nan/lib/python%' -e 's%@JAVALIBDIR@%/home/nan/lib/java%' -e 's%@LAM_BIN@%%' -e 's%@APPCONFIGDIR@%/home/nan/etc%' -e 's%@BINDIR@%/home/nan/bin%' -e 's%@MEMELOGS@%/home/nan/LOGS%' -e 's%@MEMEDB@%/home/nan/db%' -e 's%@SITE_URL@%%' -e 's%@MAX_TIME@%18000%' -e 's%@DOCDIR@%/home/nan/doc/%' MemeWebUtils.pm.in > MemeWebUtils.pm
make check-TESTS
make[2]: Entering directory `/home/nan/motif/meme_4.10.0/scripts'
make[3]: Entering directory `/home/nan/motif/meme_4.10.0'
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[3]: Entering directory `/home/nan/motif/meme_4.10.0/scripts'
make[4]: Entering directory `/home/nan/motif/meme_4.10.0'
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0'
FAIL: metatest
make[4]: Entering directory `/home/nan/motif/meme_4.10.0/scripts'
make[5]: Entering directory `/home/nan/motif/meme_4.10.0'
make[5]:Leaving directory `/home/nan/motif/meme_4.10.0'
make[4]: Nothing to be done for `all'.
make[4]:Leaving directory `/home/nan/motif/meme_4.10.0/scripts'
============================================================================
Testsuite summary for meme 4.10.0
============================================================================
# TOTAL: 1
# PASS: 0
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0
============================================================================
See scripts/test-suite.log
============================================================================
make[3]: *** [test-suite.log] Error 1
make[3]:Leaving directory `/home/nan/motif/meme_4.10.0/scripts'
make[2]: *** [check-TESTS] Error 2
make[2]:Leaving directory `/home/nan/motif/meme_4.10.0/scripts'
make[1]: *** [check-am] Error 2
make[1]:Leaving directory `/home/nan/motif/meme_4.10.0/scripts'
make: *** [test] Error 2

In addition, even if I could not install meme, wherever I typed 'meme' or 'mast' (such as nan@zihe: ~/motif/meme_4.10.0$ meme or nan@zihe:~$meme or nan@zihe:~/motif$ meme), the result of 'meme' was always wrong, but the 'mast' result seem to okay. I guess my MPI may be the problem, but I do not how to fix?

~/motif/meme_4.10.0$ meme
[zihe:15485] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357
[zihe:15485] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230
[zihe:15485] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

orte_ess_set_name failed
--> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

ompi_mpi_init: orte_init failed
--> Returned "A system-required executable either could not be found or was not executable by this user" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** The MPI_Init() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[zihe:15485] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!

nan@zihe:~/motif/meme_4.10.0$ mast

USAGE:
    mast    <motif file> <sequence file> [options]
    [-bfile <bf>]    read background frequencies from <bf>
    [-dblist]    the file specified as database contains a list of databases
    [-o <dir>]    directory to output mast results
    [-oc <dir>]    directory to output mast results with overwriting allowed
    [-hit_list]    print only a list of non-overlapping hits to stdout
    [-remcorr]    remove highly correlated motifs from query
    [-m <m>]+    use only motif(s) number <m> (overrides -mev)
    [-c <count>]    only use the first <count> motifs or all motifs when <count> is zero (default: 0)
    [-mev <mev>]+    use only motifs with E-values less than <mev>
    [-diag <diag>]    nominal order and spacing of motifs
    [-norc]        do not score reverse complement DNA strand
    [-sep]        score reverse complement DNA strand as a separate
            sequence
    [-dna]        translate DNA sequences to protein
    [-comp]        adjust p-values and E-values for sequence composition
    [-ev <ev>]    print results for sequences with E-value < <ev>
            (default: 10)
    [-mt <mt>]    show motif matches with p-value < mt (default: 0.0001)
    [-w]        show weak matches (mt<p-value<mt*10) in angle brackets
    [-best]        include only the best motif in diagrams (hit_list mode only)
    [-seqp]        use SEQUENCE p-values for motif thresholds
            (default: use POSITION p-values)
    [-mf <mf>]    in results use <mf> as motif file name
    [-df <df>]    in results use <df> as database name (ignored when -dblist specified)
    [-dl <dl>]    in results use <dl> as link to search sequence names (ignored when -dblist specified)
    [-minseqs <ms>]    lower bound on number of sequences in db
    [-nostatus]    do not print progress report
    [-notext]    do not generate text output
    [-nohtml]    do not generate html output
    [-version]    print the version and exit

