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Issues with R3.5.2

13 messages · Martin Maechler, Janh Anni, Jeff Newmiller +1 more

Janh Anni
# 
Dear R Experts,

I use Windows 10 and just installed the new R version, R3.5.2 but when I
tried to load a data file using read.table, I got an error message like
this:

*Error in file(file, "rt") : cannot open the connection*
*In addition: Warning message:*
*In file(file, "rt") :*
*  cannot open file 'StreamPCB.dat': No such file or directory*

Also, I couldn't install packages using install.packages as usual, unless I
run R as Administrator

I wonder if anyone else had the same issues and any suggestions how to fix?

Thanks a lot
Janh
Jeff Newmiller
# 
Did you by any chance use Run As Administrator to install R? If so then you need to uninstall it and delete all files created by it (e.g. Documents/R/win-lib/3.5/) and re-install using UAC as prompted.
On December 22, 2018 5:10:27 PM PST, Janh Anni <annijanh at gmail.com> wrote:

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Janh Anni
    

    

      
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Hi Jeff,

No, during the installation, there was not an option to Run as
Administration.  But *after *installation, I found that if I selected Run
as Administrator, then I could install packages using install.packages as
usual without problems.

Thanks
Janh

On Sat, Dec 22, 2018 at 8:26 PM Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
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That normally only occurs if you have at some time used elevated permissions, beyond which point you fall into a downward spiral of more permissions trouble. You are apparently already in trouble, whether it was of your own making or due to a bug in the installer.

Also, never update the system R package library... always use a personal library.

        
On December 22, 2018 6:01:44 PM PST, Janh Anni <annijanh at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Janh Anni
    

    

      
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This issue only came up after I installed R3.5.2. Never had any problems
with previous installations.  So it is likely a bug in the current
version.  Any suggestions what to do now?

On Sat, Dec 22, 2018 at 11:06 PM Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
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You could delete your 3.5 personal package library (using the File Explorer with Run as Admin if necessary) and re-install your packages without running as Admin. If that does not work try uninstalling R and re-installing 3.5.1.

        
On December 22, 2018 8:16:11 PM PST, Janh Anni <annijanh at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Martin Maechler
    

    

      
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> You could delete your 3.5 personal package library (using
    > the File Explorer with Run as Admin if necessary) and
    > re-install your packages without running as Admin. If that
    > does not work try uninstalling R and re-installing 3.5.1.

I tend to think that Jeff is right and you, Janh, *have* changed
something on your Windows box, or inadvertently during
installation of R.

I've tried our Windows Server installation (where I consciously do install
things as admin for all win server users to use it), and I can
install packages fine as simple user -- into the personal
library that is created after asking for user confirmation.

Also, given the number of R users and the (unfortunately still) high
percentage of Windows users among them,  I strongly assume we
would would have heard of it if this was a common problem..
(But then I may be wrong if the Windows users are "slow" to
 update their R version)

Martin

Merry Christmas!

    > On December 22, 2018 8:16:11 PM PST, Janh Anni

        
> <annijanh at gmail.com> wrote:

        
>> This issue only came up after I installed R3.5.2. Never
    >> had any problems with previous installations.  So it is
    >> likely a bug in the current version.  Any suggestions
    >> what to do now?
    >> 
    >> On Sat, Dec 22, 2018 at 11:06 PM Jeff Newmiller

        
>> <jdnewmil at dcn.davis.ca.us> wrote:

        
>> 
    >>> That normally only occurs if you have at some time used
    >>> elevated permissions, beyond which point you fall into a
    >>> downward spiral of
    >> more
    >>> permissions trouble. You are apparently already in
    >>> trouble, whether
    >> it was
    >>> of your own making or due to a bug in the installer.
    >>> 
    >>> Also, never update the system R package
    >>> library... always use a
    >> personal
    >>> library.
    >>> 
    >>> On December 22, 2018 6:01:44 PM PST, Janh Anni
    >>> <annijanh at gmail.com>

        
>> wrote:

        
>>> >Hi Jeff,
    >>> >
    >>> >No, during the installation, there was not an option to
    >>> Run as >Administration.  But *after *installation, I
    >>> found that if I
    >> selected
    >>> >Run >as Administrator, then I could install packages
    >>> using
    >> install.packages
    >>> >as >usual without problems.
    >>> >
    >>> >Thanks >Janh
    >>> >
    >>> >On Sat, Dec 22, 2018 at 8:26 PM Jeff Newmiller

        
>>> ><jdnewmil at dcn.davis.ca.us> >wrote:

        
>>> >
    >>> >> Did you by any chance use Run As Administrator to
    >>> install R? If so >then >> you need to uninstall it and
    >>> delete all files created by it (e.g.  >>
    >>> Documents/R/win-lib/3.5/) and re-install using UAC as
    >>> prompted.
    >>> >>
    >>> >> On December 22, 2018 5:10:27 PM PST, Janh Anni
    >> <annijanh at gmail.com>
    >>> >wrote: >> >Dear R Experts,
    >>> >> >
    >>> >> >I use Windows 10 and just installed the new R
    >>> version, R3.5.2 but >when >> >I >> >tried to load a data
    >>> file using read.table, I got an error
    >> message
    >>> >like >> >this:
    >>> >> >
    >>> >> >*Error in file(file, "rt") : cannot open the
    >>> connection* >> >*In addition: Warning message:* >> >*In
    >>> file(file, "rt") :* >> >* cannot open file
    >>> 'StreamPCB.dat': No such file or directory*
    >>> >> >
    >>> >> >Also, I couldn't install packages using
    >>> install.packages as
    >> usual,
    >>> >> >unless I >> >run R as Administrator
    >>> >> >
    >>> >> >I wonder if anyone else had the same issues and any
    >>> suggestions
    >> how
    >>> >to >> >fix?
    >>> >> >
    >>> >> >Thanks a lot >> >Janh
    >>> >> >
    >>> >> > [[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 >>
    >>> >http://www.R-project.org/posting-guide.html >> >and
    >>> provide commented, minimal, self-contained, reproducible
    >> code.
    >>> >>
    >>> >> --
    >>> >> Sent from my phone. Please excuse my brevity.
    >>> >>
    >>> 
    >>> --
    >>> Sent from my phone. Please excuse my brevity.
    >>> 

