[Bioc-devel] Incorrect order of installing dependencies on OS X in bioc-devel in travis

Alexey Sergushichev alsergbox at gmail.com
Thu Mar 23 22:14:59 CET 2017

Hello all,

I'm using travis for checking my project build and found something that
looks like a bug in how biocLite installs package dependencies. It appears
that at some point biocLite started to install them in an alphabet order,
not topological, and specifically on OS X.

I've made a small dummy package to illustrate this: see
https://github.com/assaron/travis-test and corresponding travis build

There reactome.db package should be installed but fails on osx platform in
bioc-devel version. What happens there is reactome.db is installed before
RSQLite, while reactome.db dependes on RSQLite via AnnotationDbi (
https://travis-ci.org/assaron/travis-test/jobs/214404313#L630). Compare it
with bioc-release version:
https://travis-ci.org/assaron/travis-test/jobs/214404316#L543 or bioc-devel
but on linux: https://travis-ci.org/assaron/travis-test/jobs/214389446#L928

Can anyone reproduce this behavior at their OS X machine? Is this bug in
biocLite or Travis?


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