Asking for your help and Many thanks!!

James Johnson

unread,

Feb 1, 2015, 7:47:16 PM2/1/15

to meme-...@googlegroups.com

Could you post the contents of "scripts/test-suite.log" as that will tell us what test actually failed.

xuzihe

unread,

Feb 2, 2015, 3:03:49 AM2/2/15

to meme-...@googlegroups.com

Hope for your help. The content of test-suite.log is below
========================================
meme 4.10.0: scripts/test-suite.log

=========================================

# TOTAL: 1
# PASS: 0
# SKIP: 0
# XFAIL: 0
# FAIL: 1
# XPASS: 0
# ERROR: 0

.. contents:: :depth: 2

FAIL: metatest
==============

*******************************************************************************
Testing ama . . .
ama --verbosity 1 --scoring max-odds gomo/motif.meme gomo/seqs.fasta gomo/seqs.bg 1> results/ama1/ama_09aWM_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing ama . . .
ama --pvalues --verbosity 1 --cs gomo/motif.meme gomo/seqs_red.fasta gomo/seqs.norc.bg 1> results/ama2/ama_wIpz1_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing centrimo . . .
centrimo -verbosity 1 -oc results/centrimo -flip ../doc/examples/sample-dna-Klf1.fa centrimo/dreme-Klf1.txt &> $all_messages
SUCCESS
*******************************************************************************
Testing create-priors . . .
create-priors -oc results/create-priors_out create-priors/DNaseHS_gm12878.wig &> $all_messages
Creating priors with alpha=1.0 and beta=10000
Sequence size is -1 bases.
Scores were observed for 4140 bases.
Minimum score is 1
Median score is 1
Maximum score is 3.97638
Sum of scores is 7156.07
Sum of un-normalized priors is 1.08013e+09
Sum of normalized priors = 10000
Sum of prior distribution = 1
-------------------------------------------------------------------------------
2,208c2,208
< 100000585 5.42101e-16
< 100000605 5.42101e-16
< 100000625 5.42101e-16
< 100000645 5.42101e-16
< 100000665 5.42101e-16
< 100000685 5.42101e-16
< 100000705 5.42101e-16
< 100001105 5.42101e-16
< 100001125 5.42101e-16
< 100001145 1.61777e-15
< 100001165 1.61777e-15
< 100001185 1.61777e-15
< 100001205 1.61777e-15
< 100001225 1.61777e-15
< 100001245 1.61777e-15
< 100001265 1.07994e-15
< 100001285 1.07994e-15
< 100001345 5.42101e-16
< 100001365 5.42101e-16
< 100001385 5.42101e-16
< 100001405 5.42101e-16
< 100001425 5.42101e-16
< 100001445 5.42101e-16
< 100001465 5.42101e-16
< 100001505 5.42101e-16
< 100001525 5.42101e-16
< 100001545 5.42101e-16
< 100001565 5.42101e-16
< 100001585 5.42101e-16
< 100001605 5.42101e-16
< 100001625 5.42101e-16
< 100001645 5.42101e-16
< 100001765 5.42101e-16
< 100001785 5.42101e-16
< 100001805 1.07994e-15
< 100001825 1.07994e-15
< 100001845 1.07994e-15
< 100001865 1.07994e-15
< 100001885 1.07994e-15
< 100001905 5.42101e-16
< 100001925 5.42101e-16
< 100001945 5.42101e-16
< 100002445 5.42101e-16
< 100002465 5.42101e-16
< 100002485 5.42101e-16
< 100002505 5.42101e-16
< 100002525 5.42101e-16
< 100002545 5.42101e-16
< 100002565 5.42101e-16
< 100002585 5.42101e-16
< 100002745 5.42101e-16
< 100002765 5.42101e-16
< 100002785 5.42101e-16
< 100002805 5.42101e-16
