is probably the best solution for now.
Best regards,
Thierry
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics &
e without removing the
URL for the README?
Best regards,
Thierry
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics &
Dear Dirk,
Zenodo does offer storage. The default quota are 50GB and 100 files per
record (version). See
https://help.zenodo.org/docs/deposit/manage-files/#prepare
Best regards,
Thierry
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR
. E.g. https://doi.org/10.5281/zenodo.14179531
The zen4R package makes it easy to upload and download the data from within
R. Our functions assume the data is in a local folder. Only when the data
is missing, we try to download it from Zenodo.
Best regards,
ir. Thierry Onkelinx
Statisticus
PTION meta-information ... NOTE
Author field differs from that derived from Authors@R
Author:'Thierry Onkelinx [aut, cre] (<
https://orcid.org/-0001-8804-4216>, Research Institute for Nature and
Forest (INBO)), Floris Vanderhaeghe [ctb] (<
https://orcid.org/-0002-6
t;, "A3", "digest", "abe")],
function(x) {
parse(text = x) |>
eval() |>
list()
},
vector(mode = "list", 1)
) |>
unname() |>
author2df()
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Go
Hi Dirk,
Happy to help. I'm working on a new version of the checklist package. I
could export the function if that makes it easier for you.
Best regards,
Thierry
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDE
email orcid
affiliation usage
1 Thierry Onkelinxthierry.onkel...@inbo.be -0001-8804-4216
1
2 Floris Vanderhaeghe floris.vanderhae...@inbo.be -0002-6378-6229
1
3 Peter Desmetpeter.des...@inbo.be -0002-8442
Dear Hector,
The tmp dir depends on the R session. Use tools::R_user_dir("your_package",
which = "cache") if you want a permanent cache of the files.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NAT
The cascade is even longer. prediction got archived because ffbase was no
longer available. https://cran.r-project.org/web/packages/ffbase/
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR
The goal of opencv is to provide bindings to 'OpenCV' Computer Vision
Library. Hence a much wider scope than just reading qrcodes. qrcode just
focusses creating different qrcodes. The fact that they can use each other
to test themselves is a happy coincidence.
ir. Thierry Onkelinx
S
in qrcode? And thus
requiring qrcode to list opencv as a suggested package. I know this is not
allowed when depending or importing packages.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH
Dear Tony,
Much will depend on what information you need from the output of
installed.packages()?
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team
loop.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Have
Dear Vincent,
Have a look at the spatstat package which was split into several smaller
packages (https://github.com/spatstat/spatstat). Maybe the maintainers of
that package can share some insights.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of
function.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...
ibrary") solved the problem.
So it looks like rcmdcheck ignored the first element of .libPaths(). I'm
not sure if that is a bug of rcmdcheck. Shall I report an issue?
Best regards,
Thierry
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
21-03-08
─ Packages
package * version date lib source
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.4)
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOS
That will be hard to do without your package. Note that I've suggested a
work around in my first reply.
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biom
Probably because the cache is not installed into the package. I'd check the
tar.gz file to see if the cache is present.
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Dear Jose,
I store the results of CPU intensive chunks in the package. Have a look at
https://github.com/ropensci/git2rdata/blob/master/vignettes/efficiency.Rmd.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN
/blob/bad8a4cf42049faa72a04b202c5a4dfc233b4046/vignettes/efficiency.Rmd#L293
for an example.
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team B
those
citations.
So I won't waste time arguing over this and use that time to put it on
Zenodo.
Best regards,
PS Zenodo is well funded (https://about.zenodo.org/infrastructure/) and
IMHO equally likely to be permanent as CRAN is.
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaams
Thanks for the feedback. It seems like I was under the impression that
.Rbuildignore would follow similar rules as .gitignore.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR
Dear all,
Can we add blank lines in .Rbuildignore? Or lines with only comments (line
starting with #)?
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team
Dear Dominik,
IMHO you only need to list "first order" dependencies: things that your
package directly uses. Listing higher order dependencies would be redundant
as they are listed in the packages that have them as first order dependency.
Best regards,
ir. Thierry Onkelinx
S
Dear Spencer,
I assume you are using R **3**.6.2.
Consider TinyTeX (https://yihui.org/tinytex/). I found that working fairly
easy on Windows machines, even by users without admin privileges.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of
Dear Neonira.
Whatever file you place in the inst folder, will be available for the users
when they install the package.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR
describing
and linking to the precompiled vignettes. Something like
browseURL(system.file("precompiled.html", package = "yourpackage"))
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK
fined global variable" error.
What is the proper way to use txt data in a package?
Best regards,
Thierry
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biomet
Dear Rainer,
It looks like you are using testthat. testthat has a skip_on_cran()
function. This will always skip the subsequent tests in the script unless
the environment variable NOT_CRAN is set.
