[R-SIG-Mac] update.packages() re-downloading old versions

Sun Apr 6 00:32:27 CEST 2025

This looks like a case where an attempt is made to update with type="both" which will take into account both source and binary repositories for comparison, but packages can be installed from source only if the user has the tools and acknowledged that they really want to do that. As Peter said, if you want to use binaries then it's best to use type="binary" instead since it will only compare package versions based on the available binaries - and I highly recommend that as default if you are using CRAN binaries, because type="both" is quite problematic in practice, because it is attempting to merge two sets constraints and dependence graphs [one from each type] - that may not be compatible.

In practice, this only occurs in the (short) time between the source package being published and the binary being built. The Mac builds are based on the published CRAN packages from the CRAN master, so there is always a small lag between the source package being published on CRAN and the binary becoming available (typically few hours). In some cases the lag increases, e.g. around the time of a new release (like now), because we have to re-build all packages with the new R version which takes 1-2 days.

Cheers,
Simon

> On Apr 4, 2025, at 7:47 PM, Gavin Simpson <ucfagls using gmail.com> wrote:
> 
> Hi Spencer,
> 
> I don't see a response to this, but I am too seeing this on my M3 Macbook
> Air.
> 
> It looks to me like this is update.packages() looking at whether a package
> is outdated but then downloading the latest Mac binary. I don't know if
> this is because I've not got my system set up to build from sources or not
> (I mostly use the binaries but I can build packages by hand so *shrug* -
> I'm very new to Macs).
> 
> The packages this is affecting right now are all packages that got updated
> a day or two ago and for which the mac binaries are not yet available.
> 
> All the best
> 
> G
> 
> On Thu, 14 Nov 2024 at 19:41, Spencer Graves <spencer.graves using prodsyse.com>
> wrote:
> 
>> Hello, All:
>> 
>> 
>>          "update.packages()" now identifies 6 packages with updates but
>> re-downloads the old version. In the output copied below starting,  "Thu
>> Nov 14 06:48:15 2024", it invited me to update curl, Ecfun, NLP,
>> packageRank, slam, and terra. I said yes to all. Then it reinstalled the
>> old version, not the new, for each. Then I repeated the procedure
>> starting "Thu Nov 14 06:48:33 2024", 28 seconds later, with the same
>> results.
>> 
>> 
>>          I've noticed this problem roughly 2 days ago. At that time, it
>> downloaded several packages, some correctly but two (Ecfun and terra)
>> incorrectly, as here. This was shortly after I got your email saying,
>> "Your package Ecfun_0.3-6.tar.gz has been built for Windows and will be
>> published within 24 hours in the corresponding CRAN directory."
>> 
>> 
>>          sessionInfo() is also provided below.
>> 
>> 
>>          I asked Uwe Ligges, who suggested I "ask on a sig-mac mailing
>> list if
>> this is know (to Simon in particular)?" Uwe added, "I can only tell
>> about source packages (as used under Linux) and Windows binaries where
>> this should never happen."
>> 
>> 
>>          What do you think?
>> 
>> 
>>          Thanks,
>>          Spencer Graves
>> 
>> 
>> p.s. I very much appreciate this great R community. People live better
>> the world over because of good statistical analyses that may not have
>> been done -- or done as well -- without R and CRAN.
>> 
>> 
>> *** DOCUMENTATION OF WHAT I SAW:
>> 
>> 
>>> date()
>> [1] "Thu Nov 14 06:48:15 2024"
>>> update.packages()
>> curl :
>>  Version 6.0.0 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 6.0.1 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> Ecfun :
>>  Version 0.3-2 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 0.3-6 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> NLP :
>>  Version 0.3-0 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 0.3-1 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> packageRank :
>>  Version 0.9.3 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 0.9.4 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> slam :
>>  Version 0.1-54 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 0.1-55 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> terra :
>>  Version 1.7-78 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 1.7-83 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/curl_6.0.0.tgz
>> '
>> Content type 'application/x-gzip' length 832416 bytes (812 KB)
>> ==================================================
>> downloaded 812 KB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/Ecfun_0.3-2.tgz
>> '
>> Content type 'application/x-gzip' length 1245104 bytes (1.2 MB)
>> ==================================================
>> downloaded 1.2 MB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/NLP_0.3-0.tgz
