[R-SIG-Mac] GitHub Action on macOS cannot find the latest version of a package

Thu Nov 21 20:17:23 CET 2024

Spencer,

I strongly recommend NOT selecting compilation from sources as that is non-trivial and requires a whole list of tools and libraries that you don't have - I would recommend using type="binary" in install.packages/update.packages to make sure the get the versions that haven been checked on CRAN. I’m pretty sure what you reported was just a temporary issue anyway.

If you really want to compile development versions of R packages from sources, then you'll need to follow the basic R documentation (R-admin C.3) with respect to the required tools like gfortran (see also https://mac.r-project.org/tools/ ) and also install all dependent libraries (see https://mac.r-project.org/bin/ for the version used by CRAN).

Cheers,
Simon

(sorry for the late reponse - this was stuck in my outbox for a week)

> On Nov 15, 2024, at 11:35 AM, Spencer Graves <spencer.graves using prodsyse.com> wrote:
> 
> Hello, All:
> 
> 
> 	  The problem with "update.packages()" described in my email below seems to impact also GitHub Action on macOS for my "Ecdat" package:[2] It cannot find a function I added to the most recent release of another package (‘[Ecfun]{findCountry}’).[3] It works fine on Windows and Ubuntu.
> 
> 
> 	  Suggestions?
> 	  Thanks,
> 	  Spencer Graves
> 
> 
> p.s. Thanks to Duncan Murdoch, who noted that 'install.packages("curl", type="source")' can overcome the problem mentioned in other question to R-SIG-Mac earlier today (copied below). To be precise, it worked for the first 4 of the 6 packages that were not being downloaded properly under macOS via "update.packages()":
> 
> 
> 	  *  'install.packages("slam", type="source")' aborted because, "library 'gfortran' not found".
> 
> 
> 	  * 'install.packages("terra", type="source")' aborted, complaining 'configure: error: gdal-config not found or not executable.'
> 
> 
> 	  If I needed the latest version of "slam", I would invest the time to figure out why "library 'gfortran' not found". I've had it before. I don't know why it's not available now. Similarly, if I needed the latest version of "terra", I would spend time trying to fix that.
> 
> 
> [2]
> 
> 
> https://github.com/sbgraves237/Ecdat
> 
> 
> [3]
> 
> 
> https://github.com/sbgraves237/Ecdat/actions/runs/11844366708/job/33007415589
> 
> 
> -------- Forwarded Message --------
> Subject: update.packages() re-downloading old versions
> Date: Thu, 14 Nov 2024 12:41:08 -0600
> From: Spencer Graves <spencer.graves using prodsyse.com>
> To: r-sig-mac <r-sig-mac using r-project.org>
> 
> 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)
>> 
> 
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