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
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