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mihmcl
Dec 23, 2017, 6:05:40 AM12/23/17
to MEME Suite Q&A
Being relatively computer illiterate, I've run into a problem installing the MEME Suite, and I couldn't find posts describing anything similar in the group archives:
Make tests failed for dreme1, dreme2, fasta-dinucleotide-shuffle1, meme1 through meme6, meme_psp, meme-chip1, and momo1 through momo17. In those cases the processes "exited with value 127 indicating failure." (glam tests also failed, but that appears to be a separate and less important problem with ghostscript and/or HTML conversion.)
My system:
Windows 7 64-bit
Cygwin64 6.1
Python 3.4 and 2.7 installed through Cygwin
Perl 5.22 installed through Cygwin
All the required third-party packages installed, as far as I can tell
An additional Python 3.6 installation outside of Cygwin
Logfiles for config, make, and the test suite are in a zip file here. In addition to the test errors, there are several errors in config.log, most of which appear to be related to conftest.c. Dependencies.pl reports no missing Perl packages.
Are directories missing from my $PATH? (If so, should I add them via the Windows control panel or in the Cygwin .profile or .bashrc files?) Could my Python distribution or packages be installed incorrectly?
Thanks!
Make tests failed for dreme1, dreme2, fasta-dinucleotide-shuffle1, meme1 through meme6, meme_psp, meme-chip1, and momo1 through momo17. In those cases the processes "exited with value 127 indicating failure." (glam tests also failed, but that appears to be a separate and less important problem with ghostscript and/or HTML conversion.)
My system:
Windows 7 64-bit
Cygwin64 6.1
Python 3.4 and 2.7 installed through Cygwin
Perl 5.22 installed through Cygwin
All the required third-party packages installed, as far as I can tell
An additional Python 3.6 installation outside of Cygwin
Logfiles for config, make, and the test suite are in a zip file here. In addition to the test errors, there are several errors in config.log, most of which appear to be related to conftest.c. Dependencies.pl reports no missing Perl packages.
Are directories missing from my $PATH? (If so, should I add them via the Windows control panel or in the Cygwin .profile or .bashrc files?) Could my Python distribution or packages be installed incorrectly?
Thanks!
CharlesEGrant
Dec 26, 2017, 3:31:03 PM12/26/17
to MEME Suite Q&A
In the config.log file I noticed this line:
configure:12536: checking for convert
configure:12554: found /cygdrive/c/Windows/system32/convert
configure:12566: result: /cygdrive/c/Windows/system32/convert
configure:12576: checking for gs
configure:12594: found /usr/bin/gs
configure:12606: result: /usr/bin/gs
The MEME Suite is looking for the convert utility that comes with ImageMagik image processing suite, but it's finding a Windows utility with the same name. This is probably what's causing the tests to fail. The convert utility is used to convert the EPS version of the logograms to PNG format. The convert utility isn't required as long as the GhostScript utility (gs) is present, but it's getting confused by finding the "wrong" convert in your PATH. Try re-building but using the --with-convert="" option for configure:
./configure --prefix=/home/mihmcl/meme --with-url=http://meme-suite.org --enable-build-libxml2 --enable-build-libxslt --with-convert=""
mihmcl
Dec 28, 2017, 2:59:02 PM12/28/17
to MEME Suite Q&A
Thanks for your help. The addition of --with-convert="" didn't keep the MEME Suite from finding the Windows convert utility, but I was
able to hide the file (windows/system32/convert.exe) by temporarily renaming it. Since I don't have ImageMagick, no convert utility was found at all.
Unfortunately, that didn't fix the installation errors. All
the same tests failed as before, with the same messages. The logfiles looked very similar as well (see them here).Reply all
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