On 26/12/2021 8:03 a.m., Duncan Murdoch wrote:
I've now submitted a bug report for R:
https://bugs.r-project.org/show_bug.cgi?id=18266 along with a suggested
patch to remove the first of these.
And this patch was committed to the trunk by Kurt Hornik, so it should
appear in R 4.2.0 or
I've now submitted a bug report for R:
https://bugs.r-project.org/show_bug.cgi?id=18266 along with a suggested
patch to remove the first of these.
Duncan Murdoch
On 26/12/2021 5:55 a.m., Duncan Murdoch wrote:
On 26/12/2021 12:07 a.m., Spencer Graves wrote:
Hello, All:
es:
Version 8.0 [dataset]. Minneapolis: University of Minnesota, 2018.
http://doi.org/10.18128/D010.V8.0
You'd get a format pretty close to that if you don't try to make the
title into a link, just enter it as
Steven Ruggles, Sarah Flood, Ronald Goeken,
Josiah Grover, Erin M
duced from vignettes (which is the recommended way to do things, but
isn't required) then you shouldn't have inst/doc in the source at all.
R CMD build will create it when it builds the tarball.
Duncan Murdoch
Eric.
On Fri, Dec 10, 2021 at 10:25 AM Duncan Murdoch
mailto:murdoch.dun.
Just delete the .html output from earlier runs before you run R CMD
build, and it will have no choice but to rebuild them.
Duncan Murdoch
On 10/12/2021 9:29 a.m., Eric Weine wrote:
Hello,
Sorry yes, I think that my initial post on stack overflow is a bit
misleading. I have checked the file
nto the tarball.
Duncan Murdoch
Cheers,
Simon
On Dec 10, 2021, at 10:52 AM, Eric Weine wrote:
Hello,
I'm having an issue where my vignette created using R CMD build does not
match the vignette created using devtools::build_vignettes or when I knit
with RStudio. I posted about this iss
all reads.
To handle larger ones, you need to know what size blocks you are going
to receive with each read. If that varies unpredictably, I doubt if
there's much you can do other than reducing the timeout.
Duncan Murdoch
Ben Engbers
-
CreateSocket =
un,
and add other examples that execute quickly.
Even better might be to include only the ones that execute quickly:
just like CRAN, users don't want to wait a long time for examples to
finish.
Duncan Murdoch
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to initialize the default for c as it depends on one value
of "a" or the other?
That c=a*b only works with non-standard tidyverse evaluation. It causes
other problems, e.g. the inability to pass ... properly (see
https://github.com/tidyverse/glue/issues/231 for an example).
Dunc
this should have been made illegal when R was created, but I think
it's too late to outlaw now: I'm sure there are lots of people making
use of this.
Or am I missing something?
Duncan Murdoch
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t;- body(fn)
Duncan Murdoch
Building Matrix with --no-byte-compile reduces the size of R/Matrix.rdx
by more than half, from 2.7 MB to 1 MB.
-Bill
On Sat, Oct 30, 2021 at 12:00 AM Mosqueira Sanchez, Iago
mailto:iago.mosque...@wur.nl>> wrote:
As far as I can see only cla
lazyLoadDBfetch() works and read one of them to see what's in
it, but I haven't done that.
Duncan Murdoch
Iago
On Fri, 2021-10-29 at 20:21 -0400, Duncan Murdoch wrote:
On 29/10/2021 4:23 p.m., Gábor Csárdi wrote:
You probably (accidentally?) put some large object into your
packa
sy to have them included too.
Duncan Murdoch
Gabor
On Fri, Oct 29, 2021 at 10:07 PM Mosqueira Sanchez, Iago
wrote:
I am getting warnings in some packages about the size of the R folder
* checking installed package size ... NOTE
installed size is 20.5Mb
sub-directories of 1Mb or
ndex. Presumably they go to
the end.)
Rebuild the formula after sorting.
Duncan Murdoch
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to.
When you called clone(x), you called the bit::clone generic which never
received the registration, so dispatch to clone.ff never happened.
