Many many packages in the methylation business (methylation array or
MethylSeq) define dozens of data structures (S4 classes) for the purpose
of representing methylation data. Some of the most outstanding data
structures seem to be RnBeadSet in RnBeads, MethylSet in minfi,
MethyLumiSet in
On the one hand, if the error is from curl I think this is the case
url <- "localhost:8000" ## nothing to connect to
tryCatch({
response <- GET(url)
stop_for_status(response)
content(response)
}, error = function(e) {
message(paste(class(e), collapse = " "))
stop("curl
Thanks Lori, I had not seen this page before.
Best,
Ted
On Thu, Dec 10, 2020 at 1:19 PM Kern, Lori
wrote:
> There is information on this page:
> http://bioconductor.org/developers/how-to/troubleshoot-build-report/
>
> Lori Shepherd
>
> Bioconductor Core Team
>
> Roswell Park Comprehensive
There is information on this page:
http://bioconductor.org/developers/how-to/troubleshoot-build-report/
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
Ah, I see. Ok thanks for that clarification. Do you know roughly how long
it might take to build?
On Thu, Dec 10, 2020 at 11:15 AM James W. MacDonald wrote:
> You also have a commit from yesterday in master that isn't yet reflected
> on the build machine, again because it takes time for the
Hi all,
Sometime my package got "Empty reply from server" error when I using httr
package.
The pseudo-code I used to handle error is like this:
library(httr)
APIurl <-
You also have a commit from yesterday in master that isn't yet reflected on
the build machine, again because it takes time for the build machine to
build stuff. IIRC we are over 24 hours per build, but that may be old news
(FAKE NEWS!).
On Thu, Dec 10, 2020 at 11:09 AM James W. MacDonald wrote:
It looks like you bumped it just yesterday:
commit 5a9929aed33e40c11609f3d064b114d95d95e6cb
Author: Ted Natoli
Date: Wed Dec 9 16:42:16 2020 -0500
fixing version bump
commit accd8a5871fe38a8a1f63b32b4e79d2640e86792
Author: Ted Natoli
Date: Wed Dec 9 16:32:47 2020 -0500
update
Hi James,
Thanks for the response. The corresponding changes were committed to the
master branch on November 23. The development build report seems to be
using the correct code, or at least close to it, as the most recent commit
it shows there is from December 8. I did push to both github and
Did you bump your version number? How long has it been since you committed
the changes? If you have a github repo, you remembered to push to both the
Bioconductor and GitHub repos?
On Thu, Dec 10, 2020 at 10:19 AM Ted Natoli wrote:
> Hello all,
>
> I'm trying to update the released version of
Hello all,
I'm trying to update the released version of my package, cmapR, because one
of the packages it depends on has been deprecated and hence install of
cmapR now fails.
I've followed the instructions here in order to get those changes over to
the released version of the package:
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