< 100002825 5.42101e-16
< 100002845 5.42101e-16
< 100002865 5.42101e-16
< 100002885 5.42101e-16
< 100003045 5.42101e-16
< 100003065 5.42101e-16
< 100003085 5.42101e-16
< 100003105 5.42101e-16
< 100003125 5.42101e-16
< 100003145 5.42101e-16
< 100003165 5.42101e-16
< 100003185 5.42101e-16
< 100003285 5.42101e-16
< 100003305 5.42101e-16
< 100003325 1.07994e-15
< 100003345 1.07994e-15
< 100003365 1.07994e-15
< 100003385 1.61777e-15
< 100003405 1.61777e-15
< 100003425 1.61777e-15
< 100003445 1.61777e-15
< 100003465 1.07994e-15
< 100003485 1.07994e-15
< 100003505 1.07994e-15
< 100003525 5.42101e-16
< 100003545 5.42101e-16
< 100003565 5.42101e-16
< 100003885 5.42101e-16
< 100003905 5.42101e-16
< 100003925 5.42101e-16
< 100003945 5.42101e-16
< 100003965 5.42101e-16
< 100003985 5.42101e-16
< 100004005 5.42101e-16
< 100004065 5.42101e-16
< 100004085 5.42101e-16
< 100004105 5.42101e-16
< 100004125 5.42101e-16
< 100004145 5.42101e-16
< 100004165 5.42101e-16
< 100004185 5.42101e-16
< 100004205 5.42101e-16
< 100004225 5.42101e-16
< 100004245 5.42101e-16
< 100004265 5.42101e-16
< 100004285 5.42101e-16
< 100004305 5.42101e-16
< 100004325 5.42101e-16
< 100004345 5.42101e-16
< 100004385 5.42101e-16
< 100004405 5.42101e-16
< 100004425 5.42101e-16
< 100004445 5.42101e-16
< 100004465 5.42101e-16
< 100004485 5.42101e-16
< 100004505 5.42101e-16
< 100004565 5.42101e-16
< 100004585 5.42101e-16
< 100004605 5.42101e-16
< 100004625 5.42101e-16
< 100004645 5.42101e-16
< 100004665 5.42101e-16
< 100004685 5.42101e-16
< 100004825 5.42101e-16
< 100004845 1.07994e-15
< 100004865 1.07994e-15
< 100004885 1.61777e-15
< 100004905 1.61777e-15
< 100004925 1.61777e-15
< 100004945 1.61777e-15
< 100004965 2.1556e-15
< 100004985 1.07994e-15
< 100005005 2.1556e-15
< 100005025 2.1556e-15
< 100005045 1.61777e-15
< 100005065 1.61777e-15
< 100005085 1.61777e-15
< 100005105 1.07994e-15
< 100005125 1.07994e-15
< 100005145 1.07994e-15
< 100005245 5.42101e-16
< 100005265 5.42101e-16
< 100005285 5.42101e-16
< 100005305 5.42101e-16
< 100005325 5.42101e-16
< 100005345 1.07994e-15
< 100005365 1.07994e-15
< 100005385 1.07994e-15
< 100005405 1.07994e-15
< 100005425 1.07994e-15
< 100005445 1.07994e-15
< 100005465 1.07994e-15
< 100005485 1.07994e-15
< 100005505 5.42101e-16
< 100005525 5.42101e-16
< 100005545 5.42101e-16
< 100006265 1.61777e-15
< 100006285 1.61777e-15
< 100006305 1.61777e-15
< 100006325 1.61777e-15
< 100006345 1.61777e-15
< 100006365 1.61777e-15
< 100006385 1.61777e-15
< 100006405 1.07994e-15
< 100006425 5.42101e-16
< 100006445 5.42101e-16
< 100006465 5.42101e-16
< 100006485 1.61777e-15
< 100006505 1.61777e-15
< 100006525 2.1556e-15
< 100006545 2.1556e-15
< 100006565 2.1556e-15
< 100006585 2.1556e-15
< 100006605 2.1556e-15
< 100006625 2.1556e-15
< 100006645 1.07994e-15
< 100006665 5.42101e-16
< 100006685 1.07994e-15
< 100006705 1.07994e-15
< 100006725 1.07994e-15
< 100006745 1.07994e-15
< 100006765 1.61777e-15
< 100006785 1.61777e-15
< 100006805 1.61777e-15
< 100006825 1.61777e-15
< 100006845 5.42101e-16
< 100006865 5.42101e-16
< 100006885 5.42101e-16
< 100006905 5.42101e-16
< 100007005 5.42101e-16
