Re: [Bioc-devel] EXTERNAL: Question about Wercker continuous integration

Hi Kevin, My hunch is that the image that you're working with is old. If you're working with an older image, you could run into that problem with different R versions used to install 'backports'. I would first ensure that I'm working with a clean image by stopping any active containers, removing

[Bioc-devel] on to AnnotationTrack with rtracklayer [was Re: IGV VCF demo, other suggestions? [was Re: IGV - a new package in preparation]]

I have now implemented VCF tracks for IGV, supporting both a local VCF object read and filtered by the VariantAnnotation package, and a remote webserver-hosted vcf file. In normal use I expect (and recommend) that the local VCF object will be relatively small (< 1Mb, < 50 samples - or

Re: [Bioc-devel] git push denied

On 20 March 2018 19:30, Turaga, Nitesh wrote: > Hi Laurent, > > You cannot force push. Is you GitHub repo at a position where it needs > to be synced to the Bioconductor repo? > > If so, I can force push for you and sync. I was able to push from a cloned bioc repo, but can't to

[Rd] sink(con, type = "message"): what is the reason why 'message' sinks cannot be stacked?

In ?sink we can read: "Sink-ing the messages stream should be done only with great care. For that stream file must be an already open connection, and there is no stack of connections." and: "Do not sink the messages stream unless you understand the source code implementing it and hence the

Re: [Bioc-devel] EXTERNAL: Question about Wercker continuous integration

Hi Marcel, Thanks for the reply. I tried your `wercker.yml` file (exactly as is), and still got the same issue: * creating vignettes ... ERROR Error: processing vignette 'MyPackage-vignette.Rmd' failed with diagnostics: package ‘backports’ was installed by an R version with different internals;

[Rd] WISH: Sys.setlocale() to return value invisibly

Contrary to, say, Sys.setenv(), Sys.setlocale() returns it's value visibly. This means that if you for instance add: Sys.setlocale("LC_COLLATE", "C") to your .Rprofile file, it will print: [1] "C" at startup. The workaround is to wrap the call in invisible(), but I'd argue that any "setter"

Re: [Bioc-devel] git push denied

Hi Laurent, You cannot force push. Is you GitHub repo at a position where it needs to be synced to the Bioconductor repo? If so, I can force push for you and sync. Best, Nitesh > On Mar 20, 2018, at 10:36 AM, Laurent Gatto wrote: > > > On 20 March 2018 01:58, Turaga,

[Rd] R 3.5.0 scheduled for April 23

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

Re: [Bioc-devel] EXTERNAL: Question about Wercker continuous integration

Hi Kevin, Being that I am unable to fully reproduce the issue, I can only say that I have been successful in running the steps in the Wercker build for a different package. Please do a *clean* pull of the Bioconductor image from docker hub by removing any stale images first. Here is the

Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

2018-03-20 5:12 GMT+01:00 Jennifer Bryan : > Hi Tim, > > Here's a rather long thread from previous discussions of this: > > https://stat.ethz.ch/pipermail/r-devel/2014-May/069113.html > > These two lines from R CMD check suggest the two ways the vignette code > will be

Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

Hi Tim, Here's a rather long thread from previous discussions of this: https://stat.ethz.ch/pipermail/r-devel/2014-May/069113.html These two lines from R CMD check suggest the two ways the vignette code will be run: * checking running R code from vignettes ... OK * checking re-building of

Re: [Bioc-devel] git push denied

On 20 March 2018 01:58, Turaga, Nitesh wrote: > Hi Laurent, > > Are you sure you are using either of the private keys associated with > these public keys? You have to make sure to use the correct private > key. Yes, I checked, and the keys are correct. Here's what I get in a cleanly cloned and

Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

On 2018-03-20 06:17, Johannes Ranke wrote: ... The idea exposed by Dirk is the same: requireNamespace will find the package on CRAN and will set eval=TRUE. What you want though is to avoid running a chunk on CRAN, even if the package is available. So you need to set eval=FALSE

Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

... > The idea exposed by Dirk is the same: requireNamespace will find the > package on CRAN and will set eval=TRUE. What you want though is to > avoid running a chunk on CRAN, even if the package is available. So > you need to set eval=FALSE *unconditionally*. Or conditional on the package

Re: [R-pkg-devel] Avoid reprocessing Rmd vignette

2018-03-20 4:04 GMT+01:00 Tim Keitt : > http://www.keittlab.org/ > > On Mon, Mar 19, 2018 at 6:41 AM, Dirk Eddelbuettel wrote: > >> >> On 18 March 2018 at 21:57, Tim Keitt wrote: >> | That's a great idea, however my problem is with building a vignette, not >> |

Re: [Rd] trivial typo in man/pretty.Rd

> Ben Bolker > on Mon, 19 Mar 2018 11:57:34 -0400 writes: > patch against recent SVN ... > as far as I can tell this trivial typo has been there for 20 years: >