Michael McQuaid
2025-Dec-20 19:30 UTC
[R] update.packages() fails due to searching for old versions of packages
When I try to update packages, the package manager appears to search for
old versions of the packages, despite seemingly knowing about the existence
of newer versions. Here is an example where I try to update the e1071
package and it seems to recognize that the current version is 1.7-17 but
then searches for and fails to find 1.7-16. This happens for every package
I try to update, I've just included one here for brevity. I have tried
several mirrors including wustl, utk, and iastate. I wonder if there is
some file on my system pointing to the old version. I also tried updating
from R 4.5.1 to 4.5.2, but the issue persists. I am on macOS Tahoe 26.2 on
an M1 Macbook Pro.
$ Rscript -e 'update.packages(oldPkgs=c("e1071"))'
e1071 :
Version 1.7-16 installed in /Users/mm223266/Library/R/arm64/4.5/library
Version 1.7-17 available at https://cloud.r-project.org
Update? (Yes/no/cancel)
trying URL '
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz
'
Error in download.file(urls, destfiles, "libcurl", mode =
"wb", ...) :
cannot open URL '
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz
'
In addition: Warning messages:
1: In download.file(urls, destfiles, "libcurl", mode = "wb",
...) :
downloaded length 0 != reported length 279
2: In download.file(urls, destfiles, "libcurl", mode = "wb",
...) :
cannot open URL '
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz':
HTTP status was '404 Not Found'
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
download of package ?e1071? failed
[[alternative HTML version deleted]]
Rui Barradas
2025-Dec-20 22:34 UTC
[R] update.packages() fails due to searching for old versions of packages
?s 19:30 de 20/12/2025, Michael McQuaid escreveu:> When I try to update packages, the package manager appears to search for > old versions of the packages, despite seemingly knowing about the existence > of newer versions. Here is an example where I try to update the e1071 > package and it seems to recognize that the current version is 1.7-17 but > then searches for and fails to find 1.7-16. This happens for every package > I try to update, I've just included one here for brevity. I have tried > several mirrors including wustl, utk, and iastate. I wonder if there is > some file on my system pointing to the old version. I also tried updating > from R 4.5.1 to 4.5.2, but the issue persists. I am on macOS Tahoe 26.2 on > an M1 Macbook Pro. > > $ Rscript -e 'update.packages(oldPkgs=c("e1071"))' > e1071 : > Version 1.7-16 installed in /Users/mm223266/Library/R/arm64/4.5/library > Version 1.7-17 available at https://cloud.r-project.org > Update? (Yes/no/cancel) > trying URL ' > https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz > ' > Error in download.file(urls, destfiles, "libcurl", mode = "wb", ...) : > cannot open URL ' > https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz > ' > In addition: Warning messages: > 1: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) : > downloaded length 0 != reported length 279 > 2: In download.file(urls, destfiles, "libcurl", mode = "wb", ...) : > cannot open URL ' > https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz': > HTTP status was '404 Not Found' > Warning in download.packages(pkgs, destdir = tmpd, available = available, : > download of package ?e1071? failed > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide https://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.Hello, R 4.5.2 on Windows 11, sessionInfo at end. I cannot reproduce this on Windows 11 but I am getting another error. >Rscript -e "update.packages(oldPkgs=c('e1071'))" Error in contrib.url(repos, type) : trying to use CRAN without setting a mirror Calls: update.packages -> available.packages -> unique -> contrib.url Execution halted So I don't have a default mirror set. But after explicitly passing one, it works as expected. Rscript -e "update.packages(oldPkgs=c('e1071'), repos = 'https://cloud.r-project.org')" Warning: package 'mgcv' in library 'C:/Program Files/R/R-4.5.2/library' will not be updated e1071 : Version 1.7-16 installed in C:/Program Files/R/R-4/site-library Version 1.7-17 available at https://cloud.r-project.org Update? (Yes/no/cancel) There is a binary version available but the source version is later: binary source needs_compilation e1071 1.7-16 1.7-17 TRUE installing the source package 'e1071' trying URL 'https://cloud.r-project.org/src/contrib/e1071_1.7-17.tar.gz' Content type 'application/x-gzip' length 318056 bytes (310 KB) =================================================downloaded 310 KB The version being installed is e1071_1.7-17.tar.gz >Rscript -e "packageVersion('e1071')" [1] '1.7.17' >Rscript -e "sessionInfo()" R version 4.5.2 (2025-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows 11 x64 (build 22631) Matrix products: default LAPACK version 3.12.1 locale: [1] LC_COLLATE=Portuguese_Portugal.utf8 LC_CTYPE=Portuguese_Portugal.utf8 [3] LC_MONETARY=Portuguese_Portugal.utf8 LC_NUMERIC=C [5] LC_TIME=Portuguese_Portugal.utf8 time zone: Europe/Lisbon tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_4.5.2 Hope this helps, Rui Barradas
Duncan Murdoch
2025-Dec-21 10:11 UTC
[R] update.packages() fails due to searching for old versions of packages
I see the same thing in R 4.5.2 on MacOS Sequoia 15.7.2. The problem
happens in install.packages() as well, e.g. I get the same error with
install.packages("e1071")
A workaround is to ask for `type="source"`, as long as you're
prepared
to recompile the new package.
I think the issue is that there is no binary available for the latest
1.7-17 version. The database says the binary for 1.7-16 is available,
but in fact it is not.
Duncan Murdoch
On 2025-12-20 2:30 p.m., Michael McQuaid wrote:> When I try to update packages, the package manager appears to search for
> old versions of the packages, despite seemingly knowing about the existence
> of newer versions. Here is an example where I try to update the e1071
> package and it seems to recognize that the current version is 1.7-17 but
> then searches for and fails to find 1.7-16. This happens for every package
> I try to update, I've just included one here for brevity. I have tried
> several mirrors including wustl, utk, and iastate. I wonder if there is
> some file on my system pointing to the old version. I also tried updating
> from R 4.5.1 to 4.5.2, but the issue persists. I am on macOS Tahoe 26.2 on
> an M1 Macbook Pro.
>
> $ Rscript -e 'update.packages(oldPkgs=c("e1071"))'
> e1071 :
> Version 1.7-16 installed in /Users/mm223266/Library/R/arm64/4.5/library
> Version 1.7-17 available at https://cloud.r-project.org
> Update? (Yes/no/cancel)
> trying URL '
>
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz
> '
> Error in download.file(urls, destfiles, "libcurl", mode =
"wb", ...) :
> cannot open URL '
>
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz
> '
> In addition: Warning messages:
> 1: In download.file(urls, destfiles, "libcurl", mode =
"wb", ...) :
> downloaded length 0 != reported length 279
> 2: In download.file(urls, destfiles, "libcurl", mode =
"wb", ...) :
> cannot open URL '
>
https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.5/e1071_1.7-16.tgz':
> HTTP status was '404 Not Found'
> Warning in download.packages(pkgs, destdir = tmpd, available = available,
:
> download of package ?e1071? failed
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
https://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.