< 100007025 5.42101e-16
< 100007045 5.42101e-16
< 100007065 5.42101e-16
< 100007085 5.42101e-16
< 100007105 5.42101e-16
< 100007125 5.42101e-16
< 100007265 1.07994e-15
< 100007285 1.07994e-15
< 100007305 1.07994e-15
< 100007325 1.61777e-15
< 100007345 1.61777e-15
< 100007365 1.61777e-15
< 100007385 2.1556e-15
< 100007405 1.07994e-15
< 100007425 1.07994e-15
< 100007445 2.1556e-15
< 100007465 1.61777e-15
< 100007485 1.61777e-15
< 100007505 2.1556e-15
< 100007525 1.61777e-15
< 100007545 1.61777e-15
< 100007565 1.61777e-15
< 100007585 1.61777e-15
---
> 100000585 2.3283e-06
> 100000605 2.3283e-06
> 100000625 2.3283e-06
> 100000645 2.3283e-06
> 100000665 2.3283e-06
> 100000685 2.3283e-06
> 100000705 2.3283e-06
> 100001105 2.3283e-06
> 100001125 2.3283e-06
> 100001145 6.9482e-06
> 100001165 6.9482e-06
> 100001185 6.9482e-06
> 100001205 6.9482e-06
> 100001225 6.9482e-06
> 100001245 6.9482e-06
> 100001265 4.63826e-06
> 100001285 4.63826e-06
> 100001345 2.3283e-06
> 100001365 2.3283e-06
> 100001385 2.3283e-06
> 100001405 2.3283e-06
> 100001425 2.3283e-06
> 100001445 2.3283e-06
> 100001465 2.3283e-06
> 100001505 2.3283e-06
> 100001525 2.3283e-06
> 100001545 2.3283e-06
> 100001565 2.3283e-06
> 100001585 2.3283e-06
> 100001605 2.3283e-06
> 100001625 2.3283e-06
> 100001645 2.3283e-06
> 100001765 2.3283e-06
> 100001785 2.3283e-06
> 100001805 4.63826e-06
> 100001825 4.63826e-06
> 100001845 4.63826e-06
> 100001865 4.63826e-06
> 100001885 4.63826e-06
> 100001905 2.3283e-06
> 100001925 2.3283e-06
> 100001945 2.3283e-06
> 100002445 2.3283e-06
> 100002465 2.3283e-06
> 100002485 2.3283e-06
> 100002505 2.3283e-06
> 100002525 2.3283e-06
> 100002545 2.3283e-06
> 100002565 2.3283e-06
> 100002585 2.3283e-06
> 100002745 2.3283e-06
> 100002765 2.3283e-06
> 100002785 2.3283e-06
> 100002805 2.3283e-06
> 100002825 2.3283e-06
> 100002845 2.3283e-06
> 100002865 2.3283e-06
> 100002885 2.3283e-06
> 100003045 2.3283e-06
> 100003065 2.3283e-06
> 100003085 2.3283e-06
> 100003105 2.3283e-06
> 100003125 2.3283e-06
> 100003145 2.3283e-06
> 100003165 2.3283e-06
> 100003185 2.3283e-06
> 100003285 2.3283e-06
> 100003305 2.3283e-06
> 100003325 4.63826e-06
> 100003345 4.63826e-06
> 100003365 4.63826e-06
> 100003385 6.9482e-06
> 100003405 6.9482e-06
> 100003425 6.9482e-06
> 100003445 6.9482e-06
> 100003465 4.63826e-06
> 100003485 4.63826e-06
> 100003505 4.63826e-06
> 100003525 2.3283e-06
> 100003545 2.3283e-06
> 100003565 2.3283e-06
> 100003885 2.3283e-06
> 100003905 2.3283e-06
> 100003925 2.3283e-06
> 100003945 2.3283e-06
> 100003965 2.3283e-06
> 100003985 2.3283e-06
> 100004005 2.3283e-06
> 100004065 2.3283e-06
> 100004085 2.3283e-06
> 100004105 2.3283e-06
> 100004125 2.3283e-06
> 100004145 2.3283e-06
> 100004165 2.3283e-06
> 100004185 2.3283e-06
> 100004205 2.3283e-06
> 100004225 2.3283e-06
> 100004245 2.3283e-06
> 100004265 2.3283e-06
> 100004285 2.3283e-06
> 100004305 2.3283e-06
> 100004325 2.3283e-06
> 100004345 2.3283e-06
> 100004385 2.3283e-06
> 100004405 2.3283e-06
> 100004425 2.3283e-06
> 100004445 2.3283e-06
> 100004465 2.3283e-06
> 100004485 2.3283e-06
> 100004505 2.3283e-06