Best regards,
Thierry
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid
Dear Alex,
Another idea is to use pkgdown (http://pkgdown.r-lib.org) to convert
all the documentation of your package (include the vignettes) into a
website. Then you make that available to your students, e.g. through
github pages.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
s("LM2GLMM") or
update.packages()
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Qua
Dear Bill,
The best way to fix your problem is IMHO to have it fixed in lme4. I've
cc'ed Ben Bolker (lme4 maintainer) to inform him of this problem.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BO
You can make things even a bit easier by setting "eval=myeval" and set
"myeval <- FALSE" at the top of the vignette. In case you want to update
the figures, you only have to set "myeval <- TRUE" and run the vignette.
ir. Thierry Onkelinx
Statisticus / Statist
the source has to allow that kind of usage.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics &
using pdf as
output format for the vignette? Consider using
rmarkdown::html_vignette.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie
it test can be bypassed on other systems with
testthat::skip_on_os().
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biomet
ion. I've tried Sys.chmod(file,
"000") which didn't work.
Any suggestions?
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie
Dear Nikos,
Your examples are taking too much time. Make them run faster. Or
remove some of them.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team
Dear Adrian,
Answering this would be much easier when you have access to the code.
Best regards,
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie
up to the _user_ to
provide a data.frame (and a tibble is not a data.frame). Documenting
this in the package documentation/FAQ or issuing a warning "don't use
tibble" when the package is loaded should be sufficient.
Best regards,
ir. Thierry Onkelinx
Statisticus/ Statistician
Vlaamse
regards,
ir. Thierry Onkelinx
Statisticus/ Statiscian
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Kliniekstraat 25
, ...) :
could not find function "loadMethod"
loadMethod() is NOT used in mypackage and not imported.
library(mypackage)
my_function()
Best regards,
ir. Thierry Onkelinx
Statisticus/ Statiscian
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH
Dear Olek,
One of the problems seems to be that lme4 (dependency of fishmethod) wasn't
installed during the pretest. I have no idea why.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszo
Dear Dario,
The attachments got stripped from the mail by the server. Can you provide a
link to the results of R CMD check and the source code of the package?
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie
Dear Martin,
We use Docker to create an image with R and specific versions of the
required packages. You can find our docker image and the source code at
https://hub.docker.com/r/inbobmk/rstable/
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for
Yes. That is what I meant (but too lazy to write).
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the stat
Try adding requireNamespace("ggplot2") in the function that rely on ggplot2.
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Ande
Dear Jonathon,
Is ggplot2 listed in the DESCRIPTION file? It needs to be at least in the
Suggests:
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality A
Dear Roy,
In case you create a HTML vignette you can use datatable() from the DT
package. That creates a dynamic table in the output.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg /
is to set options(error = function(){}) I assume
that this has a permanent effect on the current R session? So I should
reset that as a part of the error handling?
What would be recommended: tryCatch() or options(error = ...)? Or are there
more / better solutions?
Best regards,
ir. Thierr
Dear David,
Have you tried removing the exclamation mark in %!\VignetteEncoding{UTF-8}?
I think it should be %\VignetteEncoding{UTF-8}
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg /
between using the old version which still works but no longer maintained or
the switched to the new version which is maintained but will break existing
code.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie
Hi Roy,
Have a look at the lintr package:
https://github.com/jimhester/lintr/blob/master/README.md
It works stand alone and integrates with several editors.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie
quot;cA") has a slot of
class "maybeInla", which is defined as setClassUnion("maybeInla", c("inla",
"NULL"))
- The "cA" class uses a slot of class "cB". "cB" is imported from package
"B".
Can someone explai
Dear Russell.
The assertthat package (by Hadley) provides a has_name() function.
> library(assertthat)
> x <- data.frame(y = NA)
> has_name(x, "y")
[1] TRUE
> has_name(x, "x")
[1] FALSE
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderz
Dear Bruce,
Have a look at drat: http://dirk.eddelbuettel.com/code/drat.html I think
that is what you are looking for.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics &
.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the experiment is done m
I
"c:/R/R-32~1.3/share/texmf/tex/latex" -I
"c:/R/R-32~1.3/share/texmf/bibtex/bst"' had status 1
Does someone has a clue what is going wrong?
Best regards,
Thierry
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team
Have a look at the RODBC package. odbcConnectAcces() is only available on
Windows.
Op 19-sep.-2015 12:08 schreef "Richard Cotton" :
> I have a package that uses win.version from the utils package.
>
> I've made my R code safe to use across platforms, I check that the OS is
> Windows before calling
Hi Hadley,
Thanks for the workaround.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the stat
Dear Hadley,
I've put a reproducible example at https://github.com/ThierryO/testS4
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Klinieks
r
setMethod(
f = "bar",
signature = signature(A = "myClass"),
definition = function(
a,
b
){
bar(
a = myClass@A,
b = myClass@B
)
}
)
When I build my package I get the error "no existing definition for
function 'bar'".
Any s
et_sha1() calculates the
SHA1 for different kinds of objects. You can find the code at
http://bitbucket.org/thierry_onkelinx/n2khelper
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
team Biometrie & Kwaliteitszorg / team Biomet
oth
32-bit and 64-bit.
Best regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the
regards,
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
To call in the statistician after the experiment is done may be no m
You have no guarantee that the user has write access to those folders. So
you might want to rethink your strategy.
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality A
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