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[R-pkg-devel] Strange Additional_repositories NOTE followed by package install error

5 messages · Hugh Parsonage, Georgi Boshnakov, Neal Fultz +1 more

Original
Hugh Parsonage
# 
I am unable to reproduce a recent R CMD check failure on CRAN
concerning a package of mine: grattan.

This package Suggests: taxstats which is a large package hosted by an
Additional repository: https://hughparsonage.github.io/drat/

When I run this check locally, on travis, and on appveyor with
_R_CHECK_CRAN_INCOMING_ = true I get the expected NOTE:


* checking CRAN incoming feasibility ... NOTE
Maintainer: ?Hugh Parsonage <hugh.parsonage at gmail.com>?
Suggests or Enhances not in mainstream repositories:
  taxstats
Availability using Additional_repositories specification:
taxstats   yes   https://hughparsonage.github.io/drat/


However, on CRAN (including win-builder) I get the rather curious NOTE:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Hugh Parsonage <hugh.parsonage at gmail.com>'

Suggests or Enhances not in mainstream repositories:
  taxstats
Availability using Additional_repositories specification:
  taxstats   no   ?
  ?           ?   https://hughparsonage.github.io/drat/
Additional repositories with no packages:
  https://hughparsonage.github.io/drat/


followed by errors resulting from failures to install 'taxstats' when
code such as the following is run to re-build vignettes:

if (requireNamespace("taxstats", quietly = TRUE)){
  library(taxstats)
} else {
  templib <- tempfile()
  hutils::provide.dir(templib)
  install.packages("taxstats",
                   lib = templib,
                   repos = "https://hughparsonage.github.io/drat/",
                   type = "source")
  library("taxstats", lib.loc = templib)
}


Since the failures only occur on Windows machines, and have only
appeared recently, I have considered modifying the DESCRIPTION file to
'trick' win-builder into reinstalling taxstats, as I suspect there may
be caching issues. However, given that the 'taxstats' package takes a
fairly long time to install, I don't want to do this nor submit to
CRAN in case I am missing something else that's causing the check to
fail.
Georgi Boshnakov
# 
Is it possible that the CRAN has a more stringent check and not only check that there is a web link, But also that it is an R package repository?

This would explain the difference (but not if the lrepo is fine of course).

Georgi Boshnakov

-----Original Message-----
From: R-package-devel [mailto:r-package-devel-bounces at r-project.org] On Behalf Of Hugh Parsonage
Sent: 05 February 2018 11:29
To: r-package-devel at r-project.org
Subject: [R-pkg-devel] Strange Additional_repositories NOTE followed by package install error

I am unable to reproduce a recent R CMD check failure on CRAN concerning a package of mine: grattan.

This package Suggests: taxstats which is a large package hosted by an Additional repository: https://hughparsonage.github.io/drat/

When I run this check locally, on travis, and on appveyor with _R_CHECK_CRAN_INCOMING_ = true I get the expected NOTE:


* checking CRAN incoming feasibility ... NOTE
Maintainer: ?Hugh Parsonage <hugh.parsonage at gmail.com>?
Suggests or Enhances not in mainstream repositories:
  taxstats
Availability using Additional_repositories specification:
taxstats   yes   https://hughparsonage.github.io/drat/


However, on CRAN (including win-builder) I get the rather curious NOTE:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Hugh Parsonage <hugh.parsonage at gmail.com>'

Suggests or Enhances not in mainstream repositories:
  taxstats
Availability using Additional_repositories specification:
  taxstats   no   ?
  ?           ?   https://hughparsonage.github.io/drat/
Additional repositories with no packages:
  https://hughparsonage.github.io/drat/


followed by errors resulting from failures to install 'taxstats' when code such as the following is run to re-build vignettes:

if (requireNamespace("taxstats", quietly = TRUE)){
  library(taxstats)
} else {
  templib <- tempfile()
  hutils::provide.dir(templib)
  install.packages("taxstats",
                   lib = templib,
                   repos = "https://hughparsonage.github.io/drat/",
                   type = "source")
  library("taxstats", lib.loc = templib) }


Since the failures only occur on Windows machines, and have only appeared recently, I have considered modifying the DESCRIPTION file to 'trick' win-builder into reinstalling taxstats, as I suspect there may be caching issues. However, given that the 'taxstats' package takes a fairly long time to install, I don't want to do this nor submit to CRAN in case I am missing something else that's causing the check to fail.

______________________________________________
R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

-----Original Message-----
From: R-package-devel [mailto:r-package-devel-bounces at r-project.org] On Behalf Of Hugh Parsonage
Sent: 05 February 2018 11:29
To: r-package-devel at r-project.org
Subject: [R-pkg-devel] Strange Additional_repositories NOTE followed by package install error

I am unable to reproduce a recent R CMD check failure on CRAN concerning a package of mine: grattan.

