Unlisted Requirement fails on CentOS 7.4 w MariaDB

Bioconductor / VariantAnnotation

Annotation of Genetic Variants

https://bioconductor.org/packages/VariantAnnotation

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Unlisted Requirement fails on CentOS 7.4 w MariaDB #1

Closed lachlansimpson closed 6 years ago

lachlansimpson commented 6 years ago

I'm trying to install VariantAnnotation in R 3.4.2 on CentOS 7.4

One of the errors is

2: In install.packages(pkgs = doing, lib = lib, ...) :
  installation of package ‘RMySQL’ had non-zero exit status

I attempted to install RMySQL yesterday and that failed too - although there is a fork work around, which is less than ideal.

Two things of note:

RMySQL isn't listed as a dependency on a new install of VariantAnnotation?
The RMySQL page notes that it is being phased out for RMariaDB

mtmorgan commented 6 years ago

RMySQL is a dependency of a dependency; it's not usual in R to list recursive dependencies (of which there are 65 for VariantAnnotation, pkgs = tools::package_dependencies("VariantAnnotation", available.packages(repos=BiocInstaller::biocinstallRepos()), recursive=TRUE).

This belongs on the GenomicFeatures repository, where I'll try to reference this.