Re: [Bioc-devel] EXTERNAL: LazyData: false and accessing data in the YAML section of an Rmd document

How about in the YAML: params: configuration: NULL project_conf: NULL data: NULL Then in the first chunk something like: ```{r data-config} if(is.null(params$data)){ data(data_ionstar, package = "prolfqua") data = data_ionstar configuration = data$filtered()$config } ``` You can use a

Re: [Bioc-devel] EXTERNAL: Not possible to create runnable examples for package

Hi Kelsey, 1. If you are writing a wrapper, then do all the intermediate steps need to be exposed and exported to the end user? If you don't @export a function, you don't need an example (though it can still be useful to write one for your own purposes). If the intermediate steps do need to

Re: [Bioc-devel] Build issues under macOS

FWIW I am getting the same error in my builds on merida1 for a package that is under review: http://bioconductor.org/spb_reports/CellaRepertorium_buildreport_20200908175926.html#merida1_buildbin_anchor Similar to Matt, I have Rcpp code, but no fortran code so I am perplexed why there is any

Re: [Bioc-devel] HDF5Array failure on windows

For what it's worth, I have been getting seemingly the same error from HDF5Array, only on windows, on the package builder: https://master.bioconductor.org/checkResults/3.11/bioc-LATEST/MAST/tokay2-buildsrc.html I have been hoping it will magically go away, as I do not have access to any

Re: [Bioc-devel] Updating for 3.11

I agree with Martin that the R administration guide should be frequently consulted on Mac OS and other systems (and would have save me a couple hours of trouble shooting the other week). However it's not always updated for the most recent Mac OS perversions, as I found:

Re: [Bioc-devel] Bioc-devel Digest, Vol 182, Issue 7

Off topic, but I am curious how you maintain the parallel installs in your home directory given the Mac binary package's proclivities to dump things into /Library/Frameworks/? Do you compile from source, with appropriate --prefix to keep your installation sandboxed in ~/bin? Andrew McDavid

Re: [Bioc-devel] Pushing towards a better home for matrix generics

As a casual observer of this thread, my takeaway is that 1. the current situation is untenable (e.g. it means that Aaron would have to essentially reimplement S4 method dispatch) 2. Given the long history, and extent of reverse dependencies to Matrix, there are good reasons to not mess with

Re: [Bioc-devel] git transition for projects with prior git history

r-git-mirror? Your > non-zero commit history should be related to bioconductor git server. > > Best > > Nitesh > > Get Outlook for Android > > > > From: Vladimir Kiselev > Sent: Thursday, July 27, 5:11 PM > Subject: Re: [Bioc-devel] git transition for pro

[Bioc-devel] git transition for projects with prior git history

Is there a recommended recipe to utilize the git.bioconductor.org remote with an existing git repo that has non-zero history? I tried adding the git.bioconductor.org as a remote, making a branch, and then checking out a branch on that

Re: [Bioc-devel] Problem pushing new versions of xcms via git svn dcommit

Hi Steffen, Option 2 worked for me recently with a repo that had previous git history. I think you after you run git branch --track biocmaster bioc/master You need to run git checkout biocmaster Then you may run git svn dcommit, which should just be a null op at this point. I will

[Bioc-devel] Why can't NAMESPACE be a strict subset of DESCRIPTION Imports?

BiocCheck throws a warning when a package is listed as Imports: in DESCRIPTION but not used in the NAMESPACE. This may happen when a developer uses the fully qualified names of objects within a package. I am unclear as to the rationale for this warning. Per Hadley: It's common for packages