> 100004565 2.3283e-06
> 100004585 2.3283e-06
> 100004605 2.3283e-06
> 100004625 2.3283e-06
> 100004645 2.3283e-06
> 100004665 2.3283e-06
> 100004685 2.3283e-06
> 100004825 2.3283e-06
> 100004845 4.63826e-06
> 100004865 4.63826e-06
> 100004885 6.9482e-06
> 100004905 6.9482e-06
> 100004925 6.9482e-06
> 100004945 6.9482e-06
> 100004965 9.25816e-06
> 100004985 4.63826e-06
> 100005005 9.25816e-06
> 100005025 9.25816e-06
> 100005045 6.9482e-06
> 100005065 6.9482e-06
> 100005085 6.9482e-06
> 100005105 4.63826e-06
> 100005125 4.63826e-06
> 100005145 4.63826e-06
> 100005245 2.3283e-06
> 100005265 2.3283e-06
> 100005285 2.3283e-06
> 100005305 2.3283e-06
> 100005325 2.3283e-06
> 100005345 4.63826e-06
> 100005365 4.63826e-06
> 100005385 4.63826e-06
> 100005405 4.63826e-06
> 100005425 4.63826e-06
> 100005445 4.63826e-06
> 100005465 4.63826e-06
> 100005485 4.63826e-06
> 100005505 2.3283e-06
> 100005525 2.3283e-06
> 100005545 2.3283e-06
> 100006265 6.9482e-06
> 100006285 6.9482e-06
> 100006305 6.9482e-06
> 100006325 6.9482e-06
> 100006345 6.9482e-06
> 100006365 6.9482e-06
> 100006385 6.9482e-06
> 100006405 4.63826e-06
> 100006425 2.3283e-06
> 100006445 2.3283e-06
> 100006465 2.3283e-06
> 100006485 6.9482e-06
> 100006505 6.9482e-06
> 100006525 9.25816e-06
> 100006545 9.25816e-06
> 100006565 9.25816e-06
> 100006585 9.25816e-06
> 100006605 9.25816e-06
> 100006625 9.25816e-06
> 100006645 4.63826e-06
> 100006665 2.3283e-06
> 100006685 4.63826e-06
> 100006705 4.63826e-06
> 100006725 4.63826e-06
> 100006745 4.63826e-06
> 100006765 6.9482e-06
> 100006785 6.9482e-06
> 100006805 6.9482e-06
> 100006825 6.9482e-06
> 100006845 2.3283e-06
> 100006865 2.3283e-06
> 100006885 2.3283e-06
> 100006905 2.3283e-06
> 100007005 2.3283e-06
> 100007025 2.3283e-06
> 100007045 2.3283e-06
> 100007065 2.3283e-06
> 100007085 2.3283e-06
> 100007105 2.3283e-06
> 100007125 2.3283e-06
> 100007265 4.63826e-06
> 100007285 4.63826e-06
> 100007305 4.63826e-06
> 100007325 6.9482e-06
> 100007345 6.9482e-06
> 100007365 6.9482e-06
> 100007385 9.25816e-06
> 100007405 4.63826e-06
> 100007425 4.63826e-06
> 100007445 9.25816e-06
> 100007465 6.9482e-06
> 100007485 6.9482e-06
> 100007505 9.25816e-06
> 100007525 6.9482e-06
> 100007545 6.9482e-06
> 100007565 6.9482e-06
> 100007585 6.9482e-06
FAIL
*******************************************************************************
Testing create-priors . . .
create-priors -oc results/create-priors_out create-priors/DNaseHS_gm12878.wig &> $all_messages
Creating priors with alpha=1.0 and beta=10000
Sequence size is -1 bases.
Scores were observed for 4140 bases.
Minimum score is 1
Median score is 1
Maximum score is 3.97638
Sum of scores is 7156.07
Sum of un-normalized priors is 1.08013e+09
Sum of normalized priors = 10000
Sum of prior distribution = 1
-------------------------------------------------------------------------------
1,3c1,3
< 5.42101e-16
< 2.1556e-15
< 5.42101e-16
---
> 2.3283e-06
> 9.25816e-06
> 2.3283e-06
37c37
< 4.11997e-17
---
> 1.76951e-07
70c70
< 4.22839e-17
---
> 1.81608e-07
103c103
< 1.30104e-17
---
> 5.58794e-08
FAIL
