R help - May 2017 - Error in readRDS(dest) (was Re: Error with installed.packages with R 3.4.0 on Windows)

On Fri, 28-Apr-2017 at 07:04PM +0200, peter dalgaard wrote:

|> 
|> > On 28 Apr 2017, at 12:08 , Duncan Murdoch <murdoch.duncan at
gmail.com> wrote:
|> > 
|> > On 28/04/2017 4:45 AM, Thierry Onkelinx wrote:
|> >> Dear Peter,
|> >> 
|> >> It actually breaks install.packages(). So it is not that
innocent.
|> > 
|> > I don't think he meant that it is harmless, he meant that the fix
is easy, and is in place in R-patched and R-devel.  You should use R-patched and
you won't have the problem.
|> 
|> Read more carefully: I said that the _fix_ is harmless for this case, but
might not be so in general.
|> 
|> -pd


Apparently it isn't harmless.  
> install.packages("withr")
Error in readRDS(dest) : error reading from connection
>
> 
> sessionInfo()
R version 3.4.0 Patched (2017-05-19 r72713)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/hrapgc/local/R-patched/lib/libRblas.so
LAPACK: /home/hrapgc/local/R-patched/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8    
 [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8   
 [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] grDevices utils     stats     graphics  methods   base     

other attached packages:
[1] lattice_0.20-35

loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0    grid_3.4.0    
> 
Has anyone a workaround?

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___    Patrick Connolly   
 {~._.~}                   Great minds discuss ideas    
 _( Y )_  	         Average minds discuss events 
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)  	                      ..... Eleanor Roosevelt
	  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

On 05/22/2017 05:10 AM, Patrick Connolly wrote:
> On Fri, 28-Apr-2017 at 07:04PM +0200, peter dalgaard wrote:
>
> |>
> |> > On 28 Apr 2017, at 12:08 , Duncan Murdoch <murdoch.duncan at
gmail.com> wrote:
> |> >
> |> > On 28/04/2017 4:45 AM, Thierry Onkelinx wrote:
> |> >> Dear Peter,
> |> >>
> |> >> It actually breaks install.packages(). So it is not that
innocent.
> |> >
> |> > I don't think he meant that it is harmless, he meant that
the fix is easy, and is in place in R-patched and R-devel.  You should use
R-patched and you won't have the problem.
> |>
> |> Read more carefully: I said that the _fix_ is harmless for this case,
but might not be so in general.
> |>
> |> -pd
>
>
> Apparently it isn't harmless.
>
>> install.packages("withr")
> Error in readRDS(dest) : error reading from connection
that seems like a plain-old network connectivity issue, or perhaps an 
issue with the CRAN mirror you're using. Can you debug on your end, e.g,.

   options(error=recover)
   install.packages("withr")
   ...

then select the 'frame' where the error occurs, look around

   ls()

find the value of 'dest', and e.g., try to open dest in your  browser.

Martin Morgan
>>
>
>>
>> sessionInfo()
> R version 3.4.0 Patched (2017-05-19 r72713)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.5 LTS
>
> Matrix products: default
> BLAS: /home/hrapgc/local/R-patched/lib/libRblas.so
> LAPACK: /home/hrapgc/local/R-patched/lib/libRlapack.so
>
> locale:
>  [1] LC_CTYPE=en_NZ.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_NZ.UTF-8        LC_COLLATE=en_NZ.UTF-8
>  [5] LC_MONETARY=en_NZ.UTF-8    LC_MESSAGES=en_NZ.UTF-8
>  [7] LC_PAPER=en_NZ.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] grDevices utils     stats     graphics  methods   base
>
> other attached packages:
> [1] lattice_0.20-35
>
> loaded via a namespace (and not attached):
> [1] compiler_3.4.0 tools_3.4.0    grid_3.4.0
>>
>
> Has anyone a workaround?
>

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On Mon, 22-May-2017 at 05:43AM -0400, Martin Morgan wrote:

|> On 05/22/2017 05:10 AM, Patrick Connolly wrote:

|> >Apparently it isn't harmless.
|> >
|> >>install.packages("withr")
|> >Error in readRDS(dest) : error reading from connection
|> 
|> that seems like a plain-old network connectivity issue, or perhaps
|> an issue with the CRAN mirror you're using. Can you debug on your
|> end, e.g,.
|> 
|>   options(error=recover)
|>   install.packages("withr")
|>   ...
|> 
|> then select the 'frame' where the error occurs, look around
|> 
|>   ls()
|> 
|> find the value of 'dest', and e.g., try to open dest in your 
browser.

This is what I get
>   options(error=recover)
>   install.packages("withr")
^C

Enter a frame number, or 0 to exit   

1: install.packages("withr")
2: available.packages(contriburl = contriburl, method = method)
3: tryCatch({
    download.file(url = paste0(repos, "/PACKAGES.rds"), destfile
4: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatchOne(expr, names, parentenv, handlers[[1]])
6: doTryCatch(return(expr), name, parentenv, handler)
7: download.file(url = paste0(repos, "/PACKAGES.rds"), destfile =
dest, method

Selection: 7
Called from: eval(substitute(browser(skipCalls = skip), list(skip = 7 - which)),
    envir = sys.frame(which))
Browse[1]> dest
Error during wrapup: object 'dest' not found

That indicates to me that the problem is further back but I have no
idea how make use of that information.


Browse[1]> ls()
[1] "cacheOK"  "destfile" "extra"   
"method"   "mode"     "quiet"    "url"
Browse[1]> url
[1] "http://cran.stat.auckland.ac.nz/src/contrib/PACKAGES.rds"
Browse[1]> destfile
[1]
"/tmp/RtmpplJSrB/repos_http%3A%2F%2Fcran.stat.auckland.ac.nz%2Fsrc%2Fcontrib.rds"
Browse[1]> 

The destfile above is zero-length and I suppose is where dest is
intended to end up.

Where else should I be looking?  Earlier installations never had this
issue so I don't have anything to compare.

TIA
-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___    Patrick Connolly   
 {~._.~}                   Great minds discuss ideas    
 _( Y )_  	         Average minds discuss events 
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)  	                      ..... Eleanor Roosevelt
	  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.