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.
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_pathargument of all memes functions
options(meme_bin = "/path/to/meme/bin/")inside your R script
export MEME_BIN=/path/to/meme/binin your
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
remotes::install_github("snystrom/memes", INSTALL_opts = c("--no-html"))