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al2na / methylKit

R package for DNA methylation analysis
https://bioconductor.org/packages/release/bioc/html/methylKit.html
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cannot find -lrtmp #316

Closed GuoanQi1996 closed 8 months ago

GuoanQi1996 commented 8 months ago

Hi! I am trying to install methylKit from Github into my PC, following the command devtools::install_github("al2na/methylKit", build_vignettes=FALSE, repos=BiocManager::repositories(), dependencies=TRUE) but it errored out becuse of library dependencies missing. At first, it errored out with

ld.exe: cannot find -lcurl ld.exe: cannot find -lrtmp ld.exe: cannot find -lssl ld.exe: cannot find -lssl2 ld.exe: cannot find -lcrypto

And I download the curl library for windows and move them into .../rtools40/mingw64/lib. Then the errors only left

ld.exe: cannot find -lrtmp

When I tried to find the library rtmp, googling results only has Real-Time Media Flow Protocol, which is also abbrev as rtmp but I suspect it's not what methylKit uses. And I search all text include in the codes, no results found for the "rtmp", so it may be a other dependency of the denpendency of methylKit? So what exactly rtmp is and where could I find it please? Thank you!

alexg9010 commented 8 months ago

Hi @GuoanQi1996 ,

It has been a while since I built methylKit from source on a Windows machine, but probably you will need Rtools installed.

You may also install the latest version from Bioconductor directly: https://bioconductor.org/packages/release/bioc/html/methylKit.html

Best, Alex

GuoanQi1996 commented 8 months ago

Hi @alexg9010, appreciate your reply.

I have made a dummy mistake and now the issue is solved.

The reason I installed methylKit from github was I wanted to read the output of bismark directly, rather than needing further conversion. When I didn't know how to do this (despite the fact that the documentation clearly says "cytosineReport and coverage files from Bismark aligner can be read in to methylKit as well.", but unfortunately I didn't see that), I did some searching, and I saw a discussion about it in #16 , so I incorrectly assumed that direct reading of bismark output is a feature in "developer version" of GitHub methylKit.

Now I've noticed that this functionality is in the methRead function since at least methylKit v0.9.x , regardingless install it from GitHub or bioconductor, and the input format is sprcified via the 'pipeline' parameter.

Thanks again for you help. The issue closed.