>> '
>> Content type 'application/x-gzip' length 396405 bytes (387 KB)
>> ==================================================
>> downloaded 387 KB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/packageRank_0.9.3.tgz
>> '
>> Content type 'application/x-gzip' length 3504704 bytes (3.3 MB)
>> ==================================================
>> downloaded 3.3 MB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/slam_0.1-54.tgz
>> '
>> Content type 'application/x-gzip' length 212778 bytes (207 KB)
>> ==================================================
>> downloaded 207 KB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/terra_1.7-78.tgz
>> '
>> Content type 'application/x-gzip' length 97585776 bytes (93.1 MB)
>> ==================================================
>> downloaded 93.1 MB
>> 
>> 
>> The downloaded binary packages are in
>> 
>> /var/folders/2n/zqk768wj3818l8x2wttbc5kw0000gn/T//Rtmp7DqHrd/downloaded_packages
>>> 
>>> 
>>> date()
>> [1] "Thu Nov 14 06:48:33 2024"
>>> update.packages()
>> curl :
>>  Version 6.0.0 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 6.0.1 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> Ecfun :
>>  Version 0.3-2 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 0.3-6 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> NLP :
>>  Version 0.3-0 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 0.3-1 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> packageRank :
>>  Version 0.9.3 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 0.9.4 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> slam :
>>  Version 0.1-54 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 0.1-55 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> terra :
>>  Version 1.7-78 installed in
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library
>>  Version 1.7-83 available at https://cran.rstudio.com
>> Update? (Yes/no/cancel) y
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/curl_6.0.0.tgz
>> '
>> Content type 'application/x-gzip' length 832416 bytes (812 KB)
>> ==================================================
>> downloaded 812 KB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/Ecfun_0.3-2.tgz
>> '
>> Content type 'application/x-gzip' length 1245104 bytes (1.2 MB)
>> ==================================================
>> downloaded 1.2 MB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/NLP_0.3-0.tgz
>> '
>> Content type 'application/x-gzip' length 396405 bytes (387 KB)
>> ==================================================
>> downloaded 387 KB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/packageRank_0.9.3.tgz
>> '
>> Content type 'application/x-gzip' length 3504704 bytes (3.3 MB)
>> ==================================================
>> downloaded 3.3 MB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/slam_0.1-54.tgz
>> '
>> Content type 'application/x-gzip' length 212778 bytes (207 KB)
>> ==================================================
>> downloaded 207 KB
>> 
>> trying URL
>> '
>> https://cran.rstudio.com/bin/macosx/big-sur-arm64/contrib/4.4/terra_1.7-78.tgz
>> '
>> Content type 'application/x-gzip' length 97585776 bytes (93.1 MB)
>> ==================================================
>> downloaded 93.1 MB
>> 
>> 
>> The downloaded binary packages are in
>> 
>> /var/folders/2n/zqk768wj3818l8x2wttbc5kw0000gn/T//Rtmp7DqHrd/downloaded_packages
>>> 
>>> 
>>> 
>>> sessionInfo()
>> R version 4.4.2 (2024-10-31)
>> Platform: aarch64-apple-darwin20
>> Running under: macOS Sequoia 15.0.1
>> 
>> Matrix products: default
>> BLAS:
>> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
>> 
>> 
>> LAPACK:
>> /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;
>> 
>>  LAPACK version 3.12.0
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> time zone: America/Chicago
>> tzcode source: internal
>> 
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets
>> [6] methods   base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_4.4.2 tools_4.4.2
>> 
>> 
>> On 11/12/24 04:48, ligges using statistik.tu-dortmund.de wrote:
>>> Dear package maintainer,
>>> 
>>> this notification has been generated automatically.
>>> Your package Ecfun_0.3-6.tar.gz has been built for Windows and
>>> will be published within 24 hours in the corresponding CRAN directory.
>>> R version 4.4.2 (2024-10-31 ucrt)
>>> 
>>> All the best,
>>> Uwe Ligges
>>> (Maintainer of binary packages for Windows)
>>> 
>> 
>> _______________________________________________
>> R-SIG-Mac mailing list
>> R-SIG-Mac using r-project.org
>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>> 
> 
> 
> -- 
> Gavin Simpson, PhD [he/him/his]
> [tw] @ucfagls [OrciD] 0000-0002-9084-8413
> [web] fromthebottomoftheheap.net
> • Assistant Professor
> • Department of Animal & Veterinary Sciences, Aarhus University
> • Adjunct Professor, Department of Biology, University of Regina.
> 
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