R devel - Feb 2017 - R CMD build error during vignettes build

Hello,

I'm trying to rebuild a package (using R version 3.3.2 (2016-10-31))
that has not seen any changes since it was last built without problems
in previous R versions.  It fails during vignette building with:

---<--------------------cut
here---------------start------------------->---
$ R CMD build diveMove
* checking for file ?diveMove/DESCRIPTION? ... OK
* preparing ?diveMove?:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Quitting from lines 432-438 (diveMove.Rnw) 
Error: processing vignette 'diveMove.Rnw' failed with diagnostics:
missing values and NaN's not allowed if 'na.rm' is FALSE
Execution halted
---<--------------------cut
here---------------end--------------------->---

There are no problems running the R code resulting from tangling the
vignette.  Specifically, the code referred to in the error is a single
function call, which returns with no warnings or errors, so I have
little to hold on to.  How can I get more verbose debug from "R CMD
build"?

-- 
Seb

On 21/02/17 19:06, Sebastian P. Luque wrote:
> Hello,
>
> I'm trying to rebuild a package (using R version 3.3.2 (2016-10-31))
> that has not seen any changes since it was last built without problems
> in previous R versions.  It fails during vignette building with:
>
> ---<--------------------cut
here---------------start------------------->---
> $ R CMD build diveMove
> * checking for file ?diveMove/DESCRIPTION? ... OK
> * preparing ?diveMove?:
> * checking DESCRIPTION meta-information ... OK
> * installing the package to build vignettes
> * creating vignettes ... ERROR
> Quitting from lines 432-438 (diveMove.Rnw)
> Error: processing vignette 'diveMove.Rnw' failed with diagnostics:
> missing values and NaN's not allowed if 'na.rm' is FALSE
> Execution halted
> ---<--------------------cut
here---------------end--------------------->---
>
> There are no problems running the R code resulting from tangling the
> vignette.  Specifically, the code referred to in the error is a single
> function call, which returns with no warnings or errors, so I have
> little to hold on to.  How can I get more verbose debug from "R CMD
> build"?
>
Are you sure that the complete R code of the vignette runs without 
errors? I can't help you with getting more verbose output from 'R CMD 
build', but the error can be reproduced with other means, as outlined below.

When trying to build the vignette from the git version of your package 
(as part of R CMD build), I see the same error message. Investigating 
further, the "tangled" file diveMove.R from 
'tools::buildVignette("diveMove.Rnw")' has 68 lines and stops
short of
the code chunk "zoc" where the error occurs. Running that code
obviously
works fine.

However, 'tools::buildVignette("diveMove.Rnw", weave = FALSE)'
outputs a
longer (154 lines) diveMove.R (presumably containing the complete code 
of the vignette) which includes the chunk "zoc". Executing the code
with
source() produces the expected error. This also identifies the call 
where the error occurs:
> Error in quantile.default(Ad1.maybe.nat, probs = (1 - ascent.crit.q)) :
>   missing values and NaN's not allowed if 'na.rm' is FALSE
The error can be investigated with the usual tools, e.g. traceback() and 
debug().

-- 
Mikko Korpela
Department of Geosciences and Geography
University of Helsinki

On Wed, 22 Feb 2017 12:22:45 +0200,
Mikko Korpela <mikko.korpela at helsinki.fi> wrote:

[...]
> When trying to build the vignette from the git version of your package
> (as part of R CMD build), I see the same error message. Investigating
> further, the "tangled" file diveMove.R from
> 'tools::buildVignette("diveMove.Rnw")' has 68 lines and
stops short of
> the code chunk "zoc" where the error occurs. Running that code
> obviously works fine.
This is exactly what I failed to do -> check the tangled output to see
it is complete... It didn't occur to me to do that assuming all the code
would be there.  Even more so considering there's nothing in the CRAN
checks showing problems.

Thank you Mikko!

-- 
Seb