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

[Andrzej Oleś]

Awesome, many thanks Martin for the update!

Cheers,
Andrzej

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.
>
> Martin
>
>
>>
>> Cheers,
>> Andrzej
>>
>> On Sat, Jan 14, 2017 at 9:43 AM, Martin Morgan
>> <martin.morgan at roswellpark.org <mailto: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/
>>         <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
>>
>>                 [[alternative HTML version deleted]]
>>
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