[R] Corrupted package?

[David Winsemius]

> On Oct 31, 2018, at 11:30 AM, peter dalgaard <pdalgd using 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 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

Did you misspell "checkBuilt"? You should always present the transcript to prevent such questions.

-- 
David.


>> 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
>> 	  
>> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>> 
>> ______________________________________________
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>> and provide commented, minimal, self-contained, reproducible code.
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd.mes using cbs.dk  Priv: PDalgd using gmail.com
> 
> ______________________________________________
> R-help using 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.