[R-SIG-Mac] update.packages() re-downloading old versions
peter dalgaard
pd@|gd @end|ng |rom gm@||@com
Fri Apr 4 17:09:35 CEST 2025
You might try update.packages(type="binary").
Also, install.packages() in RStudio is not utils:::install.packages(), and is known to get its knickers in a twist sometimes, but I don't know which one of them is getting called by update.packages().
-pd
> On 4 Apr 2025, at 08.47, 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 is outdated but then downloading the latest Mac binary.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.
>
> [[alternative HTML version deleted]]
>
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--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business SchoolSolbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes using cbs.dk Priv: PDalgd using gmail.com
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