The Bioconductor build system does not have the MEME Suite installed, therefore these vignettes will not contain any R output. To view the full vignette, visit this article page on the memes website at this link
memes is an R interface to the MEME Suite family of tools, which provides several utilities for performing motif analysis on DNA, RNA, and protein sequences. It works by detecting a local install of the MEME suite, running the commands, then importing the results directly into R.
memes relies on a local install of the MEME Suite. For installation instructions for the MEME suite, see the MEME Suite Installation Guide.
Briefly, the MEME suite can be installed to a default location (~/meme/
) on Linux, MacOS, Cygwin, and Windows Linux Subsystem using the following shell commands:
# As of May 2020, version 5.1.1 is the most recent MEME-Suite version
# Please check the install guide (linked above) for more recent information
version=5.1.1
wget http://meme-suite.org/meme-software/$version/meme-$version.tar.gz
tar zxf meme-$version.tar.gz
cd meme-$version
./configure --prefix=$HOME/meme --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt
make
make test
make install
For additional troubleshooting or to learn more about install configuration, please see the Installation Guide.
memes needs to know the location of the meme/bin/
directory on your local machine. You can tell memes the location of your MEME suite install in 4 ways. memes will always prefer the more specific definition if it is a valid path. Here they are ranked from most- to least-specific:
meme_path
argument of all memes functionsoptions(meme_bin = "/path/to/meme/bin/")
inside your R scriptMEME_BIN=/path/to/meme/bin/
in your .Renviron
file, or export MEME_BIN=/path/to/meme/bin
in your ~/.bashrc
~/meme/bin/
If memes fails to detect your install at the specified location, it will fall back to the next option.
To verify memes can detect your MEME install, use check_meme_install()
which uses the search herirarchy above to find a valid MEME install. It will report whether any tools are missing, and print the path to MEME that it sees. This can be useful for troubleshooting issues with your install.
I get the following error: installation of package ‘R.oo’ had non-zero exit status
R.css
fileremotes::install_github("snystrom/memes", INSTALL_opts = c("--no-html"))