*******************************************************************************
Testing dreme . . .
dreme -oc results/dreme -v 1 -noxslt -p Klf1-200-100.s &> $all_messages
SUCCESS
*******************************************************************************
Testing dreme . . .
dreme -norc -oc results/dreme -v 1 -noxslt -p Klf1-200-100.s &> $all_messages
SUCCESS
*******************************************************************************
Testing fasta-center . . .
fasta-center -len 100 < Klf1-200.s 1> results/fasta-center1/fasta-center__R_RZ_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing fasta-dinucleotide-shuffle . . .
fasta-dinucleotide-shuffle -f Klf1-200-100.s -t -dinuc 1> results/fasta-dinucleotide-shuffle1/fasta-dinucleotide-shuffle_mVBd9_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing fimo . . .
fimo --text --motif-pseudo 0.01 fimo/MCM1.meme.html fimo/spiked.fasta 1> results/fimo1/fimo__YgXP_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing fimo . . .
fimo --text --motif 2 --motif 3 --thresh 0.01 common/crp0.meme.html motiph/spiked.fasta 1> results/fimo2/fimo_WPpkj_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing fimo . . .
fimo --text --psp fimo/GCN4_YPD.psp --prior-dist fimo/prior.dist.txt fimo/GCN4.meme fimo/GCN4_YPD.fasta 1> results/fimo3/fimo_J2E47_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing fimo . . .
fimo --text --parse-genomic-coord --psp fimo/GCN4_YPD-genomic.psp --prior-dist fimo/prior.dist.txt fimo/GCN4.meme fimo/GCN4_YPD-genomic.fasta 1> results/fimo4/fimo_tTGmo_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing gomo . . .
gomo --seed 1 --nostatus --verbosity 1 --text gomo/GO2Gene.map.csv gomo/ama.nozscoring.xml 1> results/gomo1/gomo_NLjQ9_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing gomo . . .
gomo --seed 1 --nostatus --verbosity 1 --text gomo/GO2Gene.map.csv gomo/ama.nozscoring.xml gomo/ama.nozscoring.xml 1> results/gomo2/gomo_1MlIS_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing mast . . .
mast meme/meme.crp0.oops common/crp0.s -oc results/mast1 -nohtml -nostatus &> $all_messages
SUCCESS
*******************************************************************************
Testing mast . . .
mast meme/meme.crp0.zoops common/crp0.s -oc results/mast2 -nohtml -nostatus &> $all_messages
SUCCESS
*******************************************************************************
Testing mast . . .
mast meme/meme.crp0.tcm common/crp0.s -oc results/mast3 -nohtml -nostatus &> $all_messages
SUCCESS
*******************************************************************************
Testing mcast . . .
mcast -oc results/mcast1 meme/meme.lex0.zoops common/lex0.s &> $all_messages
SUCCESS
*******************************************************************************
Testing meme . . .
meme common/crp0.s -text -mod oops -dna -revcomp -nostatus -nmotifs 2 -minw 8 1> results/meme1/meme_S1pYy_stdout 2> $error_messages
[zihe:03461] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357
[zihe:03461] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230
[zihe:03461] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132

