R tries to install old not available packages from Artifactory

Question

Solution

Delete the .RDS in the Artifactory cache.

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Problem

I have a very weird issue with using R 3.6.2 on Ubuntu and a corporate mirror of CRAN. Let's say I run the following command:

install.packages('rlang')

What I get back is that the version 0.4.2 could not be found. When I look into the repository manually I find that 0.4.2 indeed does not exist, but 0.4.3 does. First I thought that something is wrong with the PACKAGES file where the repository stores the index. But I looked into it and it points to the correct and available version of rlang.

From where does R gets the version number it puts into the query URL when install.packages() is executed?

Updates

I tried install.packages("http://private.com/src/contrib/rlang_0.4.3.tar.gz", repos=NULL) and it works. Next I will try to replicate the issue in new Ubuntu environment. Maybe I messed up while installing R and upgrading it to 3.6.2

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When I downgrade to R version 3.4.4 the issue persists. Maybe it has something to do with the corporate mirror? I will try an official one.

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Thanks to Dirks answer I found out with available.packages() that something is wrong with the mirror and not the R installation.

> AP <- available.packages()
> res <- AP[ AP[,1] == "rlang", ]
> str(res)
 Named chr [1:17] "rlang" "0.4.2" NA "R (>= 3.2.0)" NA NA ...
 - attr(*, "names")= chr [1:17] "Package" "Version" "Priority" "Depends" ...

Since the readable version of PACKAGES in the mirror contains 0.4.3 I assume that the PACKAGES.rds is at fault. Next I will try to read in that object to confirm my presumption.

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Dirk recommended me to check the timestamps of the indices and I think I found the issue. 0.4.3 was released a short time ago. While the readable index was updated just few others ago, the .rds file (probably used by R) has not been updated since 2020-01-16. And so R tries to download a version that is not part of the repository anymore.

Now I wonder who is in charge of updating the RDS file? The repository itself? I'll report back in the next time... Maybe the problem resolves itself after a random batch job updates the repository.

The rlang package:

The timestamps:

The PACKAGES content:

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I manually downloaded PACKAGES.rds and used readRDS() on it. It points to the old version. I also checked the repo that is mirrored. Its PACKAGES.rds points to the correct version. In addition I made sure that the issue persists independent from the distribution and image I'm using.

Answer 1

You can ask R that very question! The available.packages() function tells you "everything" it knows, and one entry is 'Repository'.

So:

R> AP <- available.packages()       ## all known packages given options("repos")
R> res <- AP[ AP[,1] == "rlang", ]  ## find rlang
R>
R> str(res)
 Named chr [1:17] "rlang" "0.4.3" NA "R (>= 3.2.0)" NA NA ...
 - attr(*, "names")= chr [1:17] "Package" "Version" "Priority" "Depends" ...
R> 
R> names(res)
 [1] "Package"               "Version"              
 [3] "Priority"              "Depends"              
 [5] "Imports"               "LinkingTo"            
 [7] "Suggests"              "Enhances"             
 [9] "License"               "License_is_FOSS"      
[11] "License_restricts_use" "OS_type"              
[13] "Archs"                 "MD5sum"               
[15] "NeedsCompilation"      "File"                 
[17] "Repository"           
R> 
R> res["Repository"]
                               Repository 
"https://cloud.r-project.org/src/contrib" 
R> 

No surprise here as that is the default repository for per the default configuration I use (and encode in the Debian / Ubuntu package).

Answer 2

if you do

?install.packages()

it will give you some information on the function that does the retrieval, there is a "repo" argument you can input. Most of the time if I have package install issues and are not TOO worried about exact versions running a:

install.packages("rlang", dependencies = TRUE)

usually does well for me