[Rd] improving the performance of install.packages

[Duncan Murdoch]

On 08/11/2019 6:17 p.m., Henrik Bengtsson wrote:
> I believe introducing a backward compatible force=TRUE is a good
> start, even if we're not ready for making force=FALSE the default at
> this point.  It would help simplify quite-common instructions like
> 
> if (requireNamespace("BiocManager"))
>    install.packages("BiocManager")
> BiocManager::install(...)
> 
> to
> 
> install.packages("BiocManager", force=FALSE)
> BiocManager::install(...)

If simplifying instructions is the goal, it would be even simpler to 
just install it unconditionally:

install.packages("BiocManager")

Unlike dplyr (the original example in this thread), BiocManager is a 
tiny package with no compiling needed, so it hardly needs any time to 
install.

And as previously mentioned, the backward compatible force=TRUE wouldn't 
help with the bad script at all.  In fact, the bad script could be fixed 
simply by realizing that

install.packages("tidyverse")

means it's actually a bad idea to also include

install.packages("dplyr")

because the former would install dplyr if and only if it was not already 
installed.  So it seems to me that fixing the bad script (by deleting 
one line) is the solution to the problem, not fixing R with a multistage 
series of revisions, tests, etc.

Duncan Murdoch

> 
> and more so when installing lots of packages conditionally, e.g.
> 
> if (requireNamespace("foo")) install.packages("foo")
> if (requireNamespace("bar")) install.packages("bar")
> ...
> 
> to
> 
> install.packages(c("foo", "bar", ...), force = FALSE)
> 
> Before deciding on making force=FALSE the new default, I think it
> would be valuable to play the devil's advocate and explore and
> identify all possible downsides of such a default, e.g. breaking
> existing instructions, downstream package code that uses
> install.packages() internally, and so on.
> 
> /Henrik
> 
> PS. Although the idea of having update.packages() install missing
> packages is not bad, I don't think I'm a not a fan for the sole
> purpose of risking installation instructions starting using
> update.packages() instead, which will certainly confuse those who
> don't know the history (think require() vs library()).
> 
> On Fri, Nov 8, 2019 at 3:11 PM Pages, Herve <hpages using fredhutch.org> wrote:
>>
>> Hi Gabe,
>>
>> Keeping track of where a package was installed from would be a nice
>> feature. However it wouldn't be as reliable as comparing hashes to
>> decide whether a package needs re-installation or not.
>>
>> H.
>>
>> On 11/8/19 12:37, Gabriel Becker wrote:
>>> Hi Josh,
>>>
>>> There are a few issues I can think of with this. The primary one is that
>>> CRAN(/Bioconductor) is not the only place one can install packages from. I
>>> might have version x.y.z of a package installed that was, at the time, a
>>> development version I got from github, or installed locally, etc. Hell I
>>> might have a later devel version but want the CRAN version. Not common,
>>> sure, but wiill likely happen often enough that install.packages not doing
>>> that for me when I tell it to is probably bad.
>>>
>>> Currently (though there has been some discussion of changing this) packages
>>> do not remember where they were installed from, so R wouldn't know if the
>>> version you have is actually fully the same one on the repository you
>>> pointed install.packages to or not.  If that were changed  and we knew that
>>> we were getting the byte identical package from the actual same source, I
>>> think this would be a nice addition, though without it I think it would be
>>> right a high but not high enough proportion of the time.
>>>
>>> R will build the package from source (depending on what OS you're using)
>>>> twice by default. This becomes especially burdensome when people are using
>>>> big packages (i.e. lots of depends) and someone has a script with:
>>>>
>>>
>>>
>>> install.packages("tidyverse")
>>>> ...
>>>> ... later on down the script
>>>> ...
>>>> install.packages("dplyr")
>>>>
>>>
>>> I mean, IMHO and as I think Duncan was alluding to, that's straight up an
>>> error by the script author. I think its a few of them, actually, but its at
>>> least one. An understandable one, sure, but thats still what it is. Scripts
>>> (which are meant to be run more than once, generally) usually shouldn't
>>> really be calling install.packages in the first place, but if they do, they
>>> should certainly not be installing umbrella packages and the packages they
>>> bring with them separately.
>>>
>>> Even having one vectorized call to install.packages where all the packages
>>> are installed would prevent this issue, including in the case where the
>>> user doesn't understand the purpose of the tidyverse package. Though the
>>> installation would still occur every time the script was run.
>>>
>>>
>>> The last thing to note is that there are at least 2 packages which provide
>>> a function which does this already (install.load and remotes), so people
>>> can get this functionality if they need it.
>>>
>>>
>>> On Fri, Nov 8, 2019 at 11:56 AM Joshua Bradley <jgbradley1 using gmail.com> wrote:
>>>
>>>>
>>>>
>>>> I assumed this list is used to discuss proposals like this to the R
>>>> codebase. If I'm on the wrong list, please let me know.
>>>>
>>>
>>> This is the right place to discuss things like this. Thanks for starting
>>> the conversation.
>>>
>>> Best,
>>> ~G
>>>
>>>>
>>>>
>>>
>>>        [[alternative HTML version deleted]]
>>>
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>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
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>> Seattle, WA 98109-1024
>>
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