[R] Corrupted package?

[peter dalgaard]

Hm, a source install to r-devel gave me 

Peter-Dalgaards-MacBook-Air:BUILD pd$ ls -l library/pkgconfig/R/pkgconfig.rdb
-rw-r--r--  1 pd  staff  4515 Oct 31 19:15 library/pkgconfig/R/pkgconfig.rdb
Peter-Dalgaards-MacBook-Air:BUILD pd$ ls -l library/pkgconfig/help/pkgconfig.rdb
-rw-r--r--  1 pd  staff  5748 Oct 31 19:15 library/pkgconfig/help/pkgconfig.rdb

and an install to R_3.4.1 (yes, 4...) said

$ ls -l /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/*/pkgconfig.rdb
-rw-r--r--  1 pd  admin  2432 Aug 17 11:36 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/R/pkgconfig.rdb
-rw-r--r--  1 pd  admin  5412 Aug 17 11:36 /Library/Frameworks/R.framework/Versions/3.4/Resources/library/pkgconfig/help/pkgconfig.rdb

I.e., it looks like it is the larger of your file sizes that is anomalous(?).

Did you try a straight install with install.packages("pkgconfig")? 

And, BTW, which system are you using?

-pd

> On 31 Oct 2018, at 08:22 , Patrick Connolly <p_connolly using slingshot.co.nz> wrote:
> 
> 
> I got this message while using a dplyr mutate call: 
> 
> Error in get0(oNam, envir = ns) : 
>  lazy-load database '/home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb' is corrupt
> 
> I had only just installed R-3.5.1 and updated the packages (using the
> function update.packages with the checkBuild parameter to TRUE) in the
> library I use with that version.  So, I checked the size of
> pkgconfig.rdb with the previous version from the bash prompt:
> 
>> ll `locate pkgconfig.rdb`
> 
> -rw-r--r-- 1 hrapgc hrapgc  5335 May  8 14:06 /home/hrapgc/local/R-3.5.0/library/pkgconfig/help/pkgconfig.rdb
> -rw-r--r-- 1 hrapgc hrapgc 15669 May  8 14:06 /home/hrapgc/local/R-3.5.0/library/pkgconfig/R/pkgconfig.rdb
> -rw-r--r-- 1 hrapgc hrapgc  5359 Oct 31 16:12 /home/hrapgc/local/R-3.5.1/library/pkgconfig/help/pkgconfig.rdb
> -rw-r--r-- 1 hrapgc hrapgc  4367 Oct 31 16:12 /home/hrapgc/local/R-3.5.1/library/pkgconfig/R/pkgconfig.rdb
> 
> While the pkgconfig.rdb filesize in the help directory is nearly
> identical in size to that in R-3.5.0 (and previous versions) the one
> in the R directory is very much smaller.  So the error message
> probably makes sense.
> 
> The question is: how could that have happened?  I removed the package
> and reinstalled it, but that made no difference.  Is this documented
> anywhere?
> 
> TIA
> -- 
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
>   ___    Patrick Connolly   
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-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
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