lared from: ‘bar’
'loadNamespace' or 'requireNamespace' call not declared from: ‘bar’
Right, you shouldn't refer to a package in code without mentioning it in
the DESCRIPTION file.
Does this mean it is not possible to use 'bar' anymore in 'foo'?
I do
n't do it unless that company gives you permission, and apparently
they haven't.
Duncan Murdoch
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o yours. If you do that, be sure to
give proper credit to the authors.
Duncan Murdoch
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d throw me the following NOTE:
Package has a VignetteBuilder field but no prebuilt vignette index.
Any ideas how can I include the compacted PDFs in the souce package and have a
vignette index in the same time?
When you build the tarball, use th
On 07/01/2018 12:17 PM, William Dunlap wrote:
I think that assigning something to parent.frame() is bad practice, for the
same reasons that assigning to .GlobalEnv is bad. You could instead make
an environment in your package called, say, "TSEtools.env", with
TSETools.env <- new.env()
in so
They should be suppressed if you code the link as I show above.
Duncan Murdoch
Thanks for any help.
Russ
Russell V. Lenth - Professor Emeritus
Department of Statistics and Actuarial Science
The University of Iowa - Iowa City, IA 52242 USA
Voice (319)335-0712 (Dept.
heir code explaining why they asked not to run some lines. That's such
a sensible suggestion that it should have ended the thread.
Duncan Murdoch
Georgi
-Original Message-
From: Hadley Wickham [mailto:h.wick...@gmail.com]
Sent: 19 December 2017 19:22
To: Georgi Boshnakov
Cc: To
<- file.path(tempdir(),name)
dir.create(newdir, showWarnings = FALSE)
olddir <- setwd(newdir)
write.table(sleepstudy, file = "sleepstudy.txt", row.names=FALSE,
col.names = FALSE)
r <- nparACT_flex_loop(newdir, SR = 4/60, minutes = 435)
setwd(olddir)
Duncan Murdoch
setwd(newdir)
tory.
To fix this, just save the old directory, and restore it at the end of
your example. For example,
olddir <- setwd(tempdir())
# Run the rest of the example code here
setwd(olddir)
Duncan Murdoch
The full message can be seen here:
https://CRAN.R-project.org/web/checks/check
tk2", quietly = TRUE) when you loaded it, but this is
frowned upon, because the user might not want RGtk2 in their search
list. (It might have functions with the same names as functions from
other packages, and that can mess up the user's code.)
Duncan Murdoch
It all works fine on l
e functions you need. If they are unwilling to do that, then
you could ask them to distribute your package, or distribute it yourself
(e.g. by making it available on Github).
One other possibility is that their license would allow you to copy
enough of their package into yours that you wou
copy will match the CRAN binary of R-devel, but we'll see.
Duncan Murdoch
require(XML)
Loading required package: XML
Error: package or namespace load failed for 'XML':
package 'XML' was installed by an R version with different internals; it needs
to be reinstal
Can anybody help me to short out those problem please ?
Thank you very much.
regards
Pijush
[[alternative HTML version deleted]]
Generally R mailing lists are plain text. Your message was readable as
you posted it, but if you had added code, it would likely be a mess.
Please configure your mail program to post in plain text.
Duncan Murdoch
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oesn't mess with the
search list.
But that'll likely cause warnings, unless the same condition is used in
the NAMESPACE file where there should be an entry
S3method(foo, bar)
The thing is, I'm not sure if
if (requireNamespace("A&qu
On 02/12/2017 2:19 PM, Bill Denney wrote:
On Dec 2, 2017, at 09:43, Duncan Murdoch wrote:
I don't think there's anything better than Bill's solution, though I imagine it is
possible to ask for translation of the message. For example, sqrt(-1) currently gives a
warning with
ts would complain if you tested for equality
between a warning message and the result of gettext(): it's still true
that if the English warning changed, the test would fail.
Duncan Murdoch
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not legal syntax, it doesn't indicate anything at all.
