Skip to content

PACKAGES file missing

10 messages · Joel Jacobson, Dr Eberhard W Lisse, Uwe Ligges +3 more

Original
Joel Jacobson
# 
Hi,

I'm a R newbie having some problems.

The special PACKAGES file seems to be missing for version 3.6:
https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES

This is causing install.packages() to fail, which forces installation from source:
also installing the dependencies ?sys?, ?ps?, ?markdown?, ?askpass?, ?processx?, ?knitr?, ?yaml?, ?htmltools?, ?base64enc?, ?curl?, ?mime?, ?openssl?, ?callr?, ?fs?, ?rmarkdown?, ?haven?, ?httr?, ?jsonlite?, ?readxl?, ?reprex?, ?rvest?, ?xml2?

Warning: unable to access index for repository https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6:
 cannot open URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.6/PACKAGES'
Packages which are only available in source form, and may need
 compilation of C/C++/Fortran: ?sys? ?ps? ?markdown? ?askpass?
 ?processx? ?yaml? ?htmltools? ?base64enc? ?curl? ?mime? ?openssl?
 ?fs? ?haven? ?jsonlite? ?readxl? ?xml2?
Do you want to attempt to install these from sources? (Yes/no/cancel)

Have I made som mistake or is this a real problem?

Many thanks for any help.

Best regards,

Joel Jacobson
4 days later
Dr Eberhard W Lisse
# 
Joel,

This should be a temporary issue, I can reach the failed URL.

	local({
	+   r <- getOption("repos")
	+   r["CRAN"] <- "https://cloud.r-project.org/"
	+   options(repos = r)
	+ })

	> install.packages("tidyverse")
	[...]
	trying URL 'https://cloud.r-project.org/src/contrib/tidyverse_1.3.0.tar.gz'
	Content type 'application/x-gzip' length 712837 bytes (696 KB)
	[...]

Did an upgrade (of packages) from within RStudio from same and that also
worked out well.

So, in the first instance, try again :-)-O

CRAN has many mirrors, but I strongly advise for using RStudio which
figures this out for themselves in addition to many other advantages
(such as sponsoring the mirroring service in the first place), so you
could try the closest mirror from https://cran.r-project.org/mirrors.html.

greetings, el
On 07/02/2020 18:54, Joel Jacobson wrote:
[...]
[...]
Uwe Ligges
#
On 12.02.2020 10:51, Dr Eberhard W Lisse wrote:
R Studio sponsors cloud.... but not all mirrors.

For myself, I would not use RStudio as it does what you describe: Lots 
of things I do not want to be done. So I typically never give advise 
which editor or environment to use, as that is a matter of taste.

Best,
Uwe Ligges
Dr Eberhard W Lisse
# 
You didn't give any advice. I did :-)-O And it does what the OP asked 
for :-)-O

I do some things in the command line R or even running stuff as Rscript,
but for development (and updates) an IDE such as RStudio is very helpful
even if it is not die reine Lehre :-)-O

el
On 12/02/2020 12:53, Uwe Ligges wrote:
[...]
[...]
Joel Jacobson
# 
The file was missing for sure from all mirrors also the main one. My guess is you have a cronjob that builds the new PACKAGES file that removes the old file before the new one has been created.

Best regards,

Joel
On Wed, Feb 12, 2020, at 17:01, Dr Eberhard W Lisse wrote:
Kind regards,

Joel
Uwe Ligges
#
On 12.02.2020 12:42, Joel Jacobson wrote:
Note that the mirrors do not sync at the same time. So even if the 
PACKAGES file was missing for few seconds or even minutes, it ios very 
unlikely that all mirrors lost it, too.

Best,
Uwe Ligges
Peter Dalgaard
# 
[See note from Simon Urbanek on February 7. All is related to Simon and his equipment being turned upside down a few weeks ago. -pd]

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
Thanks, indeed, there were some disruptions, but now the build machine has its own dedicated port and location in Auckland so hopefully things will settle.
I have also fortified the sync scripts to not sync with the Mac master if there is no PACKAGES file to avoid such issues in case something goes wrong.
That said, the issue should be resolved now - please use
https://mac.R-project.org
as the mirror for mac binaries until all mirrors catch up.

Cheers,
Simon

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Jeroen Ooms
    

    

      
      #
    

  


  

      
On Thu, Feb 13, 2020 at 1:55 AM Simon Urbanek

        
<simon.urbanek at r-project.org> wrote:

            

      
      
      
    

        
Thanks, that's great news.

Minor note: the server no longer allows for directory listing, is this
on purpose? E.g.
https://mac.r-project.org/bin/macosx/el-capitan/contrib/3.6/ . It's
sometimes useful to be able to see what is on the server, e.g. to see
the timestamps or file sizes of the packages.

  
  


  


      

    

    

      
      

        


  

        

      Simon Urbanek
    

    

      
      #
    

  


  

      
I kept getting bug bounties on the server since open directory listing are considered unsafe. For some parts we have a generated index files (e.g., /src and /libs), but not everywhere. I'll see if white-listing some locations would fly.

Thanks,
Simon