It makes sense: you don't want a generic in one package to interfere
with an unrelated generic in another package that happens to have the
same name.
and that would allow you to do so.
And there are other choices too: there are several packages
implementing object systems that allow objects to maintain persistent
data. I haven't used those, so this list may contain omissions and
errors: R6, R.oo, proto.
Duncan Murdoch
___
he function assigned to
plot.foo never has a different environment than the one it ends up with
(and I don't need to remember how evalq() works).
Duncan Murdoch
On Thu, Oct 21, 2021 at 12:29 AM Rolf Turner
wrote:
I have a plot method (say plot.foo()) that I want to be able to call so
problems.
What is the recommended way to create new S3-methods that get
dispatched? In earlier versions of the packages I simply exported
everything - that worked.
I import the generic and use S3method(generic, method). I don't export
the methods, so I wouldn't be able to call z &
re defunct
Alternatively, you could deprecate all of them now, but edit the main
one so it suppresses the deprecation messages in the others.
Deprecation messages are documented to have class "deprecatedWarning",
so you can suppress only those messages if you work at
rball, rather than a bug at CRAN.
Duncan Murdoch
On 09/10/2021 10:29 a.m., Mollie Brooks wrote:
[CROSSPOST from glmmTMB issue #767
https://github.com/glmmTMB/glmmTMB/issues/767]
Hi devel list,
I recently noticed that a vignette is missing a couple of equations when
installed from CRAN and wh
On 07/10/2021 5:58 p.m., Duncan Murdoch wrote:
I don't work with models like this, but I would find it more natural to
express the multiple formulas in a list:
list(d ~ p + x + y, s ~ p + w + y, p ~ z + y)
I'd really have no idea how either of the proposals below should
e this are used to working
with notation like yours, that would be a strong argument to use your
notation.
Duncan Murdoch
On 07/10/2021 5:51 p.m., Richard M. Heiberger wrote:
I am responding to a subset of what you asked. There are packages which use
multiple formulas
in their argument sequen
approaches are possible; you want to choose the one that is
easiest, and most maintainable.
Duncan Murdoch
Here's is what one datatype currently looks like:
List of 2
$ : int [1:16, 1:16, 1:16] 9 9 9 9 10 10 1 1 14 14 ...
..- attr(*, "palette")=List of 16
[snip]
$ : int
On 30/09/2021 5:21 p.m., Jeff Newmiller wrote:
What if you are on Windows but running R at the command prompt, or via cygwin,
or in the console window of RStudio?
This seems unstable to me.
Sorry, too much context missing. What's unstable?
Duncan Murdoch
On September 30, 2021 11:
rticularly frustrating experience for your
users. It would mean half the installs export the function, and half don't.
Duncan Murdoch
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s far as I know it's okay to use message() (or cat() or print(), but
message() is preferred) to give your message, just not stop() or
warning() -- those will signal a problem to CRAN that you should fix.
Duncan Murdoch
I should add that when I first ran into this awhile back I ask
also works
on Github.
You do need to make sure the man/figures directory is included in the
tarball. Check your .Rbuildignore file for patterns that might exclude it.
Duncan Murdoch
Locally, README.html works fine (both figures are shown). I think the
problem could be that
https://c
requested imports from
yours, for instance.
So if you put your startup message on .onAttach, you probably won't get
the note.
Duncan Murdoch
Thanks,
Vonn
* checking R code for possible problems ... [19s] NOTE
File 'mypackage/R/onLoad.R':
.onLoad calls:
packageStartupMess
gesting (to R-core) to simply add
Sebastian: R-core isn't involved in this. CRAN is a separate group.
Duncan Murdoch
more empty lines before "current CRAN status" and maybe it should also
say something like "(for comparison)" to clarify that these results are
not t
() function could do your translation for you.
To do the translation you want, you'd use something like
original <- "45 \u00b5m"
chartr("\u00b5\u03bc\u3382\u338c\u338d\u3395\u339b\u33b2\u33b6\u33bc",
"uu", original)
Duncan Murdoch
Is there a
at you would have created, given the name of your package. You should
look at your package source to figure out if there's an example or test
that created it but didn't delete it.
