[Bioc-devel] Dependency on devtools in biocLite()

Andrzej Oleś andrzej.oles at gmail.com
Tue Jan 17 13:15:10 CET 2017

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.


On Sat, Jan 14, 2017 at 9:43 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

> On 01/13/2017 06:29 PM, Andrzej Oleś wrote:
>> Dear all,
>> it's great that for some time now `biocLite()` also resolves package
>> dependencies for GitHub hosted packages. However, as this functionality
>> depends on devtools, an attempt to install a GitHub package when devtools
>> is not installed results in an error
>> library(BiocInstaller)
>>> biocLite("aoles/RBioFormats")
>> BioC_mirror: https://bioconductor.org
>> Using Bioconductor 3.4 (BiocInstaller 1.24.0), R 3.3.2 (2016-10-31).
>> Error: package 'devtools' not available: there is no package called
>> ‘devtools’
>> If this is the case, one would typically need to first install devtools,
>> 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
>> https://github.com/Bioconductor-mirror/BiocInstaller/blob/
>> 9965cc72d009bfcae6776a02e5abb94cbd5dd109/R/biocLite.R#L48
>> 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.
> Martin
>> Cheers,
>> Andrzej
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