Re: [Bioc-devel] Error in Vignette of package

Hi all,  I've also followed this thread as the FELLA package has problems with the vignette as well.  I have two issues (link) First:Invalid Parameter - /figure-html Warning in shell(paste(c(cmd, args), collapse = " ")) : 'convert "quickstart_files/figure-html/unnamed-chunk-12-1.png" -trim

Re: [Rd] Inconsistencies in wilcox.test

So I tried adding Infinity support for all cases. And it is (as could be expected) more complicated than I thought. It is easy to add Inf support for the test. The problems start with conf.int=TRUE. Currently confidence intervals are computed via `uniroot()` and, in the case of infinities, we

Re: [Rd] long vector support

Thank you both. I really appreciate your work developing R, and it is exciting that long vector support may be coming to writeBin(). Next time, I will come prepared with svn revision numbers to help track things down. On Sat, Dec 7, 2019 at 6:17 AM Martin Maechler wrote: > > Will L > >

[Bioc-devel] Cairo dependency problem in the OSX machine

Hello all, Recently, a package I submitted to Bioconductor failed with an error message in the OS X system. This is the link for the build: http://bioconductor.org/spb_reports/PubScore_buildreport_20191208212325.html#celaya2_buildsrc_anchor The problem was with the Cairo package, which is a

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

Hi Alex, The easiest way to do this is literally just "fetch and merge". 5371 git clone g...@github.com:al2na/methylKit.git 5372 cd methylKit 5377 git remote add upstream g...@git.bioconductor.org:packages/methylKit 5378 git fetch

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

As you can see in the branch network https://github.com/al2na/methylKit/network , I already rebased all commits to a copy of bioc master and checked the build on travis, but I was wondering whether this is the best way to do it. Because this way I am

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

The package I am talking about is methylKit, (https://github.com/al2na/methylKit ). > On 9. Dec 2019, at 16:29, Turaga, Nitesh > wrote: > > Hi, > > Please let me know which package you are talking about. > > Also, give me your GitHub package name. >

Re: [Bioc-devel] How to move package from workflow to software

Hi Julien, After re-considering how this package should go forward. Please submit your package to the https://github.com/Bioconductor/Contributions. This will put your package through the Single Package Builder which will help us review your package better. There have been significant code

Re: [Bioc-devel] Rebasing possible on bioconductor git ?

Hi, Please let me know which package you are talking about. Also, give me your GitHub package name. Nitesh > On Dec 9, 2019, at 7:24 AM, Alexander Gosdschan wrote: > > Hi, > > Somehow I missed to push a large number of commits to the bloc git master > branch before the latest release

Re: [Rd] Inconsistent behavior for the C AP's R_ParseVector() ?

On 12/9/19 2:54 PM, Laurent Gautier wrote: > > > Le lun. 9 déc. 2019 à 05:43, Tomas Kalibera > a écrit : > > On 12/7/19 10:32 PM, Laurent Gautier wrote: >> Thanks for the quick response Tomas. >> >> The same error is indeed happening when trying to

Re: [Rd] Inconsistent behavior for the C AP's R_ParseVector() ?

Le lun. 9 déc. 2019 à 05:43, Tomas Kalibera a écrit : > On 12/7/19 10:32 PM, Laurent Gautier wrote: > > Thanks for the quick response Tomas. > > The same error is indeed happening when trying to have a zero-length > variable name in an environment. The surprising bit is then "why is this >

[Rd] default col.names from data.frame not the same as as.data.frame

Hello, All:   Consider: > data.frame(matrix(1:2, 1))   X1 X2 1  1  2 > as.data.frame(matrix(1:2, 1))   V1 V2 1  1  2   I ask, because I got different default names running the same numbers through BMA:::bic.glm.matrix and BMA:::bic.glm.data.frame, so I thought I'd ask this group

[Bioc-devel] Rebasing possible on bioconductor git ?

Hi, Somehow I missed to push a large number of commits to the bloc git master branch before the latest release and now I have 50 commits on GitHub that happened before the release. What would be the best way to get the git remotes in sync again? Is it possible to rebase commits on the bioc

Re: [Rd] What should dnorm(0, 0, -Inf) return?

I have committed a fix for r-devel (dnorm only). -pd > On 9 Dec 2019, at 08:49 , Martin Maechler wrote: > >> peter dalgaard >>on Sun, 8 Dec 2019 12:11:50 +0100 writes: > >> Yes, that looks like a bug and an easily fixable one too. > > agreed. > >> However, I spy another issue:

Re: [Rd] Inconsistent behavior for the C AP's R_ParseVector() ?

On 12/7/19 10:32 PM, Laurent Gautier wrote: > Thanks for the quick response Tomas. > > The same error is indeed happening when trying to have a zero-length > variable name in an environment. The surprising bit is then "why is > this happening during parsing" (that is why are variables assigned

Re: [Bioc-devel] Error in Vignette of package

Hi Simina, thank you for reporting the remaining problem on Windows builders. I have just made an adjustment to BiocStyle which should resolve the issue. Cheers, Andrzej On Sun, Dec 8, 2019 at 4:18 PM Simina Boca wrote: > Hi all, > I've been following this conversation as I was having the

Re: [R-pkg-devel] Cannot find -ludev

Sorry for the short question :). My package requires libudev.so library which exists on Fedora Linux be default and I think it is not provided by Debian. My question is, did anyone use it before on CRAN it I need to ask the CRAN team to install it for me. Note: my package is running only on

Re: [R-pkg-devel] Cannot find -ludev

On 9/12/19 9:25 pm, Sameh M. Abdulah wrote: I am getting this error on CRAN, /usr/bin/ld: cannot find -ludev This is about as cryptic as I can recall ever seeing in the way of requests for help. I think you will need to supply just a *little* more detail (!!! :-) ) in order to have

[R-pkg-devel] Cannot find -ludev

I am getting this error on CRAN, /usr/bin/ld: cannot find -ludev --Sameh [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel

Re: [Rd] Inconsistencies in wilcox.test

I'd like to ask the developers to include some exact computation for ties into wilcox.test(). Just try wilcox.test(c(1,1,5),c(10,11)) wilcox.test(c(1,2,5),c(10,11)) The p-values differ significantly. But if I try library(exactRankTests) wilcox.exact(c(1,1,5),c(10,11))