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cannot install rgdal after updating to fedora32

4 messages · Roger Bivand, Veronica Andreo, Bennet Fauber

Original
Veronica Andreo
# 
Hi Bennet,
[cc-ing the list too]

Thanks for the explanations about the config.log file

I tried with your suggestion, but the error still appears as originally
reported

Best,
Vero

El dom., 28 jun. 2020 a las 17:00, Bennet Fauber (<bennet at umich.edu>)
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      Roger Bivand
    

    

      
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On Sun, 28 Jun 2020, Veronica Andreo wrote:

        

            

      
      
      
    

        
Please try install.packages("rgdal", repos="http://R-Forge.R-project.org", 
configure.args="--disable-loadflags") to be sure to get the current 
version.

Roger

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Veronica Andreo
    

    

      
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El dom., 28 jun. 2020 a las 19:20, Roger Bivand (<Roger.Bivand at nhh.no>)
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Yes, this works! rgdal is installed properly now :)
I didn't understand how to properly specify the command before, apologies.
And many thanks!!!

Vero

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Bennet Fauber
    

    

      
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Vero, Ista, and Roger,

I used Ista's help to get a Docker container in which I could try this.

Yes, there does seem to be something wrong with the R packages for
Fedora 32, as I am also getting this when installing packages (not
just rgdal)

Warning in file.create(f.tg) :
  cannot create file '/usr/share/doc/R/html/packages.html', reason 'No
such file or directory'
Warning in utils::make.packages.html(.Library, docdir = R.home("doc")) :
  cannot update HTML package index

I believe that they (Fedora) also did not include building the HTML
documentation for R.

The particular LDFLAG that is causing the issue seems to be this one,

    LDFLAGS='-specs=/usr/lib/rpm/redhat/redhat-hardened-ld'

as that fails with the same message, but using all the others (the
following line used the additional printing of LDFLAGS, thank you
Roger!), as in the following,

    install.packages('rgdal', repos="https://R-Forge.R-project.org",
configure.vars=c("LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now'"))

does work.  I don't know if that helps you any, Roger, but I thought
that might help if someone reports this to Fedora.  I agree with you
that they probably should be dropped.

I am confused by them having the compiler syntax `-Wl,<linker options,
comma separated>`.  I think if those were CFLAGS, that would result in
a line like

    ld -z relro --as-needed -z now

where these are the explanations from the `ld` man page.

    -z relro                    Create RELRO program header (default)
    -z now                      Mark object non-lazy runtime binding
    --as-needed                 Only set DT_NEEDED for following
dynamic libs if used

I am not working on Fedora, so my ability to pursue further is limited.

Thanks, Roger, for providing a solution so quickly!

-- bennet

        
On Sun, Jun 28, 2020 at 1:30 PM Veronica Andreo <veroandreo at gmail.com> wrote: