Re: [R-pkg-devel] Saving provenance data to the file system

I can't comment on the specific intersection of your plans and CRAN's rules, but note that you might want to check out the rappdirs package (already on CRAN and imported by some other packages) as a possible helper for whatever you decide to do. https://cran.r-project.org/package=rappdirs --

Re: [Bioc-devel] Question : GitHub-Commit changes to the released branch

Thanks so much, Lori! Best, Julie From: "Shepherd, Lori" Date: Friday, August 25, 2017 at 1:58 PM To: "Zhu, Lihua (Julie)" , "bioc-devel@r-project.org" Subject: Re: Question : GitHub-Commit changes to the

Re: [Bioc-devel] Question : GitHub-Commit changes to the released branch

The current release is RELEASE_3_5 Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of

Re: [Bioc-devel] Package changes not merging with upstream

Thanks Martin, I retried the push to upstream and it works just fine now. Thanks Matt On Fri, Aug 25, 2017 at 10:27 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 08/25/2017 01:17 PM, Matt Richards wrote: > >> Hi all, >> >> I maintain the "trena" package and I'm attempting to

[Bioc-devel] Question : GitHub-Commit changes to the released branch

Hi, I need to fix a bug in the development and released version of CRISPRseek. So far, I have successfully updated the dev version of CRISPRseek following the guides at https://www.bioconductor.org/developers/how-to/git/maintain-bioc-only/. I have a couple of question regarding commit changes

Re: [Bioc-devel] Package changes not merging with upstream

On 08/25/2017 01:17 PM, Matt Richards wrote: Hi all, I maintain the "trena" package and I'm attempting to sync the changes from my in-house Github repo with the Bioconductor version. I submitted my ssh keys last week, so essentially I'm following these instructions:

[Bioc-devel] Package changes not merging with upstream

Hi all, I maintain the "trena" package and I'm attempting to sync the changes from my in-house Github repo with the Bioconductor version. I submitted my ssh keys last week, so essentially I'm following these instructions: https://www.bioconductor.org/developers/how-to/git/sync-

Re: [Rd] Are r2dtable and C_r2dtable behaving correctly?

> On 25 Aug 2017, at 12:04 , Peter Dalgaard wrote: > >> There are three possible matrices, and these come out in proportions 1:4:1, >> the one with all cells filled with ones being >> most common. > > ... and > >> dhyper(0:2,2,2,2) > [1] 0.167 0.667 0.167 >>

[R-pkg-devel] Saving provenance data to the file system

We are working on a package that collects provenance as an R script executes, saving the provenance to the file system. In reading the rules for submitting packages to CRAN, there is this rule: > Packages should not write in the users’ home filespace, nor anywhere > else on the file system

Re: [R-pkg-devel] CRAN upload and prechecking confusion (Johannes Graumann)

You can precompute long running things in vignettes. See CRAN package mcmc for examples that do this reproducibly. -- Charles Geyer Professor, School of Statistics Resident Fellow, Minnesota Center for Philosophy of Science University of Minnesota char...@stat.umn.edu

Re: [Bioc-devel] Package not updated in build system from github

Thank you Martin! I had missed that part. Indeed maybe you can update the instructions for non-git masters (like me). On Fri, Aug 25, 2017 at 1:14 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 08/25/2017 03:36 AM, Panagiotis Moulos wrote: > >> Dear all, >> >> For some time now,

Re: [Bioc-devel] Package not updated in build system from github

On 08/25/2017 03:36 AM, Panagiotis Moulos wrote: Dear all, For some time now, my package metaseqR fails to pass the checks at the build system http://bioconductor.org/checkResults/3.6/bioc-LATEST/metaseqR/ Although I am not sure I understand the source of the problem (all is well in my local

Re: [Rd] Are r2dtable and C_r2dtable behaving correctly?

> On 25 Aug 2017, at 11:23 , Jari Oksanen wrote: > > It is not about "really arge total number of observations", but: > > set.seed(4711);tabs <- r2dtable(1e6, c(2, 2), c(2, 2)); A11 <- vapply(tabs, > function(x) x[1, 1], numeric(1));table(A11) > > A11 > 0 1

Re: [Rd] Are r2dtable and C_r2dtable behaving correctly?

It is not about "really arge total number of observations", but: set.seed(4711);tabs <- r2dtable(1e6, c(2, 2), c(2, 2)); A11 <- vapply(tabs, function(x) x[1, 1], numeric(1));table(A11) A11 0 1 2 166483 666853 14 There are three possible matrices, and these come out in

[Bioc-devel] Package not updated in build system from github

Dear all, For some time now, my package metaseqR fails to pass the checks at the build system http://bioconductor.org/checkResults/3.6/bioc-LATEST/metaseqR/ Although I am not sure I understand the source of the problem (all is well in my local systems), "Error : object ‘vsn’ is not exported by