Usethis: How to add dependency on R version?

Created on 16 Feb 2019  ·  10Comments  ·  Source: r-lib/usethis

R CMD check gives warning: Warning: package needs dependence on R (>= 2.10) (which I think comes from using use_data(... overwrite = TRUE))

Is there a way to add the dependency with use_this?

Thanks!

picture MatthieuStigler

Most helpful comment

If the running of use_data() indeed automatically implies a dependence on at least 2.10, then I also think it would be logical if use_data() would by default check whether there is a dependence already defined, and whether it is at least 2.10, and if not, or it is below it, it'd include a dependence / increase it to 2.10.

Yes, @hadley is of course right that "we do not what versions of R you wish to support", but if the above assertion is correct, then 2.10 needs to be the minimum if you run use_data(), so I think the consistent course of action would be if use_data() would handle this. The user can still change it to something higher, if he/she needs it due to other reasons.

picture tamas-ferenci on 15 Jun 2019
👍6

All 10 comments

I don't think we currently facilitate this. To the extent that we have a _good_ reason, it's because we try to avoid declaring an explicit R version dependency unless it's really necessary. But perhaps we should have a way to do this.

jennybc picture jennybc on 16 Feb 2019

I have the impression that using use_data() will create that specific dependency requirement?

Try first:

library(usethis)

path <- file.path(tempdir(), "mypkg")
create_package(path)
use_mit_license("My Name")

Gives 0 warnings/errors. Add now:

use_data(iris, overwrite = TRUE)

Gives me: 

❯ checking data for ASCII and uncompressed saves ... WARNING
    Warning: package needs dependence on R (>= 2.10)

Do you confirm? If yes, it might be good to have a function to add R version requirement, and even add it automatically with use_data? R 2.10 was released in 2009, seems safe to assume it...

Thanks!

MatthieuStigler picture MatthieuStigler on 16 Feb 2019

I think adding Depends: R (>= 2.10) is making a strong assertion that you believe your package will work with all versions of R later than 2.10, and that is not generally true. The version of R that you require is something that you as package developer have to decide, with some thought.

hadley picture hadley on 17 Mar 2019

I am not sure I made my point clearly enough. The fact is that using use_data(iris) seems to create a dependency on R 2.10! In a nutshell (full code below):

❯ checking data for ASCII and uncompressed saves ... WARNING
#>     Warning: package needs dependence on R (>= 2.10)
#> 
#> 0 errors ✔ | 2 warnings ✖ | 0 notes ✔
#> Error: R CMD check found WARNINGs

If this is the case, it seems worth considering:

  • Having a usethis::function to specify R dependency?
  • Having a message from use_data() warning the user about this?

Thanks!

Run:

library(usethis)

path <- file.path(tempdir(), "mypkg")
create_package(path)
#> ✔ Setting active project to '/tmp/RtmpTCxYQx/mypkg'
#> ✔ Creating 'R/'
#> ✔ Creating 'man/'
#> ✔ Writing 'DESCRIPTION'
#> ✔ Writing 'NAMESPACE'
use_mit_license("My Name")
#> ✔ Setting License field in DESCRIPTION to 'MIT + file LICENSE'
#> ✔ Writing 'LICENSE.md'
#> ✔ Adding '^LICENSE\\.md$' to '.Rbuildignore'
#> ✔ Writing 'LICENSE'

devtools::check(path)
#> ── Building ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── mypkg ──
#> Setting env vars:
#> ● CFLAGS    : -Wall -pedantic
#> ● CXXFLAGS  : -Wall -pedantic
#> ● CXX11FLAGS: -Wall -pedantic
#> ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#>   
   checking for file ‘/tmp/RtmpTCxYQx/mypkg/DESCRIPTION’ ...

✔  checking for file ‘/tmp/RtmpTCxYQx/mypkg/DESCRIPTION’
#> 

─  preparing ‘mypkg’:
#> 

   checking DESCRIPTION meta-information ...

✔  checking DESCRIPTION meta-information
#> 

─  checking for LF line-endings in source and make files and shell scripts
#> 

─  checking for empty or unneeded directories
#>    Removed empty directory ‘mypkg/R’
#>    Removed empty directory ‘mypkg/man’
#> ─  building ‘mypkg_0.0.0.9000.tar.gz’
#> 


#> 
── Checking ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── mypkg ──
#> Setting env vars:
#> ● _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
#> ● _R_CHECK_CRAN_INCOMING_REMOTE_    : FALSE
#> ● _R_CHECK_CRAN_INCOMING_           : FALSE
#> ● _R_CHECK_FORCE_SUGGESTS_          : FALSE
#> ── R CMD check ────────────────────────────────────────────────────────────
#>   
─  using log directory ‘/tmp/RtmpTCxYQx/mypkg.Rcheck’
#> 

─  using R version 3.5.3 (2019-03-11)
#> ─  using platform: x86_64-pc-linux-gnu (64-bit)
#> ─  using session charset: UTF-8
#> 

─  using options ‘--no-manual --as-cran’
#> ✔  checking for file ‘mypkg/DESCRIPTION’
#> ─  this is package ‘mypkg’ version ‘0.0.0.9000’
#> ─  package encoding: UTF-8
#>    checking package namespace information ...

