Level-up ShortRead package dependency version

[joey711]

This explicitly resolves (through package installation requirements) a difficult to diagnose bug derived from an old version of ShortRead package in Bioconductor. For good measure, Biostrings and data.table were also up-versioned, but the bug-resolving change is the minimum version required for ShortRead.

#263

[joey711]

@benjjneb I went and did the level-up for you, just to avoid this bug / user-confusion in the future. I agree that they should update BioC with R and dada2 version, but it remains possible to create this bug by not-updating BioC and using the latest dada2 version from GitHub; a user behavior we do want to encourage when they're motivated to try the latest features.

[spholmes]

@joey711 and @benjjneb: very important to stress that best practice is always to do all updating with BiocLite and only really bleeding edge people with the caveat that they have to know what they are doing. (homebrew is a real problem because it is used by people who think they need developer versions and then don't know how to install sources)

…

On Tue, Jun 20, 2017 at 11:24 AM, Paul J. McMurdie ***@***.*** > wrote: @benjjneb <https://github.com/benjjneb> I went and did the level-up for you, just to avoid this bug / user-confusion in the future. I agree that they should update BioC with R and dada2 version, but it remains possible to create this bug by not-updating BioC and using the latest dada2 version from GitHub; a user behavior we do want to encourage when they're motivated to try the latest features. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#265 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABJcvaNUqbn-lclp1JRv2Xd9yQMr_Q4Gks5sGA57gaJpZM4N_-HQ> .

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[benjjneb]

Thanks @joey711

@spholmes Totally agree that BioC is best and recommended installation method. But we now semi-officially support a second installation method (bioconda installation for QIIME2 plugin) which is pulling from the github repository. So it's important to keep ourselves up to date as well!