This package Suggests: taxstats which is a large package hosted by an Additional repository: https://hughparsonage.github.io/drat/

When I run this check locally, on travis, and on appveyor with _R_CHECK_CRAN_INCOMING_ = true I get the expected NOTE:


* checking CRAN incoming feasibility ... NOTE
Maintainer: ?Hugh Parsonage <hugh.parsonage at gmail.com>?
Suggests or Enhances not in mainstream repositories:
  taxstats
Availability using Additional_repositories specification:
taxstats   yes   https://hughparsonage.github.io/drat/


However, on CRAN (including win-builder) I get the rather curious NOTE:

* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Hugh Parsonage <hugh.parsonage at gmail.com>'

Suggests or Enhances not in mainstream repositories:
  taxstats
Availability using Additional_repositories specification:
  taxstats   no   ?
  ?           ?   https://hughparsonage.github.io/drat/
Additional repositories with no packages:
  https://hughparsonage.github.io/drat/


followed by errors resulting from failures to install 'taxstats' when code such as the following is run to re-build vignettes:

if (requireNamespace("taxstats", quietly = TRUE)){
  library(taxstats)
} else {
  templib <- tempfile()
  hutils::provide.dir(templib)
  install.packages("taxstats",
                   lib = templib,
                   repos = "https://hughparsonage.github.io/drat/",
                   type = "source")
  library("taxstats", lib.loc = templib) }


Since the failures only occur on Windows machines, and have only appeared recently, I have considered modifying the DESCRIPTION file to 'trick' win-builder into reinstalling taxstats, as I suspect there may be caching issues. However, given that the 'taxstats' package takes a fairly long time to install, I don't want to do this nor submit to CRAN in case I am missing something else that's causing the check to fail.

______________________________________________
R-package-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Neal Fultz
# 
It looks like the drat repo you linked to only has windows binaries for
3.2, which is probably too old for win builder? Just a guess.

On Mon, Feb 5, 2018 at 11:28 AM, Hugh Parsonage <hugh.parsonage at gmail.com>
wrote:

  
  


  


      

    

    

      
      

        


  

        

      Uwe Ligges
    

    

      
      #
    

  


  

      
1.
The repository is obviously *not* available for Windows as

https://hughparsonage.github.io/drat/bin/windows/contrib/3.5/PACKAGES

does not exist.


2.
 > Since the failures only occur on Windows machines, and have only
 > appeared recently, I have considered modifying the DESCRIPTION file to
 > 'trick' win-builder into reinstalling taxstats


-> This is strictly prohibited and you will be banned of CRAN if you try 
that.

Best,
Uwe Ligges

        
On 05.02.2018 12:28, Hugh Parsonage wrote:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Hugh Parsonage
    

    

      
      #
    

  


  

      
Thank you Uwe & Neal,

Following your suggestion, I tried inserting a binary version of the
package into the repository. I first tried inserting the package into
R 3.4; however, the note persists on winbuilder for R-release:

* using log directory 'd:/RCompile/CRANguest/R-release/grattan.Rcheck'
* using R version 3.4.3 (2017-11-30)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'grattan/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'grattan' version '1.5.3.2'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Hugh Parsonage <hugh.parsonage at gmail.com>'

Possibly mis-spelled words in DESCRIPTION:
  Grattan (18:24)
  indices (17:77)
  repos (19:34)
  taxstats (19:23)

Suggests or Enhances not in mainstream repositories:
  taxstats
Availability using Additional_repositories specification:
  taxstats   no   ?
  ?           ?   https://hughparsonage.github.io/drat/
Additional repositories with no packages:
  https://hughparsonage.github.io/drat/

 (ephemeral link: https://win-builder.r-project.org/4SMyJyP2fZcC/00check.log )

whereas when I run R CMD check --as-cran on a local machine, as well
as on appveyor, I get the expected NOTE.

?  using log directory
'C:/Users/hughp/AppData/Local/Temp/Rtmp4IHBGp/file3b0053a64c53/grattan.Rcheck'
?  using R version 3.4.3 (2017-11-30)
?  using platform: x86_64-w64-mingw32 (64-bit)
?  using session charset: ISO8859-1
?  using option '--as-cran'
?  checking for file 'grattan/DESCRIPTION'
?  checking extension type ... Package
?  this is package 'grattan' version '1.5.3.2'
N  checking CRAN incoming feasibility
   Maintainer: 'Hugh Parsonage <hugh.parsonage at gmail.com>'

   Suggests or Enhances not in mainstream repositories:
     taxstats
   Availability using Additional_repositories specification:
     taxstats   yes   https://hughparsonage.github.io/drat/

The newly inserted binary package appears to install fine on
Appveyor's instance:

Rscript -e "is.null(install.packages('taxstats', repos =
'https://hughparsonage.github.io/drat'))"
Installing package into 'c:/RLibrary'
(as 'lib' is unspecified)
trying URL 'https://hughparsonage.github.io/drat/bin/windows/contrib/3.4/taxstats_0.0.5.1415.zip'
Content type 'application/zip' length 78843919 bytes (75.2 MB)
==================================================
downloaded 75.2 MB
package 'taxstats' successfully unpacked and MD5 sums checked
The downloaded binary packages are in
C:\Users\appveyor\AppData\Local\Temp\1\Rtmp6HCDYs\downloaded_packages
[1] TRUE


I understand that available.packages() using caching, but rebooting my
computer did not change this result (I'm not sure if this is
sufficient to eliminate the possibility that caching is masking a
problem).


Sorry that this package is causing problems on CRAN. Very appreciative
of your patience.


Hugh.

        
On 6 February 2018 at 04:19, Uwe Ligges <ligges at statistik.tu-dortmund.de> wrote: