[R-pkg-devel] R CMD check --as-cran problem

[Duncan Murdoch]

On 14/01/2019 2:30 p.m., Wang, Zhu wrote:
> First, I removed the Rnw file in vignettes to make simple.
> 
> Then I followed Duncan's suggestions below, but I had the same error.
> 
> Next, in the DESCRIPTION, I added survival in Imports, and  importFrom("survival", "survfitKM") in NAMESPACE. But I still had the same error: there is no package called 'Matrix'.

I think we'd need to see at least the check log, and likely the whole 
package, to diagnose this.

Duncan Murdoch

> 
> Thanks,
> 
> Zhu
> 
> -----Original Message-----
> From: Dirk Eddelbuettel [mailto:dirk.eddelbuettel using gmail.com] On Behalf Of Dirk Eddelbuettel
> Sent: Monday, January 14, 2019 12:45 PM
> To: Duncan Murdoch
> Cc: Dirk Eddelbuettel; Wang, Zhu; r-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] R CMD check --as-cran problem
> 
> 
> On 14 January 2019 at 13:19, Duncan Murdoch wrote:
> | On 14/01/2019 12:37 p.m., Dirk Eddelbuettel wrote:
> | >
> | > On 14 January 2019 at 16:52, Wang, Zhu wrote:
> | > | Thanks Dirk and Klaus. The package Matrix is not used directly but it is used by package survival, which was called in Suggests.  So I am not sure what is the problem. But why CRAN has no such error https://cran.r-project.org/web/checks/check_results_bujar.html. I assumed the CRAN check uses the same R version 3.5.2 as I have. The problem only occurred when I used --as-cran option.
> | >
> | > Doesn't this mean that you may to ensure Matrix is present when survival
> | > might be used -- so if your package suggests survival it should also suggest
> | > Matrix?
> |
> | That shouldn't be necessary.  Since survival imports Matrix, you
> | shouldn't be able to load survival unless Matrix is available.
> | requireNamespace("survival") should fail.
> |
> | I think the problem in bujar is that it never checks
> | requireNamespace("survival"), it just calls
> | getFromNamespace('survfitKM','survival').  That will usually work (just
> | about everyone has survival installed, since it's recommended), but is
> | unsafe.  Zhu should use survival::survfitKM, but only after checking
> | that requireNamespace("survival") is successful.
> 
> Yes, I agree. I mostly tried to be helpful but my email wasn't all that
> effective in that.
> 
> Zhu: the behaviour when --as-cran is not set is irrelevant as CRAN asks you
> to test with --as-cran set, so there really is only one relevant choice.
> 
> And Duncan now kindly detailed the appropriate use case: test for a suggested
> package. Or if your use is not conditional, import from it.
> 
> Dirk
>