Duncan Murdoch
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People shouldn't be able to install your package unless the "hard"
dependencies are available.
If EBImage isn't essential to your package, you should make it a "soft"
dependency by listing it in Suggests and checking for it every time you
use it.
Duncan M
quot;))
This removes one level of processes, but the tryCatch() and processes
run within this function are still there, so it might not be sufficient
for you. In that case the only solution might be to add debugging code
into R and recompile it.
The similar command for INSTALL is tools:::.
xpr %while% parenthesized_cond
in the \usage section, and document standard usage in the \details
section and examples.
Duncan Murdoch
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On 26/07/2021 4:43 p.m., Kent Johnson wrote:
The {anytime} package by Dirk Eddelbuettel uses {BH} and generates the
same NOTE when I CMD Check it locally on Windows. It seems safe to
ignore this NOTE.
But it generates no messages on CRAN: OK all the way.
Duncan Murdoch
Kent
te those
warnings (e.g. abcADM, ACEt, etc.) to see if they're using the same
parts of Boost as you're using, and have found a way to avoid the warnings.
Duncan Murdoch
Kent
--------
*From:* Duncan Murdoch
*Sent:*
here: those functions appear to have been linked in to your
DLL, so somebody is calling them. I'd try to track down those calls and
see if there's a way to compile without them.
Duncan Murdoch
win-builder results are here:
https://win-builder.r-project.org/incoming_pretest/rt
ing R CMD build (or equivalent functions). Those may not be
recognized by the R installer, so you would need to untar them, run R
CMD build yourself, and then install the corrected tarball.
Duncan Murdoch
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y_epi_sim.net'
You can write to the directory given by tempdir(). You may still get a
note if you don't delete the files when you're done with them.
No idea about the other issue.
Duncan Murdoch
Is there a recommended path/location that I can dependably write to that
won
ernatively, he can go ahead and use :::, but just not expect his
package to be on CRAN. There are other ways to distribute packages.
Duncan Murdoch
Naturally this might be a lot of
work and risks different behaviour between your package and parallel,
but neither might be that terrible for you.
e("BIEN"))
stop("This function requires the BIEN package.")
# do things, with BIEN:: prefix on functions from that package.
and make sure your examples are also conditionalized.
You'll still get messages that they aren't available, but it won't
completely di
ly than you would in how
they should spend their time. One thing I can infer from past silence
is that they don't like discussing such things here.
Duncan Murdoch
On 16/07/2021 1:37 p.m., Kevin R. Coombes wrote:
Hi Jeff,
I think you are inferring an attitude in my initial message that
a .c
file, updated the NAMESPACE with useDynLib(mypackage, .registration = TRUE)
and have no error on my local computer.
I don't know how to fix this problem as I cannot replicate it on my
computer. Is it just a false positive ?
It's unlikely anyone could help you with this without seeing w
licensed under the AGPL, so there's some extra
motivation for companies like Google to pay for the commercial license.
That probably doesn't apply to Ben's project, though. It would likely
require all copyright holders to agree on a second non-open license.
Duncan Murdoch
O
On 07/07/2021 9:08 a.m., Uwe Ligges wrote:
On 07.07.2021 13:18, Duncan Murdoch wrote:
On 07/07/2021 5:29 a.m., David Enrique Payares García wrote:
Hello everybody,
I developed an R package that depends on packages hosted in GitHub.
In the DESCRIPTION file, I added the R packages (from
part causing the ERROR. Without seeing your
package I can't say for sure, but I would guess you have made some
unconditional use of those three packages. Since they are only
Suggested packages, you can't do that. Your package has to run even if
they are not available at all. (It may
be a
transient problem on Winbuilder.
Devel versions of R change every day, so there are more possibilities
for origins of the problem there.
Duncan Murdoch
I'll compare the dependencies between the two packages and focus on
those used by both for now, to see if it's cau
error, and a minimal change to it that does. Then perhaps you'll
understand the root cause of the error.