Is this a bug or what should I do? The function runs perfectly
in R in its usual context, and in the .Rnw file it is in a chunk
headed
It's a bug in your code. I don't know if this is what you are trying to
do, but
authors like me write better Rd files.
If you run R CMD check on your package, you'll get warnings about lines
being too long. New submissions to CRAN will have to follow these
limits, but CRAN doesn't force package authors to update to meet them.
Dunc
packages are built with
tools compatible with those that built R. (Remember, packages are
designed for distribution to diverse systems.)
If you happen to know how to override some of these settings in a safe
way on your own system, then do what you did (as recommended in the R
Admin manual, se
suggest looking in
the NAMESPACE file to be sure that something is being exported. But
you're using devtools, so I don't know if that will be informative.
Duncan Murdoch
Sys.getenv('PATH') gives the following items that are related to R and
Rtools:
c:\Rtools\bin;c:\Rtoo
Solaris
machines that CRAN tests on). It is available on MacOS.
When you submit an update, mention the issue as you discuss your
response to existing errors in CRAN tests.
Duncan Murdoch
Thanks ahead,
Berry
URLs to vignette source, CRAN html view, check results:
https://raw.githubuserc
On 09/11/2017 3:05 PM, Rolf Turner wrote:
On 09/11/17 23:40, Duncan Murdoch wrote:
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I recommend trial and
On 09/11/2017 3:05 PM, Rolf Turner wrote:
On 09/11/17 23:40, Duncan Murdoch wrote:
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I recommend trial and
On 09/11/2017 3:29 PM, Rolf Turner wrote:
... Mr. Speaker.
On 09/11/17 23:40, Duncan Murdoch wrote:
On 09/11/2017 5:06 AM, Uwe Ligges wrote:
Note the % may be a comment?
Yes, and the body should be written in Rd markup, not R. Working out
the appropriate number of escapes is painful; I
\\\%d/\\\%m/\\\%Y")}}
Duncan Murdoch
Uwe
On 09.11.2017 06:05, Rolf Turner wrote:
I tried to define a macro to produce today's date (like unto the
"\today" command in LaTeX):
\newcommand{\today}{format(Sys.date(),"%d/%m/%Y")}
I put this into my *.Rd file just befo
reverse dependencies cope with changes. If your update breaks
a revdep, you need to explain what you did to help the revdep author
cope with it, and it needs to be enough that CRAN agrees that package
author is being negligent by not adapting. Or something like that.
Duncan Murdoch
The pat
d in the extended
version with n packages having m active versions, it's m^n times as much
testing.
Duncan Murdoch
The author of 'mypackage' is free to move up to 1.7.0 when
he/she sees fit, e.g., based on what additional functionality is included
in 1.7.0.
Also, it doesn&#x
o test both.
And if mypackage depended on herpackage and hispackage that also had
multiple active versions on CRAN, things would become unwieldy very quickly.
Duncan Murdoch
Thanks
Shivaram
[1] https://github.com/goldingn/versions
On Wed, Oct 25, 2017 at 1:05 PM, Ben Bolker wrote:
On
older versions on Github
or some other repository, and explain how users can install directly
from there.
Duncan Murdoch
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, b needs to have the
units of y divided by the units of x. Its se has the same units. If
you change the units for either x or y, you'll change the appropriate
value of b and se.
Duncan Murdoch
On Fri, 6 Oct 2017 at 21:23, Iñaki Úcar wrote:
El 6 oct. 2017 19:13, "David
replace that file with a file of your
own choosing, but you would certainly not be allowed to do that if you
wanted your package to appear on CRAN.
Duncan Murdoch
Regards.
Tanvir Ahamed
Stockholm, Sweden | mashra...@yahoo.com
On Monday, October 2, 2017, 9:59:06 AM GMT+
u how
to let all of this get through to the .Rd file.
Duncan Murdoch
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On 27/09/2017 6:21 AM, Jens Oehlschlägel wrote:
On 27.09.2017 01:00, Duncan Murdoch wrote:
I think R Core would not be interested in a vote, because you'd be
voting to give them work to do, and that's really rude.
