[R] 4.5.0 | update/install BH

[Evan Cooch]

Good advice, but that approach (as you describe it) is not something I 
(or anyone I know) has needed to follow for past updates to R, and 
apparently is/was only  a consideration for BH. As per OP, every other 
package updated just fine "the old way" (which you correctly describe as 
what most of us do -- copy old /library folder to 'new' /library folder, 
and simply update everything).

On 4/24/2025 7:32 AM, peter dalgaard wrote:
> I'm puzzled. It doesn't seem to take long on MacOS, neither under 4.3.x. or 4.5.0.
>
> The tarballs for BH are like 14 MB and the Windows .zip is 21 MB, which is large, but not that large?
>
> I'm somewhat suspicious about the "package updating" techniques that some people seeme to be using. It sounds like you are copying package directories from an older version, then using update.packages(). A number of things could go wrong if you do that across an API change.
>
> At the very least, you need update.packages(checkBuilt=TRUE) (and probably you also want ask=FALSE), but I would prefer a safer strategy of just installing what that you need into a fresh install of R. I.e. something like this:
>
> In the old R do
>> pkglist <- rownames(subset(as.data.frame(installed.packages()), !(Priority %in% c("base","recommended"))))
>> save(pkglist, file="~/tmp/4.4pkglist")
> Install new version, then
>> load("~/tmp/4.4pkglist")
>> system.time(install.packages(pkglist))
> --- Please select a CRAN mirror for use in this session ---
> trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.5/abind_1.4-8.tgz'
> trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.5/ada_2.0-5.tgz'
> tryi.......
> ......ng URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.5/zoo_1.8-14.tgz'
>
> The downloaded binary packages are in
> 	/var/folders/h0/hzzhnnfd1gx7399sx_cwlhpw0000gn/T//RtmpQDl3Tj/downloaded_packages
>     user  system elapsed
>    4.574   5.235  33.213
> Warning message:
> package ‘fEcofin’ is not available for this version of R
>
> A version of this package for your version of R might be available elsewhere,
> see the ideas at
> https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages 
>> length(pkglist)
> [1] 252
>
> (most of the time was spent waiting for XQuartz and Tcl/Tk to fire up so that I could choose the CRAN mirror.)
>
>
> Actually, BH was not on the list, but
>
>> system.time(install.packages("BH"))
> trying URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.5/BH_1.87.0-1.tgz'
> Content type 'application/x-gzip' length 13900146 bytes (13.3 MB)
> ==================================================
> downloaded 13.3 MB
>
>
> The downloaded binary packages are in
> 	/var/folders/h0/hzzhnnfd1gx7399sx_cwlhpw0000gn/T//RtmpQDl3Tj/downloaded_packages
>     user  system elapsed
>    1.054   2.340   5.091
>
> -pd
>
>
>> On 23 Apr 2025, at 23:33 , Evan Cooch<evan.cooch using gmail.com> wrote:
>>
>> So, I decided to update from 4.4.3 -> 4.5.0. Updating all packages in
>> one shot (selecting all of the offered updates) failed, on all my
>> machines (Linux, Windows - lots of RAM, lots of CPU speed). So, tried
>> the updates a few at a time. Didn't take me long to discover that the
>> 'culprit' was the BH packages. For some reason, it takes a *long* time
>> for it to download/update or download/install. Even installing from a
>> local download took a long time. So long, that on my Windows machines,
>> the Rgui simply stopped responding. At all. Had to kill the process
>> manually, and try again.
>>
>> So, in case anyone else runs into this (I've replicated the problem on 5
>> different machines - 3 Windows, 2 Linux)
>>
>> 1\ if BH is included in a slew of updates you're trying to apply all at
>> once, it might clobber everything because its choking on BH, kill RGui
>> on my Windows machines. Less of an issue on my Linux boxes (good old
>> CLI), but still...
>>
>> 2\ even BH alone requires some patience. On a high-end machine (24
>> threads, 64 Gb RAM, etc etc) took almost 8 minutes to download/update.
>> Everything else (even big suckers like terra) took only seconds on said
>> machine. But BH?
>>
>>
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>>
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