Updated: Nov-04-2024
This vignette provides troubleshooting tips for common issues
encountered when using the MotifPeeker
package.
If you encounter an issue that is not covered, please open an issue on the GitHub repository.
MEME Suite Related
Error: Cannot find MEME Suite
If You have ensured that the MEME Suite is installed, but still encounter this error, set the path to the MEME suite binaries (.../meme/bin/
) using thememe_path
parameter in theMotifPeeker()
function call.Error: Failed to generate .html file.
Please ensure that the Perl dependencies required by the MEME Suite are installed, particularlyXML::Parser
, which can be installed using the following command in the terminal:bash cpan install XML::Parser
MotifPeeker()
Related
-
Function takes too long to run
It is likely de-novo motif discovery is what is taking too long to run. Try reducing the number ofworkers
if you are running out of memory while running theMotifPeeker()
function.
Additionally, follow the runtime guidance forMotifPeeker()
.
Session Info
utils::sessionInfo()
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## loaded via a namespace (and not attached):
## [1] digest_0.6.37 desc_1.4.3 R6_2.5.1 fastmap_1.2.0
## [5] xfun_0.49 cachem_1.1.0 knitr_1.48 htmltools_0.5.8.1
## [9] rmarkdown_2.28 lifecycle_1.0.4 cli_3.6.3 sass_0.4.9
## [13] pkgdown_2.1.1 textshaping_0.4.0 jquerylib_0.1.4 systemfonts_1.1.0
## [17] compiler_4.4.1 tools_4.4.1 ragg_1.3.2 bslib_0.8.0
## [21] evaluate_1.0.1 yaml_2.3.10 jsonlite_1.8.9 rlang_1.1.4
## [25] fs_1.6.5 htmlwidgets_1.6.4