[Bioc-devel] write access to git repos for two packages maintained

I have two new packages in latest release of Bioconductor, and am having issues pushing to the git repo for one. One was accepted when BioC was still using SVN, and the other after transition to git. I first entered my ssh key info into the form with the github username, and got access to the

Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...

On 10/11/17 13:10, François Michonneau wrote: A github search might be helpful to identify packages that define macros in their Rd files: https://github.com/search?utf8=%E2%9C%93=user%3Acran+extension%3Ard+newcommand=Code Thanks. Looking into it. cheers, Rolf -- Technical Editor ANZJS

Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...

A github search might be helpful to identify packages that define macros in their Rd files: https://github.com/search?utf8=%E2%9C%93=user%3Acran+extension%3Ard+newcommand=Code On Thu, Nov 9, 2017 at 6:35 PM, Rolf Turner wrote: > > On 10/11/17 12:00, Duncan Murdoch

Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...

On 10/11/17 12:00, Duncan Murdoch wrote: [Rolf Turner wrote:] ... when I do the "R CMD build" thing, when it comes to the "* building the PDF package manual" step it says "Hmm ... looks like a package" (no shit, Sherlock!) and emits a huge amount of verbose LaTeX diagnostics. "Normally"

Re: [R-pkg-devel] Macros in Rd files.

On 09/11/2017 3:05 PM, Rolf Turner wrote: On 09/11/17 23:40, Duncan Murdoch wrote: On 09/11/2017 5:06 AM, Uwe Ligges wrote: Note the % may be a comment? Yes, and the body should be written in Rd markup, not R.  Working out the appropriate number of escapes is painful; I recommend trial and

Re: [R-pkg-devel] Macros in Rd files --- supplementary question ...

On 09/11/2017 3:29 PM, Rolf Turner wrote: ... Mr. Speaker. On 09/11/17 23:40, Duncan Murdoch wrote: On 09/11/2017 5:06 AM, Uwe Ligges wrote: Note the % may be a comment? Yes, and the body should be written in Rd markup, not R.  Working out the appropriate number of escapes is painful; I

Re: [R-pkg-devel] Macros in Rd files.

On 09/11/17 23:40, Duncan Murdoch wrote: On 09/11/2017 5:06 AM, Uwe Ligges wrote: Note the % may be a comment? Yes, and the body should be written in Rd markup, not R.  Working out the appropriate number of escapes is painful; I recommend trial and error. This worked for me:  

[Bioc-devel] website

Hello everyone, We are making some updates that could affect the website. If the website is down please be patient it is intermittent and should be remedied quickly. We will try and get these updates done as soon as possible. Thank you Lori Shepherd Bioconductor Core Team Roswell Park

Re: [Rd] formatting raw vectors with names

> Lukas Stadler > on Thu, 9 Nov 2017 16:34:49 +0100 writes: > I think there’s a bug concerning the formatting of raw vectors with names: >> structure(as.raw(1:3), .Names = c("a", "", "c")) > a c > 01 02 03 >> structure(1:3,

[R-pkg-devel] R CMD INSTALL crashes with recent builds of r-devel

Dear list members, I have three packages on CRAN (asremlPlus, dae and imageData). The current versions of all three packages can be built and installed using build of 2017-06-27 r72859 development snapshot of R. I am doing this on a 64-bit laptop and a 64-bit desktop, both running Windows 10.

Re: [R-pkg-devel] issues with SOfun - package upload

Did you write it from scratch or modify the function from the package you were referencing? There may be some licensing issues you need to consider either way. -Dason On Thu, Nov 9, 2017 at 3:53 AM, LUCA BELMONTE wrote: > Dear Brian, > Dear Uwe, > > Thank you for your

[Rd] R 3.4.3 scheduled for November 30

Full schedule available on developer.r-project.org (pending auto-update from SVN) -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com

[Rd] formatting raw vectors with names

I think there’s a bug concerning the formatting of raw vectors with names: > structure(as.raw(1:3), .Names = c("a", "", "c")) a c 01 02 03 > structure(1:3, .Names = c("a", "", "c")) a c 123 The problem is that EncodeRaw does not honor the requested

Re: [Bioc-devel] annotation data not updated?

It appears that your org.Hs.eg.db and GO.db packages are still v3.4.2. Please run the command BiocInstaller::biocLite() to update your packages to the new version (v3.5.0). From: Bioc-devel on behalf of Yu, Guangchuang

Re: [Bioc-devel] annotation data not updated?

Thanks for looking into this. New versions of the OrgDbs and Db0s (v3.5.0) are now available that have up-to-date resources. Here is the output of the new org.Hs.eg.db: > x <- org.Hs.eg.db > x OrgDb object: | DBSCHEMAVERSION: 2.1 | Db type: OrgDb | Supporting package: AnnotationDbi |

Re: [Rd] check does not check that package examples remove tempdir()

> tempdir(). I think it happens because the forked process shares the > value of tempdir() with the parent process and removes it when it > exits. This is very likely the case. Pretty much the entire library can be summed up by bfork_fork, which is the following. SEXP res; pid_t pid;

Re: [R-pkg-devel] Macros in Rd files.

On 09/11/2017 5:06 AM, Uwe Ligges wrote: Note the % may be a comment? Yes, and the body should be written in Rd markup, not R. Working out the appropriate number of escapes is painful; I recommend trial and error. This worked for me:

Re: [Rd] New vcov(*, complete=TRUE) etc -- coef() vs coef()

> Fox, John > on Tue, 7 Nov 2017 22:09:03 + writes: > Dear Martin, I think that your plan makes sense. It's too > bad that aov() behaved differently in this respect from > lm(), and thus created more work, but it's not be a bad > thing that the