Excellent, thank you so much, it worked now! I had specified the package
name but perhaps should have started another email thread. What was the
issue though, was it the public key or was there something that needed to
be changed on your end? (Trying to remember for the next time)
Cheers,
Simina
On 01/31/2018 06:39 PM, Ludwig Geistlinger wrote:
Hi,
I am currently considering the following snippet:
data.ids <- paste0("d", 1:5)
f <- function(x) paste("dataset", x, sep=" = ")
res <- BiocParallel::bplapply(data.ids, function(d) f(d))
Using a recent R-devel on both a Linux machine
Hi,
I am currently considering the following snippet:
> data.ids <- paste0("d", 1:5)
> f <- function(x) paste("dataset", x, sep=" = ")
> res <- BiocParallel::bplapply(data.ids, function(d) f(d))
Using a recent R-devel on both a Linux machine and a Mac machine, this works
fine.
However, on
On 31/01/2018 8:59 AM, Mark van der Loo wrote:
I fully agree with Joris and Hadley on roxygen2.
Additionally:
I wrote and published my first package before roxygen (or roxygen2) was
available. I found editing .Rd extremely terse (especially when code is
updated). For example, the fact that
Dirk,
yes, thanks, the edge server that serves the Mac binaries to CRAN has run out
of disk space (due to size of CRAN itself) so the sync was incomplete.
It is fixed now -- you can try by using the macos master server as mirror:
https://r.research.att.com/ and it will propagate through other
Bumping this as we now have two more issue tickets filed and a fresh SO
question.
Is anybody looking at this? Simon?
Dirk
On 30 January 2018 at 15:19, Dirk Eddelbuettel wrote:
|
| I have received three distinct (non-)bug reports where someone claimed a
| recent package of mine was broken ...
Should be all fixed now.
Best,
Nitesh
> On Jan 31, 2018, at 12:31 PM, Jenkins, David wrote:
>
> Sorry about that, the RELEASE_3_6 branch on our github should be fixed now:
> https://github.com/compbiomed/ASSIGN/commits/RELEASE_3_6
>
> Thanks,
>
> David
>
> On 1/31/18, 12:00
Sorry about that, the RELEASE_3_6 branch on our github should be fixed now:
https://github.com/compbiomed/ASSIGN/commits/RELEASE_3_6
Thanks,
David
On 1/31/18, 12:00 PM, "Turaga, Nitesh" wrote:
Hi David,
Your master branch is fine now. I have
Hi David,
Your master branch is fine now. I have updated bioconductor to reflect your
master branch.
But you need to do the same thing to RELEASE_3_6 as well. There are duplicate
commits on that branch.
Please let me know once you have fixed your RELEASE_3_6.
Best,
Nitesh
> On Jan 31,
Joris,
With the large caveat that I am not Duncan, and thus am not speaking for
him, I can see an argument for his claim that I think is, more or less,
true.
roxygen2 (as far as I know as someone who uses it at least some of the
time) maps to only a subset of Rd. It is the most commonly used
On 31 January 2018 at 16:18, Barry Rowlingson
wrote:
>>
>
> Let the record also state that *gitlab* is an open source project and can be
> downloaded and self-hosted, like gogs, but unlike github.
Good to know. Nice one: https://github.com/gitlabhq/gitlabhq
Best,
Bruno,
It looks like some content in your message did not come through - please
re-send. We need to see the commands you are running, specifically what package
you're trying to access.
Valerie
On 01/30/2018 09:56 AM, bruno contrino via Bioc-devel wrote:
Hello,
I am having some issues
Dear Dr. Pfaff,
Thank you for this, creating a package out of single file was my
oriingal question, but not only creating and also maintaining it that
way so R package is an artifact of the development process rather than
"manually maintained" structure. I will have look at your sources.
Best,
I pretty much agree. I tried using roxygen when it was first released but
couldn't stand putting documentation in comments, especially for complex,
S4-based software. Rd is easy to read and write and lets me focus on the
task of writing documentation (focus is the hardest part of any task for
me).
Similarly, I created this example a couple of years ago:
https://github.com/yihui/rlp which shows that you can create a package
from R Markdown documents (or any documents that knitr supports).
Basically you can start with an R Markdown document, and after
clicking a button in RStudio, you will
On Tue, Jan 30, 2018 at 11:07 PM, Suzen, Mehmet
wrote:
> This might be off topic, but if R-core development ever moves to git,
> I think it would make sense to have its own git service hosted by a
> university, rather than using
> github or gitlab. It is possible via
Dear All:
stepping in late, but @Joris, if you would like to take 'from a single file'
literally,
have a look at:
https://github.com/bpfaff/lp4rp
(lp4rp: literate programming for R packages);
Cheers,
Bernhard
ps: incidentally, within the noweb-file roxygen is employed.
I fully agree with Joris and Hadley on roxygen2.
Additionally:
I wrote and published my first package before roxygen (or roxygen2) was
available. I found editing .Rd extremely terse (especially when code is
updated). For example, the fact that there are no spaces allowed between }
and { in
Hi Simina,
You should have access now. The missing information in all the previous
communications was the name of the package you were trying to access.
Nitesh
> On Jan 30, 2018, at 10:51 PM, Simina Boca wrote:
>
> Sure! This is for the MultiMed package, not swfdr, so I
On Wed, Jan 31, 2018 at 1:41 PM, Duncan Murdoch
wrote:
> On 31/01/2018 6:33 AM, Joris Meys wrote:
>
> 3. given your criticism, I'd like your opinion on where I can improve the
>> documentation of https://github.com/CenterForStatistics-UGent/pim. I'm
>> currently busy
Dear list,
At the European Bioconductor Meeting in December 2017, a group of us
decided to develop a common interface for interactive visualization of
single-cell ‘omics data. Two months (and over 500 commits) later, we are
proud to present the alpha release of iSEE, a package for interactive
(Please do not quote without attribution)
On 30 January 2018 at 20:44, Hadley Wickham wrote:
| Personally, I think the biggest problem with package.skeleton() is
| that it assumes that the source of truth is objects in an environment.
| This seems the wrong way around to me.
Basically
On 31/01/2018 6:33 AM, Joris Meys wrote:
3. given your criticism, I'd like your opinion on where I can improve
the documentation of https://github.com/CenterForStatistics-UGent/pim.
I'm currently busy updating the help files for a next release on CRAN,
so your input is more than welcome.
On 31/01/2018 6:33 AM, Joris Meys wrote:
Dear Duncan,
With all respect, but I strongly disagree on your stance regarding
roxygen2 for multiple reasons:
1. It is in my humble opinion not correct to evaluate a tool based on
the abuse of some users. It's not because people write packages with
On 30/01/2018 11:39 PM, Hadley Wickham wrote:
On Tue, Jan 30, 2018 at 4:55 PM, Duncan Murdoch
wrote:
On 30/01/2018 4:30 PM, Kenny Bell wrote:
In response to Duncan regarding the use of roxygen2 from the point of view
of a current user, I believe the issue he brings
Dear Duncan,
With all respect, but I strongly disagree on your stance regarding roxygen2
for multiple reasons:
1. It is in my humble opinion not correct to evaluate a tool based on the
abuse of some users. It's not because people write packages with bad
documentation, that roxygen2 is to blame.
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