--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

orte_ess_set_name failed
--> Returned value A system-required executable either could not be found or was not executable by this user (-127) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):

ompi_mpi_init: orte_init failed
--> Returned "A system-required executable either could not be found or was not executable by this user" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
*** The MPI_Init() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.

[zihe:3461] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
-------------------------------------------------------------------------------
meme exited with value 1 indicating failure.
FAIL
*******************************************************************************
Testing meme . . .
meme common/crp0.s -text -mod zoops -dna -revcomp -nostatus -nmotifs 2 -minw 8 1> results/meme2/meme_uUMoD_stdout 2> $error_messages
[zihe:03464] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357
[zihe:03464] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230
[zihe:03464] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132

[zihe:3464] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
-------------------------------------------------------------------------------
meme exited with value 1 indicating failure.
FAIL
*******************************************************************************
Testing meme . . .
meme common/crp0.s -text -mod tcm -dna -revcomp -nostatus -nmotifs 2 -minw 8 1> results/meme3/meme_ELTFl_stdout 2> $error_messages
[zihe:03467] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357
[zihe:03467] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230
[zihe:03467] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132

[zihe:3467] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
-------------------------------------------------------------------------------
meme exited with value 1 indicating failure.
FAIL
*******************************************************************************
Testing meme . . .
meme common/psp_test.s -psp common/psp_test.psp -minsites 5 -dna -revcomp -minw 7 -maxw 12 -nostatus -text 1> results/meme4/meme_Ny_jO_stdout 2> $error_messages
[zihe:03470] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357
[zihe:03470] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230
[zihe:03470] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132

