R CMD check issue

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R CMD check issue

R devel mailing list
I'm running "R CMD check" for 600+ of the packages that depend on survival, and at the end
look for
     grep Status *.Rcheck/00check.log  | grep ERROR

to find any that failed.   But by accident I just looked at the log for the Greg package,
which finishes with the lines found below.  Is the final note of WARNING rather than ERROR
on purpose, or an error?   If the former, will adding a search for "Quitting from" suffice?

By the way, the failure shown was an (uncaught) bug in cox.zph wrt putting dimnames on one
of the result matrices.

Terry T
----------------------

--- re-building ‘timeSplitter.Rmd’ using rmarkdown
Loading required package: forestplot
Loading required package: grid
Loading required package: checkmate
Loading required package: Gmisc
Loading required package: Rcpp
Loading required package: htmlTable

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

     filter, lag

The following objects are masked from 'package:base':

     intersect, setdiff, setequal, union

Quitting from lines 408-412 (timeSplitter.Rmd)
Error: processing vignette 'timeSplitter.Rmd' failed with diagnostics:
length of 'dimnames' [1] not equal to array extent
--- failed re-building ‘timeSplitter.Rmd’

SUMMARY: processing the following file failed:
   ‘timeSplitter.Rmd’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
‘/home/therneau/research/surv/Hg/survsubmit/xtest/Greg.Rcheck/00check.log’
for details.



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Re: R CMD check issue

Hugh Parsonage
The warning is that the vignette failed to be rebuilt due to an error in
its code. The error log was truncated.

Of course for practical purposes errors and warnings both constitute check
failures

On Thu, 29 Aug 2019 at 1:56 am, Therneau, Terry M., Ph.D. via R-devel <
[hidden email]> wrote:

> I'm running "R CMD check" for 600+ of the packages that depend on
> survival, and at the end
> look for
>      grep Status *.Rcheck/00check.log  | grep ERROR
>
> to find any that failed.   But by accident I just looked at the log for
> the Greg package,
> which finishes with the lines found below.  Is the final note of WARNING
> rather than ERROR
> on purpose, or an error?   If the former, will adding a search for
> "Quitting from" suffice?
>
> By the way, the failure shown was an (uncaught) bug in cox.zph wrt putting
> dimnames on one
> of the result matrices.
>
> Terry T
> ----------------------
>
> --- re-building ‘timeSplitter.Rmd’ using rmarkdown
> Loading required package: forestplot
> Loading required package: grid
> Loading required package: checkmate
> Loading required package: Gmisc
> Loading required package: Rcpp
> Loading required package: htmlTable
>
> Attaching package: 'dplyr'
>
> The following objects are masked from 'package:stats':
>
>      filter, lag
>
> The following objects are masked from 'package:base':
>
>      intersect, setdiff, setequal, union
>
> Quitting from lines 408-412 (timeSplitter.Rmd)
> Error: processing vignette 'timeSplitter.Rmd' failed with diagnostics:
> length of 'dimnames' [1] not equal to array extent
> --- failed re-building ‘timeSplitter.Rmd’
>
> SUMMARY: processing the following file failed:
>    ‘timeSplitter.Rmd’
>
> Error: Vignette re-building failed.
> Execution halted
>
> * checking PDF version of manual ... OK
> * DONE
>
> Status: 1 WARNING
> See
> ‘/home/therneau/research/surv/Hg/survsubmit/xtest/Greg.Rcheck/00check.log’
> for details.
>
>
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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