Voting about other people's work is indeed a problem. This
detail, and listing all
changes to CRAN and Bioconductor packages that would be necessary to
implement it. That's a lot of work! Do you have time to do it?
Duncan Murdoch
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ct not. The Writing R Extensions manual describes the problem:
Fortran I/O initialization can interfere with the C I/O used by R.
This won't happen on all platforms, so it's really difficult for you to
be sure your uses are safe.
The recommended way to handle this is to do
all packages. So run
update.packages(type = "source") and you should get the same versions.
Duncan Murdoch
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sense for both of you to package it.
Assuming the jar file isn't already on CRAN, and it really is necessary
for your package, and your package adds something to CRAN, they'll
probably allow it. You should include a comment with your submission
explaining why you need the excepti
to this, I
would be happy to hear about it as if there is a problem with the
plotrix package I would like to fix it. Thanks.
I just tried this, and had no problem. So I think you'll need to see
the logs of exactly what problem André was seeing.
Duncan Murdoch
Jim
Original message
On 16/08/2017 8:31 AM, Dirk Eddelbuettel wrote:
On 16 August 2017 at 12:51, peter dalgaard wrote:
| > On 16 Aug 2017, at 11:11 , Berry Boessenkool
wrote:
| >
| > if a function in a package uses graphics::legend in the code, but does not
import it in the namespace, shouldn't there be a warning
ns are welcome!
Nothing that you've written is reproducible by others. See if you can
put together a short self-contained series of instructions that display
the problems (or just one of them). It might involve installing from
Github, or making a package tarball available somewhere
package build purpose
#' to import the usefull function.
#' @return NULL
#' @export
#' @import dplyr dbplyr DBI magrittr RPostgreSQL tidyr
#'
#' @examples
#' fun_import()
fun_import <- function(){
NULL
}
Not sure why you'd want these 13 lines instead o
hecking examples ..." and don't complete the tests.
How to solve it
Shiny apps are interactive, and the tests are performed in a batch
session, so one simple approach is to change your example to
if (interactive())
runclt()
Duncan Murdoch
Link to source code https://1drv.
CRAN
message was correct.
Phil, it would be helpful if you explained how you really produced that
tarball, so people know how not to do it.
Duncan Murdoch
Phil
On Wed, Jul 26, 2017 at 10:30 AM, Duncan Murdoch
mailto:murdoch.dun...@gmail.com>> wrote:
On 26/07/2017 9:05 AM
nce 2012. Not sure why it showed up in
your check.
Duncan Murdoch
(Full report in link below)
best,
Simon
<https://win-builder.r-project.org/incoming_pretest/170726_112041_mgcv_1818/00check.log>
-- Simon Wood, School of Mathematics, University of Bristol BS8 1TW UK
+44 (
g run by CRAN. If not, the bug is in the build code that you ran.
You can get a listing of the contents from within R using
untar("mirtCAT_1.6.tar.gz", list = TRUE)
When I do that, the partial.rdb file is entry 28.
Duncan Murdoch
Phil
On Wed, Jul 26, 2017 at 7:06 AM, Duncan Mu
n anyone shed some light on this
warning and my difficulty in reproducing the message? Thank you in advance.
How did you produce the tar.gz file? If you did it in some way other
than running "R CMD build ...", don't do that. When I run R CMD build,
I do get the
functions
(or equivalent ones). This might be more successful if you write the
help pages and send them a Github pull request explaining your need,
since that makes it essentially no immediate work (just long term
support work).
Duncan Murdoch
Thank you i
You can also use the "data" directory if you want to make them available
to users using the data() function.
Duncan Murdoch
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ot sure if this is also true of R-hub, but it does
offer checks on other platforms.
Duncan Murdoch
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placed it),
then report on the bug list, or on R-devel.
