Re: [R] Corrupted package?[solved]

[Patrick Connolly]

On Thu, 01-Nov-2018 at 08:51PM +1300, Patrick Connolly wrote:

|> On Wed, 31-Oct-2018 at 07:30PM +0100, peter dalgaard 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

[...]

I searched and found someone had a message about a corrupted package
and found the problem disappeared when R was restarted.  So, I tried
that, And. sure enough, it worked!

It would have been good to get some understanding of those strange
file sizes, but I suspect it will remain one of Life's little
mysteries.

That might help someone else who gets a corrupt package message.

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___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.

Re: [R] Corrupted package?

[Patrick Connolly]

On Wed, 31-Oct-2018 at 07:30PM +0100, peter dalgaard 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(?).
|> 

That's very strange.  If I look further back, the large size is
historical in my experience.

ll `locate pkgconfig.rdb`

-rw-r--r-- 1 hrapgc hrapgc  5356 Aug  8  2017 
/home/hrapgc/local/R-3.4.4/library/pkgconfig/help/pkgconfig.rdb
-rw-r--r-- 1 hrapgc hrapgc 13377 Aug  8  2017 
/home/hrapgc/local/R-3.4.4/library/pkgconfig/R/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

Yet when I look at my home machine that I use sometimes:

> ll `locate pkgconfig.rdb`
-rw-r--r-- 1 pat pat  5349 Sep 13  2017 
/home/pat/local/R-3.2.3/library/pkgconfig/help/pkgconfig.rdb
-rw-r--r-- 1 pat pat 13374 Sep 13  2017 
/home/pat/local/R-3.2.3/library/pkgconfig/R/pkgconfig.rdb
-rw-r--r-- 1 pat pat  5355 Feb  2  2018 
/home/pat/local/R-3.4.3/library/pkgconfig/help/pkgconfig.rdb
-rw-r--r-- 1 pat pat 13392 Feb  2  2018 
/home/pat/local/R-3.4.3/library/pkgconfig/R/pkgconfig.rdb
-rw-r--r-- 1 pat pat  5356 Apr 13  2018 
/home/pat/local/R-3.4.4/library/pkgconfig/help/pkgconfig.rdb
-rw-r--r-- 1 pat pat 13392 Apr 13  2018 
/home/pat/local/R-3.4.4/library/pkgconfig/R/pkgconfig.rdb
-rw-r--r-- 1 pat pat  5351 Jul  3 20:38 
/home/pat/local/R-3.5.0/library/pkgconfig/help/pkgconfig.rdb
-rw-r--r-- 1 pat pat  4349 Jul  3 20:38 
/home/pat/local/R-3.5.0/library/pkgconfig/R/pkgconfig.rdb

Similar sizes, but not corresponding to the same R versions!!

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

Another interesting story:

> install.packages("pkgconfig")
trying URL 'http://cran.stat.auckland.ac.nz/src/contrib/pkgconfig_2.0.2.tar.gz'
Content type 'application/x-gzip' length 6024 bytes
==
downloaded 6024 bytes

This session PID is 24632:
begun at 2018-11-01 11:11:41:
* installing *source* package ‘pkgconfig’ ...
** package ‘pkgconfig’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Error in unloadNamespace(pkg_name) : 
  namespace ‘pkgconfig’ is imported by ‘dplyr’ so cannot be unloaded
* removing ‘/home/hrapgc/local/R-3.5.1/library/pkgconfig’
* restoring previous ‘/home/hrapgc/local/R-3.5.1/library/pkgconfig’

The downloaded source packages are in
‘/tmp/RtmpQ3KfLM/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("pkgconfig") :
  installation of package ‘pkgconfig’ had non-zero exit status



 So I used this approach:

echo 
'options(repos=list(CRAN="https://cloud.r-project.org;));install.packages("pkgconfig",
 depend = TRUE)' | R --vanilla

That was "successful", even if corrupted.

|> 
|> And, BTW, which system are you using?
|> 

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/hrapgc/local/R-3.5.1/lib/libRblas.so
LAPACK: /home/hrapgc/local/R-3.5.1/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_NZ.UTF-8   LC_NUMERIC=C  
 [3] LC_TIME=en_NZ.UTF-8LC_COLLATE=en_NZ.UTF-8
 [5] LC_MONETARY=en_NZ.UTF-8LC_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] bindrcpp_0.2.2 ggthemes_4.0.1 cowplot_0.9.3  ggrepel_0.8.0 
 [5] quanteda_1.3.4 topicmodels_0.2-7  rvest_0.3.2xml2_1.2.0
 [9] wordcloud_2.6  RColorBrewer_1.1-2 wordcloud2_0.2.1   tm_0.7-5  

Re: [R] Corrupted package?

[David Winsemius]

> On Oct 31, 2018, at 11:30 AM, peter dalgaard  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  
>> 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
>>
>> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>> 
>> __
>> R-help@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.
> 
> -- 
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
> 
> __
> R-help@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.

__
R-help@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.

Re: [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  
> 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
> 
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
> 
> __
> R-help@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.

-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

__
R-help@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.

[R] Corrupted package?

[Patrick Connolly]

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
  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

__
R-help@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.