What is the question?
On 3/26/20 17:36, 유도영 wrote:
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Bioc-devel@r-project.org mailing list
Hi Paul,
I can reproduce this on my laptop. See full output below (it's big!).
Make sure to use a recent version of R devel (I updated mine 3 days
ago). The error seems to occur in MotIV's C/C++ code (in
/home/hpages/R/R-4.0.r78037/library/MotIV/libs/MotIV.so on my machine).
2 unrelated
Hi,
Is this expected behavior (R-3.6.0)?
dat <- cbind(x = 1:10, y = 10:1)
ylab <- substitute(X[t], list(t = 2))
plot(dat, ylab = ylab) # works (correctly displays ylab)
boxplot(dat, ylab = ylab) # fails
boxplot(dat, ylab = as.expression(ylab)) # works
Thanks & cheers,
M
On 2020-03-26 4:02 a.m., Martin Maechler wrote:
>> Ben Bolker
>> on Wed, 25 Mar 2020 21:09:16 -0400 writes:
>
> > I've discovered an infelicity (I guess) in qbeta(): it's not a bug,
> > since there's a clear warning about lack of convergence of the numerical
> >
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Dear Bioc,
I have added the lasted HOCOMOCO motifs to MotifDb but changed no code. The
package 1.29.6 dumps core during in the bioc devel linux build, and fails
perhaps similarly on windows.
http://bioconductor.org/checkResults/devel/bioc-LATEST/MotifDb/malbec2-buildsrc.html
Any
Simon,
The link I provided to the httpuv issue has detailed information about
the error:
https://github.com/rstudio/httpuv/issues/260
The error occurs when I run the following (although note, depending on
which mirror you use, the recent CRAN server issues may result in
problems downloading
If I do install.packages("dplyr", type = "source"), I see:
Installing package into ‘/Users/hadley/R’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/dplyr_0.8.5.tar.gz'
Content type 'application/x-gzip' length 1378766 bytes (1.3 MB)
Winston,
the Mac CRAN build builds a package only if either is true:
1) the package has not passed checks
2) there is a new version of the package since last successful build+check
The old build machine doesn't have the capacity to do full re-builds (it would
take over 24h - currently the
> Ravi Varadhan
> on Thu, 26 Mar 2020 18:33:43 + writes:
> This is also strange:
> qbeta <- function (p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p =
FALSE)
> {
> if (missing(ncp))
> .Call(C_qbeta, p, shape1, shape2, lower.tail, log.p)
> else
I see changes pushed to the RELEASE_3_10 branch from today. Please see the
top section of this documentation that describes timing and expected changes.
http://bioconductor.org/developers/how-to/troubleshoot-build-report/
It will take 24-48 hours to appear on the build report and landing
Dear Sir or Madam,
Ariane Schad forwarded the e-mail below from Kayla E. Interdonato to me
regarding the MBQN Bioconductor package.
I tried to push the newest version to the release branch using the
following commands:
**
git fetch upstream
git checkout -b RELEASE_3_10 upstream/RELEASE_3_10
I have two questions about the CRAN machines that build binary
packages for Mac. When a new version of a package is released,
(A) Do the downstream dependencies get re-checked?
(B) Do the downstream dependencies get re-built?
I have heard (but do not know for sure) that the answer to (A) is
This is also strange:
qbeta <- function (p, shape1, shape2, ncp = 0, lower.tail = TRUE, log.p = FALSE)
{
if (missing(ncp))
.Call(C_qbeta, p, shape1, shape2, lower.tail, log.p)
else .Call(C_qnbeta, p, shape1, shape2, ncp, lower.tail,
log.p)
}
Since the default value is
Despite the need to focus on pbeta, I'm still willing to put in some effort.
But I find it really helps to have 2-3 others involved, since the questions back
and forth keep matters moving forward. Volunteers?
Thanks to Martin for detailed comments.
JN
On 2020-03-26 10:34 a.m., Martin Maechler
> J C Nash
> on Thu, 26 Mar 2020 09:29:53 -0400 writes:
> Given that a number of us are housebound, it might be a good time to try
to
> improve the approximation. It's not an area where I have much expertise,
but in
> looking at the qbeta.c code I see a lot of
usually it is considered very bad practice to simply copy code between packages
-- any bug-fixes or changes in behavior in the up-stream package are not
reflected in the copied code, and 'bit rot' eventually settles in, where the
copied code is no longer functioning correctly.
It is much
Hello there
Is it possible to get Drosophila virilis genome as a BSGenome data package?
e.g. this one
https://metazoa.ensembl.org/Drosophila_virilis/Info/Annotation/
Like to do genome analysis/comparison in BioConductor to another species
which is closely related, but further from Drosophila
Hello,
I am creating a new package that I would like to submit to Bioconductor.
It's essentially a C code, which is called by R (using Rcpp).
One of the C functions within my package, is the C code of the R optimize
function (obtained from a C file of the folder:
Given that a number of us are housebound, it might be a good time to try to
improve the approximation. It's not an area where I have much expertise, but in
looking at the qbeta.c code I see a lot of root-finding, where I do have some
background. However, I'm very reluctant to work alone on this,
I do see changes on our git server from today March 26 th so maybe this has
been resolved?
But generally that means you need to do a
fetch --all # gets all branches from remotes
and do a
git pull upstream master # this gets any changes from the upstream remote
master branch
It is always
Thank you very much for your feedback, Martin and Hervé
Our goal is to make the package available in R as well for users who are more
familiar with this programming language. Python would run behind the scenes, as
kindly suggested by Hervé; basilisk seems a very good option.
Thanks again for
Dear Lori,
Thanks for your help. I went according to your advice but I permanently get
error in the upstream mode, here is the output:
mintty screen dump
Minoo@DESKTOP-PGH7233 MINGW64 ~/Desktop/IMMAN (master)
$ git push origin master
git Enumerating objects: 9, done.
It's a pretty extreme case, try e.g. curve(pbeta(x, shape1, shape2), n=10001),
and (probably -- I can't be bothered to work out the relation between beta
shapes and F df parameters this morning...) outside what is normally
encountered in statistical analyses. Notice though, that you have
> Ben Bolker
> on Wed, 25 Mar 2020 21:09:16 -0400 writes:
> I've discovered an infelicity (I guess) in qbeta(): it's not a bug,
> since there's a clear warning about lack of convergence of the numerical
> algorithm ("full precision may not have been achieved"). I can
OK couple of "=" were missing.
I think I completed the upload.
Thanks a lot.
Best wishes.
*Stefano *
Stefano Mangiola | Postdoctoral fellow
Papenfuss Laboratory
The Walter Eliza Hall Institute of Medical Research
+61 (0)466452544
Il giorno gio 26 mar 2020 alle ore 18:15 stefano
ha
Thanks a lot for the acceptance, and the time spent on review.
Although my Bioconductor and github accounts share an ssh key I still get
_
rstudio-2 251 % git remote add upstream g...@git.bioconductor.org:
packages/tidybulk.git
rstudio-2 254 % git fetch upstream
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