    > -- 
    > Sent from my phone. Please excuse my brevity.

    > ______________________________________________
    > 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
    > http://www.R-project.org/posting-guide.html and provide
    > commented, minimal, self-contained, reproducible code.

  
  


  


      

    

    
1 day later

    

      
      

        


  

        

      Janh Anni
    

    

      
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Hello Jeff, Martin,

I deleted 3.5.2 as suggested and tried 3.5.1 but still had the same
problems.  I still couldn't use read.table to load a data file and still
had an error message when I tried to install a package. Usually after
installing a new version of R, I would go to the R icon on the desktop,
right click on it, click on Properties and then specify the folder that
contains my data files in the "Start in" box, so that R automatically has
access to my data files.  Could that possibly be causing problems with
these newer versions of R? Also, there?s never a prompt during the
installation to Run as Administrator, so that could not possibly be the
cause

 I also just tried Version 3.4.4, and had no problems whatsoever either
with using read.table to load data files or downloading packages.  So there
must be some changes from version 3.5 onward that created the issues.
Hopefully this will be looked at more closely by the team with  a view to
resolving the issues

Thanks,

Janh

On Sun, Dec 23, 2018 at 1:31 AM Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
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On December 24, 2018 11:14:40 AM PST, Janh Anni <annijanh at gmail.com> wrote:

            

      
      
      
    

        
No.

            

      
      
      
    

        
Yes, you have to go out of your way to Run As Administrator (RAA). However, regardless of how you initially encountered a problem, once you did that there could be any number of files contaminated with permissions issues.

Specifically, I said to delete your 3.5 personal package library, but your description is not specific so I suspect you may not have done that. However, any file modified by you intentionally or not while using RAA could be causing your problems now, so now it is up to you to find those files somehow.

            

      
      
      
    

        
I doubt the "team" will spend much time looking at this based on your descriptions so far. They need something reproducible, and the fact that you already used RAA to "fix" the problem makes anything you did prior to that almost impossible to reproduce.

fortunes:::fortune(337)

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Janh Anni
    

    

      
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I am sorry I forgot to mention - I just looked in the
Documents\R\win-Library directory and only found folders for previous R
versions, specifically R3.0, 3.1 and 3.4.  So I must have deleted the R3.5
folder as you initially advised or it was removed during the
un-installation.  Unless I am misunderstanding what you mean by the R3.5
personal package library?  Thanks again

On Mon, Dec 24, 2018 at 4:28 PM Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Jeff Newmiller
    

    

      
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Yes, that would be the personal library.

There is one question in the installer that asks if you would like to create a personal library... I have always said yes, but I could imagine that saying no could lead to problems.

        
On December 24, 2018 2:43:24 PM PST, Janh Anni <annijanh at gmail.com> wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
    

      
      
    

  


  


      

    

    

      
      

        


  

        

      Janh Anni
    

    

      
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Oddly enough, I must have done a dozen installations and re-installations
since this issue arose but don't recall ever being asked if I wished to
create a personal library.  I do recall being offered the option to install
R to a different folder other than the usual Program Files folder, or to
choose custom installation rather than the usual defaults, or to create a
desk shortcut or quick launch shortcut and so on.  But this whole RAA issue
is sobering - the fact that clicking Run as Administrator at some point or
the other, either intentionally or inadvertently can suddenly render R
inoperable ...........

On Mon, Dec 24, 2018 at 6:09 PM Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Amit Mittal
    

    

      
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It asks you when you install packages after loading the current workspace TYPICALLY WHEN CORE PACKAGES ARE NOT SUFFICIENT

BR
Amit



Amit Mittal 
5th year - PhD in Finance and Accounting 
IIM Lucknow 
http://ssrn.com/author=2665511 
*Top 10%, downloaded author since July 2017



From: Janh Anni
Sent: Tuesday, December 25, 2018 5:07 AM
To: Jeff Newmiller
Cc: r-help at r-project.org
Subject: Re: [R] Issues with R3.5.2

Oddly enough, I must have done a dozen installations and re-installations
since this issue arose but don't recall ever being asked if I wished to
create a personal library.  I do recall being offered the option to install
R to a different folder other than the usual Program Files folder, or to
choose custom installation rather than the usual defaults, or to create a
desk shortcut or quick launch shortcut and so on.  But this whole RAA issue
is sobering - the fact that clicking Run as Administrator at some point or
the other, either intentionally or inadvertently can suddenly render R
inoperable ...........

On Mon, Dec 24, 2018 at 6:09 PM Jeff Newmiller <jdnewmil at dcn.davis.ca.us>
wrote:

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        
______________________________________________
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 http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.