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MadsAlbertsen / mmgenome

Please use mmgenome2 instead. Tools for extracting individual genomes from metagenomes
https://kasperskytte.github.io/mmgenome2/
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Difficulty installing #38

Open KasperSkytte opened 6 years ago

KasperSkytte commented 6 years ago

When installing mmgenome from scratch with: source("https://bioconductor.org/biocLite.R") biocLite("Biostrings") devtools::install_github("madsalbertsen/mmgenome/mmgenome") it stops when installing a required package Rtsne.multicore with the error:

"Error in FUN(X[[i]], ...) : Invalid comparison operator in dependency: >= "

Simply using biocLite("madsalbertsen/mmgenome/mmgenome") instead causes no trouble!

anaya1 commented 6 years ago

Hi Kasper, I am really struggling installing mmgenome on my Mac OS X El Capitan system. I have a following message:

biocLite("madsalbertsen/mmgenome/mmgenome") BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30). Installing github package(s) ‘madsalbertsen/mmgenome/mmgenome’ Downloading GitHub repo madsalbertsen/mmgenome@master from URL https://api.github.com/repos/madsalbertsen/mmgenome/zipball/master Installing mmgenome Downloading GitHub repo RGLab/Rtsne.multicore@master from URL https://api.github.com/repos/RGLab/Rtsne.multicore/zipball/master Installing Rtsne.multicore '/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file --no-environ --no-save --no-restore \ --quiet CMD INSTALL \ '/private/var/folders/9c/62h8z0yj7nv50l9zkmrw6_z80000gn/T/RtmpMpIoyA/devtools2ae1fe15aec/RGLab-Rtsne.multicore-7b4f8c6' \ --library='/Library/Frameworks/R.framework/Versions/3.4/Resources/library' --install-tests

ERROR: dependency ‘Rtsne.multicore’ is not available for package ‘mmgenome’

KasperSkytte commented 6 years ago

Hi Anna!

Try with devtools::install_github("RGLab/Rtsne.multicore") first and then reinstall mmgenome.

I am currently working on mmgenome2 and it is almost done. Just need a get started guide and more information on the webpage, then it will be moved to Mads' github page and people should start using that instead. So hopefully this will be fixed in mmgenome2. Things have changed compared to mmgenome1, but hopefully for the better :)

anaya1 commented 6 years ago

Thanks Kasper, I truly believe that the mmgenome package is OK but there is sth wrong with Rtsne.multicore package compilation on Mac system. See this post, https://github.com/RGLab/Rtsne.multicore/issues/5. Unfortunately I don't know how to compile this package so will ask someone to help me. I will let you know once the problem is fixed. And looking forward to mmgenome2 !! Cheers, Anna

KasperSkytte commented 6 years ago

The package is only used in mmload to calculate t-SNE of tetramers. So if you dont use it anyways, it would probably be easier to make your own mmgenome package on GitHub. Just fork mmgenome, and remove line 26 and 27 (and the comma at line 25 ofc) from the DESCRIPTION file in the mmgenome folder. Then you would be able to install mmgenome without Rtsne.multicore with biocLite("anaya1/mmgenome/mmgenome") and hopefully it will work fine. Remember to set BH_SNE = FALSE in mmload then.

Alternatively install a specific commit before tSNE was added to mmgenome, so fx 6a673e2f62b52079998d801506d6fb65ebb2ff10, with fx biocLite("madsalbertsen/mmgenome/mmgenome", ref = "6a673e2")

anaya1 commented 6 years ago

Hi Kasper, You are genius, it looks like mmgenome is installed an alternative option using fx 6a673e2. I will test it and let you know how it goes. Thanks.

KasperSkytte commented 6 years ago

Thanks. You're welcome :)