Hello again Duncan,
I could see the two successes were ... creations and that the
others weren't.
I worry though that in searching for a solution, you need to end up with
something that is as simple for authors as what little effort is needed for
fig.alt; having looked at the HTML, I'd rathe
Thanks very much for your response.
The two images where the tags showed up are regular figures, using
lattice and base graphics. There are also a lot of rgl figures, which
have HTML code like this in the source .html file:
class="rglWebGL html-widget ">
(Looks like I should think about
thank,
I was wondering if my idea regarding the implementation is correct.
I took the idea from Tiago Olivoto and wrote an additional function that checks
if limma is installed.
Here is a mockup based on Tiago�s package:
check_limma<- function(){
if(!requireNamespace("limma", quietly = T
Hello Duncan,
I guess a few people might expect me to contribute to your request. First I'll
assure you that two graphics do have an alt tag which my screen reader is
telling me about, so in a sense that is success. I did not check with multiple
screen readers or different browsers because I wo
Packages can only be installed from the repositories listed and only CRAN is
the default so only CRAN package are guaranteed to work. I'd like to add that
the issue below is exactly why, personally, I would not recommend using
Bioconductor package as strong dependency (imports/depends), because
I received a request a few days ago to add alt text to the plots in the
HTML vignettes for the rgl package.
That was easy to do, and I did it, but realized most of the graphics
that rgl produces are not in format, they are WebGL canvases, and
those don't support the same method of adding alte
I will implement the changes you recommended into my package. Thank you for
your help.
I wasn´t ignoring your advice, I am just confused because other sources like
Stackoverflow gave me contradicting information and I wanted to be sure.
I will write if I encounter other problems which fit tha
You keep repeating basically the same questions, and appear to be
ignoring the advice you've received. That's partly understandable,
because some of it (what you find in places like StackOverflow) is
wrong, but I think you should trust what I said, and what Ivan, Martin
and Uwe said. Uwe is a
В Fri, 17 Mar 2023 12:29:51 +
"Ruff, Sergej" пишет:
> The problem is that a local installation of my package (via USB-stick
> for example) can´t install the dependencies from CRAN.
>
> The package works perfectly fine, if the dependencies are
> preinstalled.
This is a similar, but different
The user should set the CRAN+BioC via setRepositories() and then run
install.packages() will install all dependencies automatically.
Of course, if you install from a local repository without the required
packages or from a USB drive, R cannot resolve dependencies.
Best,
Uwe Ligges
On 17.03.2
Really.Whats a problem i have when all dependencies arent prei installed. I
thought the problem would be solved once my package is available on CRAN.
Here is a recent question I had regarding the same issue:
I am currently working on a r-package. I would like to submit my r package to
CRAN, b
On 17.03.2023 13:09, Ruff, Sergej wrote:
Thanks,
I thought about changing it to "Imports", but will it cause any issues when
CRAN runs checks on my package and limma isn´t available on CRAN?
No, BioC is a mainstream repository.
Best,
Uwe Ligges
Von:
On 17/03/2023 6:19 a.m., Ruff, Sergej wrote:
In my example I have the following lines:
### Differential expression analysis with limma
group = gl(2, n)
design = model.matrix(~ group)
fit1 = limma::lmFit(X, design)
fit = limma::eBayes(fit1)
The R CMD Check returns no Errors or Notes if Limma is
Thanks,
I thought about changing it to "Imports", but will it cause any issues when
CRAN runs checks on my package and limma isn´t available on CRAN?
Von: Ivan Krylov
Gesendet: Freitag, 17. März 2023 12:31:23
An: Ruff, Sergej
Cc: r-package-devel@r-project.org
В Fri, 17 Mar 2023 11:02:18 +
"Ruff, Sergej" пишет:
> I would like to ask, if I need to add something to the
> DESCRIPTION-file when declaring Bioconductor dependencies for CRAn
> Submission.
Strictly speaking, no. Once you list limma under Suggests, it's
possible and proper to install your
Thanks.
I would like to ask, if I need to add something to the DESCRIPTION-file when
declaring Bioconductor dependencies for CRAn Submission.
Right now I only listed limma under "suggests".
I asked online and get conflicting answers. Some recommend adding biocViews:
above suggests and some
В Fri, 17 Mar 2023 10:19:37 +
"Ruff, Sergej" пишет:
> Thats the source of my worries. Will the same error appear when CRAN
> checks the examples of my package? Or should I not be worried?
Yes, part of CRAN checks is running your package without the packages
listed under Suggests:
https://www
In my example I have the following lines:
### Differential expression analysis with limma
group = gl(2, n)
design = model.matrix(~ group)
fit1 = limma::lmFit(X, design)
fit = limma::eBayes(fit1)
The R CMD Check returns no Errors or Notes if Limma is pre-installed. If limma
is not pre-installed
On 17/03/2023 6:06 a.m., Ruff, Sergej wrote:
I was wondering how CRAN will handle Limma when running the automatic check.
I am worried that my package will be rejected if Limma won�t install from
Bioconductor on a clean version of R. Leading to an Error and Note during the
check.
I am using
I was wondering how CRAN will handle Limma when running the automatic check.
I am worried that my package will be rejected if Limma won�t install from
Bioconductor on a clean version of R. Leading to an Error and Note during the
check.
I am using Limma only for an example in my functions desc
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