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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