Duncan Murdoch
On 06/07/2021 3:11 p.m., Alex Chubaty wrote:
FWIW I'm having the same issue with package NetLogoR (
https://github.com/PredictiveEcology/NetLogoR/)
Passing window
On Mon, Jul 5, 2021 at 11:01 AM Duncan Murdoch <mailto:murdoch.dun...@gmail.com>> wrote:
On 05/07/2021 10:32 a.m., Ben Bolker wrote:
> I'm running into trouble checking a new release of the
'broom.mixed'
> package
<https://cran.r-project.o
nd that was
compiled on Windows. Perhaps someone else knows how to demangle those
names?
Duncan Murdoch
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o mention it.
Yes, seems related. If you're depending on a package that won't build,
your tests will fail.
Perhaps you can reduce your dependence to Suggests, which will give a
note on the failure to load, but no more.
I don't know if this is under your control, but I b
#x27;d agree in the normal case where the package is still active on CRAN.
In the case where a package has unaddressed issues with no response to
CRAN from the maintainer, they'd probably be quite happy to have someone
volunteer to take over.
Duncan Murdoch
7;t try to create it.
Feel free to ignore me (and I'll go away! :-) ).
I agree the warning shouldn't be ignored, but I believe it was created
by R CMD check, not by Spencer directly. So the real question is: why
was it already there?
Duncan Murdoch
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I'm back in civilization for a few days, and have submitted a PR to
Hmisc: https://github.com/harrelfe/Hmisc/pull/143 .
Duncan Murdoch
On 23/06/2021 8:51 a.m., Gilbert Ritschard wrote:
Thanks for this suggestion.
Pushing the investigation a bit further, I found that the error result
On 24/06/2021 5:53 p.m., Gábor Csárdi wrote:
Actually, I see somewhat different things in RStudio, for me there is
no pre-clean (with the default options AFAIR).
I'm not using the default options, as I said.
Duncan Murdoch
I can reproduce the rebuilding for rgl, but not for other pac
On 24/06/2021 5:22 p.m., Gábor Csárdi wrote:
On Thu, Jun 24, 2021 at 10:31 PM Duncan Murdoch
wrote:
[...]
I'm working in RStudio on a Mac, in case that makes any difference.
Yes, RStudio probably does its own thing in "Install and restart". The
pre-clean of course removes t
On 24/06/2021 4:52 p.m., Dirk Eddelbuettel wrote:
On 24 June 2021 at 16:31, Duncan Murdoch wrote:
| This does the full compile again, so it's slow.
ccache fixes that (as it has its own cache). It also works on macOS.
I haven't tried ccache: shouldn't "make"
On 24/06/2021 3:44 p.m., Gábor Csárdi wrote:
On Thu, Jun 24, 2021 at 8:55 PM Duncan Murdoch wrote:
[...]
A disadvantage of the devtools method is that a regular build after
load_all() seems to do a full 75 sec build: load_all caches things for
itself, but doesn't put them in the same pla
As Dirk said, you can also use command line options to suppress building
vignettes or other things if they take too long.
Duncan Murdoch
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ERROR to a NOTE
if that's the only issue), and then your package wouldn't get this error.
I'd do so myself, but I have very expensive Internet access most of the
time for the next few weeks.
Duncan Murdoch
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sure about that. I think the devtools submit functions
use that file to fill in the web form. I don't think you normally
include it in the tarball, though things might have changed.
Duncan Murdoch
I believe that's where the CRAN maintainers look for info like that
u only get that message if "multiarch" tests are requested. If CRAN
is running with --no-multiarch it won't show up.
Duncan Murdoch
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ntact the matrixcalc maintainer,
and help them to fix the issues so that matrixcalc doesn't get archived.
They may or may not be willing to work with you.
I'd say my third choice is the best choice in the short term, and 2nd or
4th would be good long term solutions.
Duncan Murdoch
Thanks!
> On Wed, Jun 2, 2021 at 1:08 PM Duncan Murdoch
wrote:
> [...]
>> > search. It would be nice to know if there's an automatic way to
answer
>> > the question
>> >
>> > "Why does package xxx appear to require yyy?"
