From hugh@p@r@on@ge @end|ng |rom gm@||@com  Wed Aug 28 18:36:38 2019
From: hugh@p@r@on@ge @end|ng |rom gm@||@com (Hugh Parsonage)
Date: Thu, 29 Aug 2019 02:36:38 +1000
Subject: [Rd] R CMD check issue
In-Reply-To: <771925$ca6l3c@ironport10.mayo.edu>
References: <771925$ca6l3c@ironport10.mayo.edu>
Message-ID: <CAJmOi+MKg97Qj0wTJZ+mTVNqxJFpt7KdhwR=CKdGxLjnsVkoog@mail.gmail.com>

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 <
r-devel at r-project.org> 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]]
>
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> https://stat.ethz.ch/mailman/listinfo/r-devel
>

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[Rd] R CMD check issue
Hugh Parsonage