My colleague points out that these typos are probably still present
because almost no-one has the stamina to read that far down in ?switch ...
cheers
Ben Bolker
Index: switch.Rd
===
--- switch.Rd (revision 76766)
+++
(Reposting..)
Hi everyone,
I am getting following two warnings when I submit my R package (perfectphyloR)
to CRAN.
Warning 1: * checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
'perfectphyloR.html',
On 02/07/2019 11:00 a.m., Georgi Boshnakov wrote:
...
if(getRversion() >= "2.15.1") utils::globalVariables(c("."))
Using such a general pattern eventually and inevitably will prevent the check
from reporting legitimate bugs.
I believe globalVariables() takes a vector of names, not a
On 2/07/19 11:13 PM, Ivan Krylov wrote:
Could R CMD check be using valgrind to run the examples? Valgrind has
to interpret CPU instructions manually to be able to warn about
results of code execution depending on memory values it considers
undefined, so it is much slower than execution on a
On 02/07/2019 5:31 a.m., Rolf Turner wrote:
Many thanks to Henrik Bengtsson and Martin Maechler for pointing out
that I can monitor progress by looking at the file
"mypkg.Rcheck/mypkg-Ex.Rout"
e.g. by using "tail -f". This strategy indeed revealed where the hangup
was happening. I
Hi all,
I updated my github repository with a bug fix, and want to push this
change to the bioconductor git repo. I don't have the rights to do that
for some reason, so I logged in to check.
I logged in here:
https://git.bioconductor.org/BiocCredentials/permissions_by_user/
I see:
Hi all,
I updated my github repository with a bug fix, and want to push this
change to the bioconductor git repo. I've somehow lost the rights to do
that, so I logged in to check my keys.
I logged in here:
https://git.bioconductor.org/BiocCredentials/permissions_by_user/
I see:
> ...
> if(getRversion() >= "2.15.1") utils::globalVariables(c("."))
Using such a general pattern eventually and inevitably will prevent the check
from reporting legitimate bugs.
One alternative is to list explicitly the variables in question and make sure
that they are not commonly used
raúl
On Tue, 2 Jul 2019 at 14:18, Berlanga, Antonio J
wrote:
>
> Hi r-package-devel,
>
> I've submitted my first package but it failed the CRAN pre-tests on
> NOTES. I got:
>
> - my email
>
> - an extra non-standard file (which I have now added to .Rbuildignore)
>
> - NOTEs on "no visible global
Hi,
On Tue, 2019-07-02 at 09:50 +, Martin Morgan wrote:
> Do you think this approach could be re-cast in the same way that
> https://github.com/Bioconductor/bioconductor_full has done, so that
> the container has all the software to _support_ the packages needed
> for the jupyter notebook,
Many thanks, Herve!
- Paul
> On Jun 24, 2019, at 7:17 PM, Pages, Herve wrote:
>
> Hi Paul,
>
> After a long hunt, the software package causing these daily
> reinstallations of BSgenome.Hsapiens.UCSC.hg38 has been
> identified and his maintainer contacted.
>
> Sorry for the inconvenience
Hi r-package-devel,
I've submitted my first package but it failed the CRAN pre-tests on
NOTES. I got:
- my email
- an extra non-standard file (which I have now added to .Rbuildignore)
- NOTEs on "no visible global function definition"
The first two I assume are harmless. The third I do not
Could R CMD check be using valgrind to run the examples? Valgrind has
to interpret CPU instructions manually to be able to warn about
results of code execution depending on memory values it considers
undefined, so it is much slower than execution on a real CPU.
One way to verify that on a
On 2/07/19 9:45 PM, Iñaki Ucar wrote:
Which line of code is it?
Dunno that it's very enlightening, without having access to the package,
but the two lines involved are:
fit <- ldFit(inLogs,predictor="logDose",link="logit")
x3 <- cvCompare(fit,nrep=5)
The first line runs
It's a pain in the neck, but even more basic than inserting browser()
calls all over the place (but possibly useful in this situation) would
be inserting appropriate cat() statements all over the place ... (and
maybe using cat() with proc.time() to report on elapsed time as you go?)
(As for
Do you think this approach could be re-cast in the same way that
https://github.com/Bioconductor/bioconductor_full has done, so that the
container has all the software to _support_ the packages needed for the jupyter
notebook, but that the user must do some kind of initialization to install the
Which line of code is it?
Iñaki
On Tue, 2 Jul 2019 at 11:32, Rolf Turner wrote:
>
>
> Many thanks to Henrik Bengtsson and Martin Maechler for pointing out
> that I can monitor progress by looking at the file
>
> "mypkg.Rcheck/mypkg-Ex.Rout"
>
> e.g. by using "tail -f". This strategy
Many thanks to Henrik Bengtsson and Martin Maechler for pointing out
that I can monitor progress by looking at the file
"mypkg.Rcheck/mypkg-Ex.Rout"
e.g. by using "tail -f". This strategy indeed revealed where the hangup
was happening. I wrapped a line of the examples in \dontrun{}
Hi,
last week over a beer some of us realized that (technically)
it is possible to run most[1] Rmd vignettes as Jupiter Notebook.
So I created https://github.com/sneumann/bioc_notebooks
which takes some example packages and creates a Docker container
with converted vignettes. The resulting
Sorry, it was a mistake. CC the list.
于 2019年7月2日 GMT-07:00 上午12:17:01, Jeff Newmiller 写到:
>I recommend that you "reply-all" to keep the mailing list included.
>
>
>On July 1, 2019 11:30:23 PM PDT, Jialin Ma wrote:
>>Hi Jeff,
>>
>>Thanks for your reply. I would like to clarify a little bit:
>>
> Henrik Bengtsson
> on Mon, 1 Jul 2019 20:36:26 -0700 writes:
> FWIW, when running R CMD check mypkg_1.0.tar.gz
> the example output is captured to the file
> 'mypkg.Rcheck/mypkg-Ex.Rout', so you could monitor that
> one for what's going on.
> /Henrik
Yes,
This is entirely within your OS's installation of Tcl/Tk and X11: the
latter both allocated and freed. We've seen it before (even had it as
bug report on R). Please check your OS is fully up-to-date and if so
report it there.
On 01/07/2019 15:55, Therneau, Terry M., Ph.D. via R-devel wrote:
> Jennifer Bryan writes:
Thanks: fixed with c76763 in the trunk.
Best
-k
> Hello,
> I'm seeing a nuisance warning when I run `R CMD check --as-cran
> whatever_x.y.z.tar.gz`.
> I generally work with these options set:
> options(
> warnPartialMatchArgs = TRUE,
> warnPartialMatchAttr =
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