On 02/06
ice to know if there's an automatic way to answer
the question
"Why does package xxx appear to require yyy?"
Duncan Murdoch
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7;s a level of complexity I'd rather not get into.
I wouldn't call it "complex", but it could be tedious.
Duncan Murdoch
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true.
2. Leave in the fda dependency, but make the test conditional, i.e. change
if (fda::CRAN())
to
if (requireNamespace("fda") && fda::CRAN())
I'd do number 1, or just assume everything is being run on CRAN.
Duncan Murdoch
On 23/05/2021 6:49 p.m., Spencer Graves w
I don't see where the connection is, but it's almost certainly coming in
through your unconditional use of "fda::CRAN()". Since "fda" is not a
hard requirement, this should be conditional on having it installed.
Duncan Murdoch
On 23/05/2021 5:25 p.m., Spencer G
might be enough for you, but I think the 2nd line
_R_CHECK_FORCE_SUGGESTS_: false
may be more important: you use ks, it imports plot3D, plot3D imports
misc3d, but it only suggests rgl and tkrplot: so that would let ks load
without XQuartz support.
Duncan Murdoch
On 23/05/2021 3:09 p.m., Spencer Graves wrote:
Hi,
s
run: |
install.packages(c('tinytex', 'ks')) # Maybe tinytex is
already there?
tinytex::parse_install(
text = "! LaTeX Error: File `tikz.sty' not found."
)
shell: Rscript {0}
Duncan Murdoch
On 23/05/2021 11
On 22/05/2021 10:05 p.m., Spencer Graves wrote:
Hello:
What do you suggest I do to enable GitHub Action to process "sos.Rnw"
properly?
The development version of my "sos" package passes "R CMD check" on
my Mac but fails in all four platforms under GitHub Action on
https:
usual", there may be a problem at your end
stopping you from downloading the info.
Duncan Murdoch
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ls to find them.
Duncan Murdoch
/
/
/Instead of passing the private R package environment to C, is there a
way to alter the namespace so that files in the "R" directory of the
package can be read by the C code but not exported to users? There are
specialized export and import f
it will need manual
intervention to ignore the automatic rejection.
Following Dirk's advice is thus advisable (passing the auto checks is
better than requiring manual intervention on every update), but not
strictly necessary.
Duncan Murdoch
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your package for "col_ed"
to see where it is being used. Then figure out why R thinks you are
trying to get it from the cli package.
Duncan Murdoch
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uldn't list knitr in both Depends and Suggests.
Duncan Murdoch
*
*
And my vignette includes:
*title: "title"
author: "name"
output: rmarkdown::html_vignette
vignette: >
%\VignetteIndexEntry{title}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}*
*
gested package in your
DESCRIPTION file.
Duncan Murdoch
Sincerely,
Danielle
*title: "title of this vignette"author: "name"output:
markdown::html_vignettevignette: > %\VignetteIndexEntry{vignette title}
%\VignetteEngine{knitr::markdown} %\VignetteEncoding{UTF-8}*
_
t that will always be true, even
if one version is "endorsed by R Core".
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On 26/04/2021 8:55 a.m., Duncan Murdoch wrote:
I had been under the mistaken impression that warnings in test code
would lead to NOTEs or WARNINGs in R CMD check, but they are ignored.
I think the only outcomes from running test code are OK or ERROR, the
latter happening when R exits with a non
ch, and is fairly inconvenient to keep up to date.
Duncan Murdoch
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re is "environment(rgl.init)", which is the
private environment within the package.
Then in C code, save that environment:
rglNamespace = in_namespace;
and use it later:
result = eval(PROTECT(lang2(PROTECT(install("rglFonts")),
PROTECT(ScalarString(mkChar(family), r
evaluate them in the
package namespace environment.
Duncan Murdoch
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On 25/04/2021 12:56 p.m., Duncan Murdoch wrote:
On 25/04/2021 12:46 p.m., Dirk Eddelbuettel wrote:
...
It has long been true that the main test runners (RUnit, testthat, now also
tinytest) are automagically included, which is a defensible (if undocumented)
special rule.
