[R] 4.5.0 | update/install BH

[peter dalgaard]

[oops, forgot to copy r-help, which could be rather important to do, so resending]

There's a difference between "getting away with in the past" and "safe to do".... 

I just had another conversation (off-line) with someone getting bitten by the change to md5sum(), and I'm 99% sure it happened because copying the old library overwrote the new tools package with the old one, an updated package tried to call tools::md5sum(bytes=....), and things blew up. 

So even though people have apparently gotten away with copying the old folder in the past, they probably actually created a bastardized installation, where some system packages was actually from a previous version (which of course is inconsequential if and only if they weren't actually changed by the update...).

- pd


> On 24 Apr 2025, at 14:31 , Evan Cooch <evan.cooch using gmail.com> wrote:
> 
> 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?
>>> 
>>> 
>>> 	[[alternative HTML version deleted]]
>>> 
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> 

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com