✔  checking package namespace information
#>    checking package dependencies ...

✔  checking package dependencies (1.5s)
#> 

✔  checking if this is a source package
#> ✔  checking if there is a namespace
#>    checking for executable files ...

✔  checking for executable files
#> 

✔  checking for hidden files and directories
#> ✔  checking for portable file names
#> ✔  checking for sufficient/correct file permissions
#> 

✔  checking serialization versions
#>    checking whether package ‘mypkg’ can be installed ...

✔  checking whether package ‘mypkg’ can be installed (554ms)
#> 

   checking installed package size ...

✔  checking installed package size
#> 

   checking package directory ...

✔  checking package directory
#>    checking DESCRIPTION meta-information ...

✔  checking DESCRIPTION meta-information
#> 

✔  checking top-level files
#> ✔  checking for left-over files
#> ✔  checking index information
#>    checking package subdirectories ...

✔  checking package subdirectories
#> 

   checking whether the package can be loaded ...

✔  checking whether the package can be loaded
#> 

   checking whether the package can be loaded with stated dependencies ...

✔  checking whether the package can be loaded with stated dependencies
#> 

   checking whether the package can be unloaded cleanly ...

✔  checking whether the package can be unloaded cleanly
#> 

   checking whether the namespace can be loaded with stated dependencies ...

✔  checking whether the namespace can be loaded with stated dependencies
#> 

   checking whether the namespace can be unloaded cleanly ...

✔  checking whether the namespace can be unloaded cleanly
#> 

   checking loading without being on the library search path ...

✔  checking loading without being on the library search path
#> 

   checking examples ...

─  checking examples ... NONE
#> 


#>    
#> 



#> ── R CMD check results ────────────────────────────── mypkg 0.0.0.9000 ────
#> Duration: 3.5s
#> 
#> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Created on 2019-03-17 by the reprex package (v0.2.1)

Now use add_data():

library(usethis)

path <- file.path(tempdir(), "mypkg")
create_package(path)
#> ✔ Setting active project to '/tmp/RtmpMZIYxZ/mypkg'
#> ✔ Creating 'R/'
#> ✔ Creating 'man/'
#> ✔ Writing 'DESCRIPTION'
#> ✔ Writing 'NAMESPACE'
use_mit_license("My Name")
#> ✔ Setting License field in DESCRIPTION to 'MIT + file LICENSE'
#> ✔ Writing 'LICENSE.md'
#> ✔ Adding '^LICENSE\\.md$' to '.Rbuildignore'
#> ✔ Writing 'LICENSE'
use_data(iris)
#> ✔ Creating 'data/'
#> ✔ Saving 'iris' to 'data/iris.rda'

devtools::check(path)
#> ── Building ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── mypkg ──
#> Setting env vars:
#> ● CFLAGS    : -Wall -pedantic
#> ● CXXFLAGS  : -Wall -pedantic
#> ● CXX11FLAGS: -Wall -pedantic
#> ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
#>   
   checking for file ‘/tmp/RtmpMZIYxZ/mypkg/DESCRIPTION’ ...

✔  checking for file ‘/tmp/RtmpMZIYxZ/mypkg/DESCRIPTION’
#> 

─  preparing ‘mypkg’:
#> 

   checking DESCRIPTION meta-information ...

✔  checking DESCRIPTION meta-information
#> 

─  checking for LF line-endings in source and make files and shell scripts
#> 

─  checking for empty or unneeded directories
#>    Removed empty directory ‘mypkg/R’
#>    Removed empty directory ‘mypkg/man’
#> ─  looking to see if a ‘data/datalist’ file should be added
#> ─  building ‘mypkg_0.0.0.9000.tar.gz’
#> 


#> 
── Checking ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────── mypkg ──
#> Setting env vars:
#> ● _R_CHECK_CRAN_INCOMING_USE_ASPELL_: TRUE
#> ● _R_CHECK_CRAN_INCOMING_REMOTE_    : FALSE
#> ● _R_CHECK_CRAN_INCOMING_           : FALSE
#> ● _R_CHECK_FORCE_SUGGESTS_          : FALSE
#> ── R CMD check ────────────────────────────────────────────────────────────
#>   
─  using log directory ‘/tmp/RtmpMZIYxZ/mypkg.Rcheck’
#> 

─  using R version 3.5.3 (2019-03-11)
#> ─  using platform: x86_64-pc-linux-gnu (64-bit)
#> ─  using session charset: UTF-8
#> 

─  using options ‘--no-manual --as-cran’
#> 

✔  checking for file ‘mypkg/DESCRIPTION’
#> ─  this is package ‘mypkg’ version ‘0.0.0.9000’
#> 

─  package encoding: UTF-8
#> ✔  checking package namespace information
#>    checking package dependencies ...

✔  checking package dependencies (954ms)
#> 

✔  checking if this is a source package
#> ✔  checking if there is a namespace
#>    checking for executable files ...