Duncan Murdoch
library(lubridate)
# today() does not behave as I expected
tz(now(tzone = "EET"))
tz(today(tzone = "EET")) # UTC!!
today("America/New_York") == today("Asia/Tokyo") # FALSE with no w
eople would find offensive.
However, CRAN's opinion is relevant if you want them to distribute it
for you. Name changes cause extra work for them so please don't do it
unnecessarily, and if you do think it's necessary, explain your
reasoning to them when you submit.
Duncan Murd
characters, so you could easily avoid the
note by removing or shortening the "third_party" directory name, which
should be under your control. If you have others where that is not
sufficient, you can think about renaming other directories, though I can
see that wouldn't be desi
initions, so you'll need to do some more work to
reconstruct the calls. That may have been done already; hopefully if so
someone else will point out where.
Duncan Murdoch
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run every function that you are exporting. If you had done that
originally, this error would never have slipped through testing.
Duncan Murdoch
Arnab Kumar Maity
Department of Statistics
Texas A&M University
3143 TAMU, Room 401A
College Station, TX 77843
aku...@stat.tamu
on a
different computer and testing it there first, to be sure that there
aren't any other problems with it.
Duncan Murdoch
Arnab Kumar Maity
Department of Statistics
Texas A&M University
3143 TAMU, Room 401A
College Station, TX 77843
aku...@stat.tamu.edu<mailto:arnabkrma...@stat.ta
rror, ?
Error: could not find function "fil"
fil() is a function of this package. The data with this package is getting
attached fine.
Any idea what is going wrong with the submission? Your help is much appreciated.
Duncan Murdoch replied that my NAMESPACE file doesn't export anythin
some directory under inst, e.g.
inst/images. Then R code system.file("images/foo.png", package = "pkg")
will give you the filename.
In most cases this isn't necessary, because in most vignettes figures
are produced by the R code, but obviously there are exceptions.
a
bug. We don't know that install.packages has the same bug.
Duncan Murdoch
Also posted on SO: http://stackoverflow.com/questions/44028355/r-force-
download-of-specific-package-versions-in-description-file
Thanks,
Martin
[[alternative HTML version deleted]]
___
if (requireNamespace("ggplot2")) ggplot2::ggplot()
else ... (optional warning that you need it) ...
Duncan Murdoch
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and
Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Q
function like foo_example().
I'd say it's better to show users how to find the folder, rather than
hiding that where they can't see it. Examples should be for learning,
not just to produce magic output.
Duncan Murdoch
HTH,
Zhian
-
Zhian N. Kamvar, Ph. D.
Postdoctoral Re
at package.
Duncan Murdoch
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le".
Not sure what you mean by "import". What are you starting with? What
do you want to end up with?
Duncan Murdoch
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foo <- dplyr::foo
else
stop("You need to install the dbplyr package, because dplyr::foo has
moved there.")
will allow you to use foo() anywhere (as long as its interface is the
same in both packages, of course).
Duncan Murdoch
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;static", and it doesn't matter
if the names in separate files clash. (At least this is true in C; I
assume C++ is similar.) Just make sure that the exported names don't
clash, and put them all into one DLL.
Duncan Murdoch
Best,
M.
On May 05, 2017, at 09:26 AM, Uwe Ligges
w
g LaTeX.
You can also try
R CMD Rd2pdf --no-clean foo.Rd
to see what LaTeX got produced from the foo.Rd man page. That will
likely contain an error if the full manual does.
Duncan Murdoch
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On 23/04/2017 7:53 PM, Rolf Turner wrote:
On 24/04/17 11:36, Duncan Murdoch wrote:
On 23/04/2017 6:18 PM, Rolf Turner wrote:
On 23/04/17 23:05, Duncan Murdoch wrote:
Looks like
extern void F77_NAME(mnnd)(double *, double *, int *, double *,
double *);
to me.
One more (I hope it'
On 23/04/2017 6:18 PM, Rolf Turner wrote:
On 23/04/17 23:05, Duncan Murdoch wrote:
Looks like
extern void F77_NAME(mnnd)(double *, double *, int *, double *,
double *);
to me.