It's a bad
On 25/04/2021 12:46 p.m., Dirk Eddelbuettel wrote:
On 25 April 2021 at 12:27, Duncan Murdoch wrote:
| On 25/04/2021 11:35 a.m., Dirk Eddelbuettel wrote:
| > I last wrote about that four years ago under the title "Suggests != Depends"
| > http://dirk.eddelbuettel.com
On 25/04/2021 11:35 a.m., Dirk Eddelbuettel wrote:
On 25 April 2021 at 11:14, Duncan Murdoch wrote:
| What I haven't tried to do is check any of them if *none* of the
| suggested packages is available. Packages should still build and check
| without ERRORs in this case, though I'd ex
On 25/04/2021 8:49 a.m., Duncan Murdoch wrote:
The current CRAN release of rgl fails on winUCRT because of missing
dependencies:
'htmlwidgets', 'htmltools', 'knitr', 'jsonlite', 'shiny', 'magrittr',
'crosstalk', 'manip
ons, Dirk!), 'base64enc'
gets a NOTE (hurray Simon!). 'rlang' is failing a test because of a
missing suggested dependency on 'glue'. At that point I stopped searching.
Does anyone have a list of packages that actually need fixes? I'd like
to help those maintainers with the necessary updates.
Duncan Murdoch
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,
and specify it using "--test-dir=". One of the scripts there can run
the files in the regular tests directory, so you get both sets with that
option, but CRAN will only run the regular ones.
Duncan Murdoch
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e, but you aren't listing all the articles.
Duncan Murdoch
I already have this metadata in the vignette:
vignette: >
%\VignetteIndexEntry{Acoustic data sets in NatureSounds}
%\usepackage[utf8]{inputenc}
%\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
I can
hat
in your results, the testing package may need to replace reference
values. I think I'd be uncomfortable doing that.
Duncan Murdoch
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ave class c("mesh3d", "unorderedList",
"ignoreNULL"), and comparison methods like base::all.equal() or
waldo::compare() would ignore the unimportant differences.
The hardest thing here would be to agree on the class names and what
they imply.
Duncan Murdoch
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gestions for ways to hide internal layouts of
objects from users. That seems a lot harder.
Duncan Murdoch
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On 16/04/2021 7:40 a.m., brodie gaslam wrote:
An all.equal method? This might not work with 3rd edition though
(untested), and I'm not sure what method registration requirements
would exist for the user.
It already has one, but it isn't used by testthat 3.
Dunc
izes the
objects, but that seems very specific to testthat version 3. I'd like
ideas for something more robust.)
Duncan Murdoch
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predict(arimaGGM,newxreg = 1:100)
the data is also attached to the mail :)
No, it wasn't. If you want more specific help, you should include a
self-contained example in the text of your message.
Duncan Murdoch
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'raster' and 'sp' packages).
I wasn't suggesting that my code was a solution, it's just a hint about
what is going wrong. I don't know how the coastline plot determines the
bounds of the plot region, but if that isn't working, then you'd have
probl
up. Maybe that's enough
of a hint for you:
library(DEPONS2R)
data("coastline")
library(rgdal)
coastline2 <- spTransform(coastline, crs(bathymetry))
plot(coastline2, col="lightyellow2")
data("bathymetry")
plot(bathymetry, add=TRUE)
This puts the legend
x27;t seem possible for a fix on my end.
You need to let us see the message about the submission failure if you
want us to give you advice about it.
Duncan Murdoch
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Here's a better way to do the file-at-a-time check:
Load the .Rd file in RStudio, and click on Preview. Copy the whole
examples section to a test.R file. RStudio will mark all the syntax
errors, but won't be fooled by the \% escapes, since the Preview handled
them.
Duncan Murd
ing the test.R file into
RStudio; it'll put markers beside each syntax error. Unfortunately, it
thinks
checkAllUnique(tmpTib \%>\% pull(1))
is a syntax error: those escapes are required in Rd, but are illegal in R.
I don't know if there's a way to do it directly from t
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