[Bioc-devel] Dependency on devtools in biocLite()
andrzej.oles at gmail.com
Fri Jan 20 16:29:08 CET 2017
Awesome, many thanks Martin for the update!
On Thu, Jan 19, 2017 at 8:08 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:
> On 01/17/2017 07:15 AM, Andrzej Oleś wrote:
>> Thanks Martin!
>> I see your point - then I suggest that at least the call to
>> `devtools::install` is guarded by a customized more informative error
>> massage, something along the lines:
>> Package 'devtools' missing: please install it (e.g., by a call to
>> `install.packages('devtools')`) and re-run your biocLite command.
> I've updated the error message in 1.25.3; thanks for the suggestion.
>> On Sat, Jan 14, 2017 at 9:43 AM, Martin Morgan
>> <martin.morgan at roswellpark.org <mailto:martin.morgan at roswellpark.org>>
>> On 01/13/2017 06:29 PM, Andrzej Oleś wrote:
>> Dear all,
>> it's great that for some time now `biocLite()` also resolves
>> dependencies for GitHub hosted packages. However, as this
>> depends on devtools, an attempt to install a GitHub package when
>> is not installed results in an error
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2
>> Error: package 'devtools' not available: there is no package
>> If this is the case, one would typically need to first install
>> and rerun the biocLite command. I was wondering whether it would
>> make sense
>> to modify the behavior such that before attempting to call
>> `devtools::install` in
>> first check for devtools availability and try to automatically
>> install it
>> if missing (maybe by prompting the user). What do you think?
>> I'm not a fan of automatic package installation, e.g., because a
>> user (e.g., me) might have a configuration of library paths that
>> they are trying to maintain. This leads me down the slippery slope
>> of not wanting to offer to install a package, either, because again
>> the offer would be too narrow, some users (again, e.g., me) will
>> reject it and prefer to have control, and so why not have a standard
>> work flow -- user fixes package installation to their satisfaction
>> and tries again -- rather than a conditional work flow.
>> On the other hand the error message "package 'devtools' not
>> available: there is no package called 'devtools'" seems to be poorly
>> worded -- there is a package devtools, and it is available, just not
>> in the current installation. One could try to provide a better
>> message, but one would rather the message were improved upstream so
>> all similar situations were handled the same; at least this way the
>> user has to learn only once what the message means.
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