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leffj / mctoolsr

Microbial community analysis tools in R
http://leffj.github.io/mctoolsr/
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biomformat update issue R v3.3.3 #25

Closed hhollandmoritz closed 7 years ago

hhollandmoritz commented 7 years ago

I'm having trouble updating mctoolsr, the issue seems to be a conflict with bioconductor's version of the biomformat package and R version 3.3.3.

`Downloading GitHub repo leffj/mctoolsr@master from URL https://api.github.com/repos/leffj/mctoolsr/zipball/master Installing mctoolsr '/usr/lib64/R/bin/R' --no-site-file --no-environ --no-save --no-restore --quiet CMD INSTALL \ '/tmp/RtmpkqqHZi/devtools4a08550199e8/leffj-mctoolsr-2265f34' \ --library='/home/hannah/R/x86_64-redhat-linux-gnu-library/3.3' --install-tests

ERROR: dependency ‘biomformat’ is not available for package ‘mctoolsr’

I tried following this solution to install the development version of biomformat as specified in this discussion before updating mctoolsr and it did not work. Any advice would be appreciated.

https://groups.google.com/forum/#!topic/qiime-forum/_TVPiqabwvs

install.packages("devtools") # if not already installed devtools::install_github("biom", "joey711")

hhollandmoritz commented 7 years ago

Okay, after restarting R and trying it again, the posted solution works. Not sure what changed, but if anyone else has this problem, hopefully it'll be helpful.