GEOquery no longer exports gunzip

[sof202]

Description

This has actually been the case the past 2 years. Because bigmelon doesn't specify a version for GEOquery, the version likely to be installed (>2.73.2) no longer has the 'dead' gunzip code:

error message:

> library(bigmelon)
Error: package or namespace load failed for ‘bigmelon’:
 object ‘gunzip’ is not exported by 'namespace:GEOquery'

Relevant commit to GEOquery: seandavi/GEOquery@b3f8134

Fix

Unfortunately, bioconductor aren't ones for backwards compatability and frequently remove older versions of packages from their repository (Only >2.80 is available currently). As such, I'd prefer to specify that the package should be installed via GitHub (remotes) instead. This can still be accomplished from within the DESCRIPTION file.

[sof202]

I imagine there is probably a replacement for GEOquery::gunzip as it was labelled as dead code. The solution given in #18 is a minimal solution to the problem that is quick to implement.

A more ideal solution would use the latest version of GEOquery and the geotogds would be refactored to no longer use GEOquery::gunzip.

What would you prefer?