On 1. May 2020, at 15:50, Vinh Tran <tran at bio.uni-frankfurt.de> wrote:
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 processed & filtered phylogenetic profile.
#' @name finalProcessedProfile
#? ?
#? ?
NULL
The command ?finalProcessedProfile still works fine :-)
Many thanks for your help!
Best,
Vinh
--------------------------------
Dr. Vinh Tran
Dept. for Applied Bioinformatics
Inst. for Cell Biology and Neuroscience
Goethe University Frankfurt
Biologicum, Room 3.209
Phone +49 (0)69/798-42118
On 1. May 2020, at 15:05, Vincent Carey <stvjc at channing.harvard.edu> wrote:
does
@docType data
help here?
On Fri, May 1, 2020 at 8:52 AM Martin Morgan <mtmorgan.bioc at gmail.com <mailto:mtmorgan.bioc at gmail.com>> 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 you want
#' @rdname
#' @name
#' @description
#' @usage
#' @details
#' @return
#' @examples
NULL
But as Kasper says it could well be that there's a better roxygen2 solution (and that it doesn't make sense to choose data storage format based on perceived document tool limitation).
Martin
?On 5/1/20, 8:17 AM, "Bioc-devel on behalf of Kasper Daniel Hansen" <bioc-devel-bounces at r-project.org <mailto:bioc-devel-bounces at r-project.org> on behalf of kasperdanielhansen at gmail.com <mailto:kasperdanielhansen at gmail.com>> wrote:
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
GitHub or email list?
Best,
Kasper
On Fri, May 1, 2020 at 5:51 AM Vinh Tran <tran at bio.uni-frankfurt.de <mailto:tran at bio.uni-frankfurt.de>> wrote:
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 cannot
find any other solutions yet except using "LazyData: true?.
Best regards,
Vinh
--------------------------------
Dr. Vinh Tran
Dept. for Applied Bioinformatics
Inst. for Cell Biology and Neuroscience
Goethe University Frankfurt
Biologicum, Room 3.209
Phone +49 (0)69/798-42118
On 30. Apr 2020, at 16:02, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com <mailto:kasperdanielhansen at gmail.com>> wrote:
This seems really weird, and I don't think you should be using lazyData to
get a message to disappear. Is there a GitHub page where we can browse the
code and do you have the full output of R CMD check somewhere?
On Thu, Apr 30, 2020 at 9:05 AM Vinh Tran <tran at bio.uni-frankfurt.de <mailto:tran at bio.uni-frankfurt.de>>
wrote:
Dear Kasper,
Many thanks for your reply. Yes, I am using data() to load the data.
However, the problem is, when I checked my package using CMD Check, it
threw me the warning that I am using that data only in the example but not
in code. I see the disadvantages of LazyData, but I just want to know in
this case, how can I solve that issue by not using LazyData. If you have
any solutions, I am very appreciated!
Btw, I added ?LazyData: true? to the DESCRIPTION and the warning went
away. So, I am not sure if it must always be uppercase.
Best regards,
Vinh
--------------------------------
Dr. Vinh Tran
Dept. for Applied Bioinformatics
Inst. for Cell Biology and Neuroscience
Goethe University Frankfurt
Biologicum, Room 3.209
Phone +49 (0)69/798-42118
On 30. Apr 2020, at 14:55, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com <mailto:kasperdanielhansen at gmail.com>> wrote:
If you don't have lazy data on, you should be able to load the data by
using data(). Let us say you example data is called expData.
With lazy data
print(expData)
Without lazy data you need explicit loading
data(expData)
print(expData)
For the purpose of examples, there is also a user-level advantage of
using an explicit data() statement: the user can see that the data comes
from somewhere, instead of appearing out of nowhere. For examples, I
actually only see advantages of not using lazyData, because of these
explicit statements.
My historical impression: I would say that when lazyData was introduced,
it seems to me that the intention was widespread use. It seems to me that
the tides have turned against lazy data and the official recommendation is
to not use it unless you have good reasons. One disadvantage with
widespread use of lazyData is that the names of these objects have to be
accessible somewhere.
Note: one thing I have realized very belatedly is that the lazyData field
is a boolean, the right statements are one of
lazyData: TRUE
lazyData: FALSE
For example, I think it has to be all uppercase.
Best,
Kasper
On Wed, Apr 29, 2020 at 6:05 PM Vincent Carey <stvjc at channing.harvard.edu <mailto:stvjc at channing.harvard.edu>>
wrote:
I see this is guideline 7 at
https://bioconductor.org/developers/package-guidelines/ <https://bioconductor.org/developers/package-guidelines/>
I have used LazyData: TRUE so that [pkgname]::[entity] can be used
instead
of data(). The
claim that it is "rarely a good thing" and slows down package loading can
be weighed against
convenience. I am not sure you should use LazyData to avoid a
documentation warning
however. Can you give more details on what package is generating the
warning?
On Wed, Apr 29, 2020 at 5:34 PM Vinh Tran <tran at bio.uni-frankfurt.de <mailto:tran at bio.uni-frankfurt.de>>
wrote:
Dear Bioc members,
I have just encountered a warning during the CHECK that some data
are used in the documents but not in code (e.g. ?Variables with usage
documentation object ?ppTree? but not in code"). They are the demo
that I am using only in the examples for demonstrate the usage of some
functions. Adding LazyData: True to the DESCRIPTION can solve that
but according to the package guidelines it is not recommended. Could
please show me what should I do in this case? The demo data is only
15 KB at max.
Many thanks for your advices!
Best regards,
Vinh
--------------------------------
Dr. Vinh Tran
Dept. for Applied Bioinformatics
Inst. for Cell Biology and Neuroscience
Goethe University Frankfurt
Biologicum, Room 3.209
Phone +49 (0)69/798-42118
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