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ocbe-uio / DIscBIO

A user-friendly R pipeline for biomarker discovery in single-cell transcriptomics
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[WIP] Binder support #4

Closed minrk closed 4 years ago

minrk commented 4 years ago

this adds install.R following the directions

It hasn't run to completion (it takes a long time to run the given commands), so I don't have verification that it works, yet.

wleoncio commented 4 years ago

Thank you for your contribution, @minrk. I'll check the request ASAP. For now, I'm just changing the merging base because master is reserved for the Bioconductor submission (the branch is suspended while we await the repo reviewers).

minrk commented 4 years ago

I'm not understanding this error when it attempts to build DIscBIO:

Installation failed: 'BiocInstaller' must be installed to install Bioconductor packages

but BiocManager has superseded BiocInstaller. Do you know how to avoid this?

In the end, installation succeeds and the notebook appears to work:

Binder

wleoncio commented 4 years ago

I'm not understanding this error when it attempts to build DIscBIO:

Installation failed: 'BiocInstaller' must be installed to install Bioconductor packages

but BiocManager has superseded BiocInstaller. Do you know how to avoid this?

In the end, installation succeeds and the notebook appears to work:

Binder

I am new to working with Bioconductor, so I need to study a bit more before I can confidently comment about the BiocManager and BiocInstaller packages. For now, I am trying to reproduce this error message. Where did you get it?

In any case, I suppose installing BiocInstaller should satisfy the validation checker's desire for its existence. From StackOverflow, the following worked on my machine:

install.packages("BiocInstaller", repos="http://bioconductor.org/packages/2.13/bioc")
minrk commented 4 years ago

Attempting the local install with:

devtools::install_local(getwd())

gives the error, followed by

BiocInstaller' must be installed to install Bioconductor packages.
Would you like to install it? This will source <https://bioconductor.org/biocLite.R>.

1: Yes
2: No

Selecting 2 aborts, selecting 1 fails with:

Installation failed: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install

But I cannot figure out what's requesting the installation of bioconductor packages.

minrk commented 4 years ago

Installing BiocInstaller does appear to work, even though it's not supposed to be used anymore, thanks!