One more (I hope it's the last!) question:
One of my subroutines has an argument of type *logical*. There
On 23/04/2017 6:38 AM, Rolf Turner wrote:
On 23/04/17 21:57, Duncan Murdoch wrote:
On 22/04/2017 5:25 PM, Rolf Turner wrote:
(1) I found that having an R function with the same name as that of a
routine (Fortran subroutine in this case) that it called, causes all
sorts of chaos. I had a
:
subroutine mnnd(x,y,n,dminbig,dminav)
implicit double precision(a-h,o-z)
.
I.e. the "actual types are "double precision",
"double precision", "integer", "double precision",
"double precision".
ader Rmd. This way R CMD build could build both pdf and html
versions of the output.
That's another solution. My suggestion would be simpler: just pick one
of PDF or HTML, and give the user instructions to produce the other if
necessary, but don't produce it for them.
Duncan Murdo
urce there.
There are ways to bend the rules that some people use (e.g. if running R
CMD build takes too long, some people find tricky ways to copy vignette
outputs without building them), but those are likely pretty fragile. As
you appear to have found.
Duncan Murdoch
_
y to clean
it up a bit and then maybe the error messages will be less obscure.)
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.g. I don't). If you are willing to volunteer to do this (or can
recruit someone to do it), go ahead. Assuming you do a good job, we can
put your patches into the base code.
Duncan Murdoch
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ngset <- function() { ... }
if (transaction) {
DBI::dbBegin(conn)
}
tryCatch(
longset()
error = function(e){
if (transaction) {
dbRollback(conn)
}
stop(e)
}
)
Duncan Murdoch
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On 01/03/2017 2:17 AM, Henrik Bengtsson wrote:
On Tue, Feb 28, 2017 at 2:47 PM, Duncan Murdoch
wrote:
On 28/02/2017 5:17 PM, Patrick Schratz wrote:
Thanks Duncan, that was the problem! Although the Rbuildignore entry
pointed to the main dir
No, it contains patterns, not paths, and is
ource directory". Put ^ at the beginning if you want to refer to the
main dir.
Hadley, reporting what gets omitted might be a good suggestion, but it
might report too much in a package with compiled code (the .o files will
generally be omitted; rgl has 51 of those in src...).
Duncan Murdo
ou want to check on your own, please use the `dev` branch;
https://github.com/pat-s/sperrorest/tree/dev
pandoc-citeproc: stable 0.10.4.1 (bottled), HEAD
pandoc: stable 1.19.2.1 (bottled), HEAD
Your .Rbuildignore file says not to include Biblio.bib. Don't do
r" package, I have checked that correctness is at the mercy of
the order of loading of the packages, even though the "bar" package
imports the "foo" package. So that doesn't seem to work either.
Before committing to making 'bar' an S4 class, does anyone
On 10/02/2017 5:28 PM, Jonathon Love wrote:
hi duncan,
On 11/2/17 01:44, Duncan Murdoch wrote:
On 10/02/2017 8:52 AM, Jonathon Love wrote:
hi uwe,
On 10/2/17 23:40, Uwe Ligges wrote:
On 10.02.2017 03:19, Jonathon Love wrote:
hi,
i'm trying to include some greek characters
rocessed differently in UTF-8 locales versus
others. So you might get away with doing this if Roxygen2 always runs
in a UTF-8 locale, but on Windows you will see problems.
Duncan Murdoch
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u explicitly import pdf() from grDevices, that won't happen.
Duncan Murdoch
Thank you,
Cathy Lee Gierke
*“Darkness cannot drive out darkness: only light can do that. Hate cannot
drive out hate: only love can do that.” *
*“The arc of the moral universe is long, but it bends towards justic
in the old version
of R that Cathy was using. Messages in current versions are clearer.
Duncan Murdoch
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hat the old versions will eventually go away. (Or
just re-implement the old ones using the new ones.)
You can call the .Deprecated() function from the old ones to warn users
every time they are used.
