Dear Kasper,
I think the issue was not with the loading data in the examples of the
functions, but with the Rd documents of the datasets themselves, where it says
“usage{data_name}” instead of “usage{data(data_name)}”. These Rd documents are
however automatically created using roxygen2. I still
Your diagnose sounds reasonable to me. I don't use roxygen2 myself, so I
can't really help here (and this is one of several reasons: it adds another
layer of potential problems to the documentation process). Perhaps someone
who uses roxygen2 can comment? Or perhaps they (roxygen2 developers) have a
One can write arbitrary documentation pages in roxygen2; the page doesn’t have
to rely on automatic generation from data objects. For instance filling in the
following template would get you (close to) what you want
#' @rdname
#' @name
#' @description
#' @usage
#' @details
#' @return
#' @example
does
@docType data
help here?
On Fri, May 1, 2020 at 8:52 AM Martin Morgan
wrote:
> One can write arbitrary documentation pages in roxygen2; the page doesn’t
> have to rely on automatic generation from data objects. For instance
> filling in the following template would get you (close to) what
Hello Bioconductor community,
Since releasing the 3.11.0 versions of the db0 packages, we have added in more
recent GO information. Therefore a newer 3.11.1 version of db0s are now
available (arabidopsis.db0 is now at version 3.11.2).
The new OrgDbs and TxDbs for Bioconductor 3.11 are now avail
Dear all,
Following Martin's guide, I added @name to the rd comment and replace the
dataset name by NULL, the warning went away.
Previously, it was:
#' An example of a final processed & filtered phylogenetic profile.
#’ …
#’ …
"finalProcessedProfile"
Now, it becomes
#' An example of a final pro
org.At.tair.db has been updated and will be undeprecated. This package will
remain in Bioconductor.
On 3/30/20, 11:37 AM, "Bioc-devel on behalf of Shepherd, Lori"
wrote:
The Bioconductor Team is continuing to identify packages that will be
deprecated in the next release to allow for the
Dear all,
So the final solution for this issue is:
- using @name to define the name of the data set, instead of writing it under
the rd comment block (solved the warning of R CMD Check: "Variables with usage
in documentation but not in code")
- using @docType data (thanks Vincent) to avoid the
Hi Lori,
we have recently submitted OpenStats package to Bioconductor and it is
approved, however, I do not have permission to commit to the repository.
When I check the in
https://git.bioconductor.org/BiocCredentials/permissions_by_user/, I see
that I have only access to PhenStat package. Please
Hi Hamed,
It seems you had two usernames for whatever reason, I've corrected the
issue. You should see access to both your packages now.
Best,
Nitesh
--
Bioconductor Core Team
On 5/1/2020 11:06 AM, Hamed Haseli wrote:
Hi Lori,
we have recently submitted OpenStats package to Bioconductor an
Thanks very much Nitesh, It is now in perfect working order.
Regards.
Hamed.
Hamed Haseli.M
| Hamed Haseli.M, PhD (Statistics)
| Data Scientist, Mouse Informatics
| E: hame...@ebi.ac.uk
| P: +44(0) 1223 494 451
| M:
Dear Nitesh,
Thanks for your help!
I just changed my subscription to the new address, and updated the DESCRIPTION
of the packages accordingly.
Best regards,
Héctor.
On 30 Apr 2020 at 17:57 +0200, Nitesh Turaga , wrote:
Please see forwarded message.
On Thu, Apr 30, 2020 at 11:55 AM Nitesh Tura
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