✔  checking for executable files
#> 

✔  checking for hidden files and directories
#> ✔  checking for portable file names
#> ✔  checking for sufficient/correct file permissions
#> 

✔  checking serialization versions
#>    checking whether package ‘mypkg’ can be installed ...

✔  checking whether package ‘mypkg’ can be installed (477ms)
#> 

   checking installed package size ...

✔  checking installed package size
#> 

   checking package directory ...

✔  checking package directory
#>    checking DESCRIPTION meta-information ...

✔  checking DESCRIPTION meta-information
#> 

✔  checking top-level files
#> ✔  checking for left-over files
#> ✔  checking index information
#>    checking package subdirectories ...

✔  checking package subdirectories
#> 

   checking whether the package can be loaded ...

✔  checking whether the package can be loaded
#> 

   checking whether the package can be loaded with stated dependencies ...

✔  checking whether the package can be loaded with stated dependencies
#> 

   checking whether the package can be unloaded cleanly ...

✔  checking whether the package can be unloaded cleanly
#> 

   checking whether the namespace can be loaded with stated dependencies ...

✔  checking whether the namespace can be loaded with stated dependencies
#> 

   checking whether the namespace can be unloaded cleanly ...

✔  checking whether the namespace can be unloaded cleanly
#> 

   checking loading without being on the library search path ...

✔  checking loading without being on the library search path
#> 

   checking for missing documentation entries ...

W  checking for missing documentation entries
#> 

   Undocumented code objects:
#>      ‘iris’
#>    Undocumented data sets:
#>      ‘iris’
#>    All user-level objects in a package should have documentation entries.
#>    See chapter ‘Writing R documentation files’ in the ‘Writing R
#>    Extensions’ manual.
#> ✔  checking contents of ‘data’ directory
#>    checking data for non-ASCII characters ...

✔  checking data for non-ASCII characters
#> 

   checking data for ASCII and uncompressed saves ...

W  checking data for ASCII and uncompressed saves
#> 

     Warning: package needs dependence on R (>= 2.10)
#>    checking examples ...

─  checking examples ... NONE
#> 


#>    See
#>      ‘/tmp/RtmpMZIYxZ/mypkg.Rcheck/00check.log’
#>    for details.
#>    
#> 




#> 
── R CMD check results ────────────────────────────── mypkg 0.0.0.9000 ────
#> Duration: 3.3s
#> 
#> ❯ checking for missing documentation entries ... WARNING
#>   Undocumented code objects:
#>     ‘iris’
#>   Undocumented data sets:
#>     ‘iris’
#>   All user-level objects in a package should have documentation entries.
#>   See chapter ‘Writing R documentation files’ in the ‘Writing R
#>   Extensions’ manual.
#> 
#> ❯ checking data for ASCII and uncompressed saves ... WARNING
#>     Warning: package needs dependence on R (>= 2.10)
#> 
#> 0 errors ✔ | 2 warnings ✖ | 0 notes ✔
#> Error: R CMD check found WARNINGs

Created on 2019-03-17 by the reprex package (v0.2.1)

MatthieuStigler picture MatthieuStigler on 17 Mar 2019

You were quite clear. usethis can not automatically add a dependency on an R version because we do not what versions of R you wish to support.

hadley picture hadley on 17 Mar 2019

No, the add R dependency automatically is just subsidiary to my main point (and should be discarded). Main question is: can usethis provide a functionality so that user can add R dependency?

This request is motivated by the fact that using use_data() seems to create an (implicit) dependency on R 2.10, according to the R CMD check. Hadley, do you agree with that premise? If no, please discard indeed that whole message. If yes, do you think usethis can help the user solve that dependency issue?

Thanks

MatthieuStigler picture MatthieuStigler on 17 Mar 2019
👍4

If the running of use_data() indeed automatically implies a dependence on at least 2.10, then I also think it would be logical if use_data() would by default check whether there is a dependence already defined, and whether it is at least 2.10, and if not, or it is below it, it'd include a dependence / increase it to 2.10.

Yes, @hadley is of course right that "we do not what versions of R you wish to support", but if the above assertion is correct, then 2.10 needs to be the minimum if you run use_data(), so I think the consistent course of action would be if use_data() would handle this. The user can still change it to something higher, if he/she needs it due to other reasons.

tamas-ferenci picture tamas-ferenci on 15 Jun 2019
👍6

I feel this issue still deserve attention. @hadley , would you mind giving it a second thought?

@tamas-ferenci summarized it well: if using use_data() indeed automatically implies a dependency to R 2.10 (which I believe is true, see code above, but I might be wrong), should usethis not check that the required version is not at least 2.10?

Currently using usethis::use_data() requires adjusting manually the DESCRIPTION file, which undermines the nice workflow of usethis

MatthieuStigler picture MatthieuStigler on 20 Apr 2020

@MatthieuStigler what is the problem? use_data() automatically adds a dependency on R 2.10.

hadley picture hadley on 20 Apr 2020

oh my bad, hadn't realized it was actually included (my mistake was to run use_description and not re-run use_data after that), sorry about that!

MatthieuStigler picture MatthieuStigler on 20 Apr 2020
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