Corrupted package?

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Corrupted package?

Patrick Connolly-4

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

______________________________________________
[hidden email] 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.
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Re: Corrupted package?

Peter Dalgaard-2
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 <[hidden email]> 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
>  
> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>
> ______________________________________________
> [hidden email] 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: [hidden email]  Priv: [hidden email]

______________________________________________
[hidden email] 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.
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Re: Corrupted package?

David Winsemius


> On Oct 31, 2018, at 11:30 AM, peter dalgaard <[hidden email]> 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 <[hidden email]> 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
>>  
>> ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
>>
>> ______________________________________________
>> [hidden email] 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: [hidden email]  Priv: [hidden email]
>
> ______________________________________________
> [hidden email] 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.

______________________________________________
[hidden email] 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.
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Re: Corrupted package?

Patrick Connolly-4
In reply to this post by Peter Dalgaard-2
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-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: ## <probably unnecessary detail>
 [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_0.3.2        xml2_1.2.0        
 [9] wordcloud_2.6      RColorBrewer_1.1-2 wordcloud2_0.2.1   tm_0.7-5          
[13] NLP_0.2-0          tidytext_0.2.0     forcats_0.3.0      stringr_1.3.1    
[17] purrr_0.2.5        readr_1.1.1        tidyr_0.8.2        tibble_1.4.2      
[21] ggplot2_3.1.0      tidyverse_1.2.1    knitr_1.20         slam_0.1-43      
[25] RcppParallel_4.4.1 tokenizers_0.2.1   dplyr_0.7.7        lattice_0.20-35  

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.19      here_0.1          lubridate_1.7.4   rprojroot_1.3-2  
 [5] assertthat_0.2.0  digest_0.6.18     R6_2.3.0          cellranger_1.1.0
 [9] plyr_1.8.4        backports_1.1.2   stats4_3.5.1      httr_1.3.1      
[13] pillar_1.3.0      rlang_0.3.0.1     curl_3.2          lazyeval_0.2.1  
[17] readxl_1.1.0      rstudioapi_0.8    data.table_1.11.8 Matrix_1.2-14    
[21] selectr_0.4-1     htmlwidgets_1.3   munsell_0.5.0     broom_0.5.0      
[25] compiler_3.5.1    janeaustenr_0.1.5 spacyr_0.9.91     modelr_0.1.2    
[29] pkgconfig_2.0.2   htmltools_0.3.6   tidyselect_0.2.5  crayon_1.3.4    
[33] withr_2.1.2       SnowballC_0.5.1   grid_3.5.1        nlme_3.1-137    
[37] jsonlite_1.5      gtable_0.2.0      magrittr_1.5      scales_1.0.0    
[41] cli_1.0.1         stringi_1.2.4     stopwords_0.9.0   fastmatch_1.1-0  
[45] tools_3.5.1       glue_1.3.0        hms_0.4.2         parallel_3.5.1  
[49] colorspace_1.3-2  bindr_0.1.1       haven_1.1.2       modeltools_0.2-22
>
 </probably unnecessary detail>

|> -pd
|>
[..]

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

______________________________________________
[hidden email] 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.
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Re: Corrupted package?[solved]

Patrick Connolly-4
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
         
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.

______________________________________________
[hidden email] 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.