alexg9010
commented
1 year ago Hi @desmodus1984,
The recommended way to install methylKit from within R would be via Bioconductor:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("methylKit")If you are installing methylKit via Conda and are facing conflicts, sometimes it helps to install into a fresh environment.
Concerning your update, it seems like you are missing curl headers to build rhtslib and a common solution seems to be installing libcurl-dev. This may require root privileges, so could be difficult to achieve on compute clusters.
Best Alex
Hi,
I tried installing methylkit in R but I got an error: Error in install_github("al2na/methylKit", build_vignettes = FALSE, repos = BiocManager::repositories(), : could not find function "install_github"
Then, I found that it is also available in conda, and I got an error: conda install -c bioconda bioconductor-methylkit Collecting package metadata (current_repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source. Collecting package metadata (repodata.json): done Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: \ Found conflicts! Looking for incompatible packages. This can take several minutes. Press CTRL-C to abort. failed
UnsatisfiableError: The following specifications were found to be incompatible with your system:
Could you help me tell what can I do to install it? I work in a computer cluster with Linux installed.
Thanks;
Update: I tried installing it again. I managed to install R in Linux, and this time I got different error: hfile_libcurl.c:47:10: fatal error: curl/curl.h: No such file or directory 47 | #include <curl/curl.h> | ^
~~~~ compilation terminated. make[1]: [Makefile.Rhtslib:135: hfile_libcurl.o] Error 1 make[1]: Leaving directory '/tmp/RtmpQQkXm3/R.INSTALL32d77c12749967/Rhtslib/src/htslib-1.15.1' make: [Makevars.common:22: htslib] Error 2 ERROR: compilation failed for package ‘Rhtslib’I followed the instructions as stated in the website.
Thanks;