Re: [Rd] Why R should never move to git

> So I created a branch within my fork, and committed the change there. But > Github provides no way to create a pull request that only includes the new > stuff! > Every attempt I made would have included everything from both bug fixes. I have been doing some tests, and I think that this issue

Re: [Rd] Why R should never move to git

Yes, indeed Gitlab GUI Core Code is Open Source (Libre / Community Edition): https://gitlab.com/gitlab-org/gitlab-ce > But his instructions required command-line git, and my main claim is that > Github is not good enough to do the kinds of things I want to do and R Core > would need to do. > >

Re: [Rd] R-gui sessions end when executing C-code

SEXP eta = PROTECT(allocVector(REALSXP,H_c)); n_prot++; double *eta_c; eta_c = REAL(eta); for (i=0;i

[Rd] R-gui sessions end when executing C-code

Hi I'm trying to develop some C code to find the fixpoint of a contraction mapping, the code compiles and gives the right results when executed in R. However R-gui session is frequently terminated. I'm suspecting some access violation error due to the exception code 0xc005 In the error

[Bioc-devel] cannot git (the package Pi)

Dear Lori, I have an issue accessing my package called ‘Pi’. Following the instruction detailed at http://bioconductor.org/developers/how-to/git/maintain-bioc-only/, I have submit my SSH public key (shown in red): $ cat ~/.ssh/id_dsa.pub ssh-dss

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

It is important but not completely clear how to address. I think it has been written that bioc package checking should make minimal use of the internet, and most checking concerning manipulation of net-derived objects should use "mocks". One possible approach is to test with calls to the

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

Thanks Mike and Hervé! Somehow, errors in examples that are caused by the state (or absence) of things on the internet should have a different status in my view than ones that reflect local state of R and packages - and distinguishing this could make maintenance of the package corpus & builds

Re: [Rd] Best practices in developing package: From a single file

On Thu, Feb 1, 2018 at 9:20 AM, Gabriel Becker wrote: > On Thu, Feb 1, 2018 at 5:24 AM, Lionel Henry wrote: > > > On 31 janv. 2018, at 09:08, Gabriel Becker wrote: > > > > > it *actively discourages* the bits it doesn't directly

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

Hi Wolfgang, Mike, We didn't have a successful build of GenomicFeatures in devel for many days because of all kinds of problems with the examples that try to access the Ensembl marts. The latest of which being: https://support.bioconductor.org/p/105565/ (which also affects GenomicFeatures in

Re: [Rd] Best practices in developing package: From a single file

On 01/02/2018 12:20 PM, Gabriel Becker wrote: [ lots deleted...] Or perhaps you could imagine two help systems, akin to --help and man for command line tools, one of which is minimalist showing usage, etc, generated by roxygen comments, and one of which is much more extensive, and not tied to

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

The error TxDbFromBiomart looks like it might be related to a biomaRt change I made recently to submit queries using httr rather than RCurl. Others have reported something similar (e.g https://support.bioconductor.org/p/104502/) and I raised the timeout from 10 to 60 seconds. I guess with the old

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

Thanks Hervé! This seems to take a long time to propagate. As of now, https://bioconductor.org/packages/devel/bioc/html/GenomicFeatures.html still shows 1.31.3. ( Btw, there's also an error in the build report which seems to come from a rather excessive-looking example in the

Re: [Rd] Best practices in developing package: From a single file

On Thu, Feb 1, 2018 at 6:20 PM, Gabriel Becker wrote: > > Or perhaps you could imagine two help systems, akin to --help and man for > command line tools, one of which is minimalist showing usage, etc, > generated by roxygen comments, and one of which is much more extensive,

Re: [Rd] as.list method for by Objects

> Henrik Bengtsson > on Thu, 1 Feb 2018 10:26:23 -0800 writes: > On Thu, Feb 1, 2018 at 12:14 AM, Martin Maechler > wrote: >>> Michael Lawrence >>> on Tue, 30 Jan 2018