Re: [Bioc-devel] mcols Function Not Found for Windows Build

Hi Dario, You're missing several imports. The CHECK results on the other platforms contains "no visible global function definition" notes for several symbols including 'mcols': https://bioconductor.org/checkResults/3.7/bioc-LATEST/ClassifyR/malbec2-checksrc.html Not sure why these missing

[Bioc-devel] mcols Function Not Found for Windows Build

Good day, I notice an error happening when the vignette of ClassifyR is checked by tokay2. mcols is not found. I viewed the check reports of S4Vectors, and there are some Warnings for all operating systems, but no platform has Error, so it's unlikely to be related to the problem. Is there a

[Rd] speeding up R compilation

Hello all, First, a small advert for this: https://hughjonesd.shinyapps.io/rcheology/ which lists functions in core R going back to 3.0.1. Second, I'm trying to extend this back to 2.0.0. That involves building many versions of R from source on a Docker image of Debian Sarge. (Shades of 2006,

Re: [Rd] clusterApply arguments

On 03/15/2018 05:25 PM, Henrik Bengtsson wrote: On Thu, Mar 15, 2018 at 3:39 AM, wrote: Thank you for your answer! I agree with you except for the 3 (Error) example and I realize now I should have started with that in the explanation. From my point of view

Re: [Rd] clusterApply arguments

On Thu, Mar 15, 2018 at 3:39 AM, wrote: > Thank you for your answer! > I agree with you except for the 3 (Error) example and > I realize now I should have started with that in the explanation. > > From my point of view > parLapply(cl = clu, X = 1:2, fun = fun, c = 1)

Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Rpolyhedra 0.2.2

On 15/03/2018 1:38 AM, alejandro baranek wrote: Hi list: Please someone can help me with the stranges errors I recivied after a minor bugfix in my package? tests ok, devtools::check() ok, TRAVIS CI ok... What is the problem? The main problem in the log is this one: * checking top-level files

Re: [Bioc-devel] Best practice on commit

Hi, Just to clarify, all software packages are built and checked every night, independently of whether their version got bumped or not. The version bump only allows the modified package to propagate to the public repo and become available via biocLite(), possibly replacing the previous version

Re: [R-pkg-devel] [CRAN-pretest-archived] CRAN submission Rpolyhedra 0.2.2

The NOTEs look harmless, the WARNING is this (InternalException (HostCannotConnect "badges.ropensci.org" [connect: failed (Connection refused (WSAECONNREFUSED))])) so badges did not want to speak to win-builder. Doesn't look like something you can deal with, except by removing the offending

[R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Rpolyhedra 0.2.2

Hi list: Please someone can help me with the stranges errors I recivied after a minor bugfix in my package? tests ok, devtools::check() ok, TRAVIS CI ok... What is the problem? Best, Ale. -- Forwarded message -- From: Date: 2018-03-15 1:39 GMT-03:00

Re: [R-pkg-devel] Weird error message during R CMD Check

I don’t think the suggestion below will work as it would need to be a connection string to a database that the winbuilder computer (and whatever account) that is running would have access to. It would be better to use \dontrun{} so that the examples aren’t run. This is what is done in RODBC

Re: [Bioc-devel] Best practice on commit

On Sun, Mar 11, 2018, at 4:10 AM, Egon Willighagen wrote: > But previously I learned that when you push > something to the repository, you should bump the question, so currently I > do this for every change I made, leaving a ridiculous number of minor > release and really short NEWS entries... I

[Bioc-devel] updating experiment data package MethylAidData

Dear all, We are looking to update the MethylAidData experiment data package by adding an additional dataset. We are not sure what the appropriate steps towards this are. Can we just update the package and push to the bioconductor git with a version bump (like with a software package)? Or is

Re: [Rd] truncation/rounding bug with write.csv

So, I come in this morning, and I also find that the behavior is not Happening any longer as well. Perhaps it has to do with Memory utilization and some built-in safeguards to avoid Memory Problems by truncating the numerics? It's extermely frustrating that it I can no longer make this happen.

Re: [Rd] clusterApply arguments

Thank you for your answer! I agree with you except for the 3 (Error) example and I realize now I should have started with that in the explanation. >From my point of view parLapply(cl = clu, X = 1:2, fun = fun, c = 1) shouldn't give an error. This could be easily avoided by using all the

Re: [R-pkg-devel] Dealing with not so temporary files

Hi Gabor, That's indeed the case, but I see good reasons for the CRAN policy when we take reproducability into account. Afaik, CRAN and R always strived to provide tools that give the same output regardless of the machine they're running on when opened in a fresh R session. If packages store

Re: [R-pkg-devel] Dealing with not so temporary files

This seems to be a good occasion to note that the CRAN policy does not seem to conform the industry standards. Applications can actually store user level configuration information, cached data, logs, etc. in the user's home directory, and there standard way to do this. Here is the Apple