Duncan Murdoch
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On 29/12/2016 6:50 PM, Duncan Murdoch wrote:
On 29/12/2016 2:58 PM, Roy Mendelssohn - NOAA Federal wrote:
HI All:
If any cares, the offending line is in the ggplot2 file utilities.r where it
has:
#' A waiver object.
#'
#' A waiver is a "flag" object, sim
h waiver() tries to put a class on NULL,
structure() puts it on a length-zero list instead. R-devel's complaint
is unnecessary here, but could be avoided with the code change
waiver <- function() structure(list(), class = "waiver")
I've cc'd Hadley to let him kno
vignette won't build
on R-devel.
Duncan Murdoch
-Roy
On Dec 29, 2016, at 10:38 AM, Duncan Murdoch wrote:
On 29/12/2016 1:24 PM, Ben Bolker wrote:
Sorry, correction/clarification to my last post: it's *not* a bug in
ggplot2, rather apparently (?) it's something in base R
n or later. (Since
the change to R-devel is very recent, it may change again.)
Duncan Murdoch
cheers
Ben
On 16-12-29 01:16 PM, Roy Mendelssohn - NOAA Federal wrote:
Hi All:
I am working on a new submission of my xtractomatic package (the
main change being the use of https). I deve
list of
"reverse " on https://CRAN.R-project.org/package=Rcpp (where is
Depends, Imports, Suggests, or LinkingTo).
Duncan Murdoch
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ate an account for you. Because of spammers, we no longer
allow automatic registrations.
Duncan Murdoch
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first?
They should both happen around the same time. It doesn't matter what order.
If one happens too much before the other, things are likely to go wrong
and cause both you and CRAN extra work.
Duncan Murdoch
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PACK_LIBS) $(BLAS_LIBS) $(FLIBS)
I don't know if you need LAPACK and Fortran libs; try it without those
if you want. R will set the macros appropriately when it is built.
Duncan Murdoch
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ethod; instead, it simply exports the function 'manchoo.bar' and moves
'foo' to Suggests
And a third way is for the developer of 'bar' to allow it to be dual
licensed as GPL 2 or 3, or something else more permissive than GPL 3.
They may not be able to do that
hat it will be a requirement for submission from now on.
Documentation updates will be showing up as we find them.
Duncan Murdoch
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ewest Rdevel, everything worked fine.
This has been fixed as of revision 71616.
Duncan Murdoch
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On 01/11/2016 1:10 PM, Henric Winell wrote:
On 2016-11-01 17:01, Uwe Ligges wrote:
> On 01.11.2016 15:56, Duncan Murdoch wrote:
>> On 01/11/2016 9:49 AM, Rampal Etienne wrote:
>>> Dear all,
>>>
>>> When I try to build a Windows binary in RStudio using R-devel
round it by specifying the library path explicitly. Since you were
installing into a temporary library, that's a little tricky, but for
most people it should be easy.
I'll see if I can track it down and fix it.
Duncan Murdoch
I have updated RStudio, Rtools and Rdevel
ata, and nobody else will (without going through
some contortions). Some of the newer object systems support this
approach, but you don't need to use them, you can just return a function
(or a list of functions) and make calls to it/them.
I hope this helps.
Duncan Murdoch
___
eed to declare your
dependencies.
It sounds as though there's a bug somewhere, in R, RStudio,
gWidgetRGtk2, or Windows. You're in the unenviable position of having
to find and fix it. (CRAN won't care if this only affects RStudio, and
you might get away with an install that doesn&
t kind of
error shouldn't cause your package to fail to be accepted. However, we
don't do those tests, because we currently don't have the resources to
do so.
Duncan Murdoch
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Linux, Windows, OS X. If you can, add Solaris:
once you're accepted onto CRAN, you'll be tested there as well.
Duncan Murdoch
Lorenzo
On 19 October 2016 at 22:36, Dirk Eddelbuettel wrote:
For this subproblem:
On 19 October 2016 at 22:14, Lorenzo Busetto wrote:
| On Linux bu
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