Corrupted package?

On 31 Oct 2018, at 08:22 , Patrick Connolly <p_connolly at 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   
{~._.~}                   Great minds discuss ideas    
_( Y )_  	         Average minds discuss events 
(:_~*~_:)                  Small minds discuss people  
(_)-(_)  	                      ..... Eleanor Roosevelt
	  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

On Oct 31, 2018, at 11:30 AM, peter dalgaard <pdalgd at gmail.com> wrote:

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 at 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