[zihe:3470] Abort before MPI_INIT completed successfully; not able to guarantee that all other processes were killed!
-------------------------------------------------------------------------------
meme exited with value 1 indicating failure.
FAIL
*******************************************************************************
Testing motiph . . .
motiph --seed 0 --bg 2 --pseudocount 0.01 --text motiph/spiked.aln motiph/yeast.tree motiph/MCM1.meme.html 1> results/motiph1/motiph_9EOat_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing motiph . . .
motiph --seed 0 --bg 2 --pseudocount 0.01 --text --output-pthresh 1 --motif 2 --motif 3 motiph/spiked.aln motiph/yeast.tree common/crp0.meme.html 1> results/motiph2/motiph_JNrRf_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing psp-gen . . .
psp-gen -revcomp -pos psp-gen/one-peak-dna.fasta -neg psp-gen/all-A.fasta 1> results/pspgen1/psp-gen_olLFp_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing psp-gen . . .
psp-gen -alpha prot -maxrange -triples -pos psp-gen/one-peak-protein.fasta -neg psp-gen/all-A.fasta 1> results/pspgen2/psp-gen_QDA0T_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing qvalue . . .
qvalue --header 1 --append --column 2 --seed 7718 qvalue/uniform.txt 1> results/qvalue1/qvalue_5Y12Z_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing spamo . . .
spamo -oc results/spamo1 -verbosity 1 -znoxslt -margin 20 -shared 1 spamo/limits.fasta spamo/primary.meme spamo/secondary.meme &> $all_messages
SUCCESS
*******************************************************************************
Testing spamo . . .
spamo -oc results/spamo2 -verbosity 1 -znoxslt -margin 20 -shared 1 spamo/random.fasta spamo/primary.meme spamo/secondary.meme &> $all_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist allr -text -incomplete-scores common/sample.meme common/sample.meme 1> results/tomtom.out.allr/tomtom_oIKrd_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist ed -text -incomplete-scores common/sample.meme common/sample.meme 1> results/tomtom.out.ed/tomtom_IVPYH_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist kullback -text -incomplete-scores common/sample.meme common/sample.meme 1> results/tomtom.out.kullback/tomtom_ol80L_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist sandelin -text -incomplete-scores common/sample.meme common/sample.meme 1> results/tomtom.out.sandelin/tomtom_rYL4f_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist blic1 -text -incomplete-scores common/sample.meme common/sample.meme 1> results/tomtom.out.blic1/tomtom_sc8Dv_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist blic5 -text -incomplete-scores common/sample.meme common/sample.meme 1> results/tomtom.out.blic5/tomtom_sN6BN_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist allr -text common/sample.meme common/sample.meme 1> results/tomtom.complete.out.allr/tomtom_Kmypb_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist ed -text common/sample.meme common/sample.meme 1> results/tomtom.complete.out.ed/tomtom_m6NUv_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist kullback -text common/sample.meme common/sample.meme 1> results/tomtom.complete.out.kullback/tomtom_WclaY_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist sandelin -text common/sample.meme common/sample.meme 1> results/tomtom.complete.out.sandelin/tomtom_Twc6e_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist blic1 -text common/sample.meme common/sample.meme 1> results/tomtom.complete.out.blic1/tomtom_owFrM_stdout 2> $error_messages
SUCCESS
*******************************************************************************
Testing tomtom . . .
tomtom -verbosity 1 -seed 1 -dist blic5 -text common/sample.meme common/sample.meme 1> results/tomtom.complete.out.blic5/tomtom_rOl2u_stdout 2> $error_messages
SUCCESS
*******************************************************************************

CharlesEGrant

unread,

Feb 3, 2015, 8:41:23 PM2/3/15

to meme-...@googlegroups.com

It looks like there might be a couple of different problems here.

First, it looks like there is a bug in our test for 'create-priors'. You can ignore that failure, and we'll fix the bug in the test in a future release.

Second, it looks like there is a problem with the configuration of OpenMPI on your machine:

zihe:03464] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 357
[zihe:03464] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../../../../orte/mca/ess/singleton/ess_singleton_module.c at line 230
[zihe:03464] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable either could not be found or was not executable by this user in file ../../../orte/runtime/orte_init.c at line 132
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

Helping install and configure OpenMPI is beyond the scope of help we can offer. You'll need to work with your local system administrator for that. However, I did notice that you seem to be configuring and building the MEME Suite under your own user account

nan@zihe:~/motif/meme_4.10.0$ make

but running the tests as root:

$nan@zihe:~/motif/meme_4.10.0$ sudo make test

The root account frequently has it's working environment configured differently than ordinary user accounts. This might be part of the problem. There shouldn't be any need to run the tests as root. The only step that might need root permissions is the 'make install' step. Unfortunately the testing folders in your distribution directory are now going to contain a bunch of files owned by root, which may cause problems if you try to run the tests from your own account. I'd suggest getting a clean copy of the the MEME suite distribution, and re-running 'configure', 'make', and 'make test', all under your own account.

Our apologies for the 'create-priors' testing bug. We'll get that fixed shortly.

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