similar to: [Bioc-devel] package citations

Just thought I would mention that the issue below (and in https://stat.ethz.ch/pipermail/r-devel/2013-April/066318.html) is still not resolved. It hasn't been a big problem, but it potentially could be, if a critical package were to have this error on release day, then all its dependencies would fail to build, which would probably require us to postpone our release. See the complete thread

I'm trying to load an annotation file on a new R installation on a new machine (Win 7 x64, R 2.15.0) Loading this package fails; I've tried re-installing R and BioC from scratch, including all new packages etc, to no avail. Any ideas? > require("hugene10sttranscriptcluster.db") Loading required package: hugene10sttranscriptcluster.db Loading required package: AnnotationDbi

>>>>> Kasper Daniel Hansen <kasperdanielhansen at gmail.com> >>>>> on Fri, 19 May 2017 20:09:24 -0400 writes: > I rebuilt R with > export LC_CTYPE=en_US.UTF-8 > and the test still fail. Surprisingly, when I run R from the bin directory > and execute the test code, it runs without error: >> oloc <-

Yes, you are absolutely right and I'm pretty sure this will be fixed in one way or another. IMO, the failing test should simply use all.equal.POSIXt's new argument check.tzone=FALSE. Two simple alternatives modifying all.equal.POSIXt behaviour: - make check.tzone=FALSE the default: this is inconsistent with other arguments of all.equal methods, always defaulting to stricter checks -

Aaaah ... and argh - I should have better not to post R question at midnight, especially when I know it forks the process and it's not using threads. Brain meltdown. (So, we'll proceed trying to use pthreads in matrixStats also for Windows). Sorry for the noise and thanks Kasper. Henrik On Aug 15, 2015 02:52, "Kasper Daniel Hansen" <kasperdanielhansen at gmail.com> wrote:

On 05.10.2015 23:47, Andrew Robinson wrote: > As a fourth option, I wonder if the first author could fork the package? > > Presumably, appropriately cited, a fork is permitted by the license under > which it was released. Then the original package, by both authors, still > exists (and a final version could point to the new one) and the new > package, citing the previous version

Adrian, Responses inline On Tue, Oct 6, 2015 at 1:58 PM, Adrian Du?a <dusa.adrian at unibuc.ro> wrote: > Hi Gabriel, > > On Tue, Oct 6, 2015 at 10:59 PM, Gabriel Becker <gmbecker at ucdavis.edu> > wrote: > >> [...] >> >> At the very least, this is seems to be a flagrant violation of the >> *spirit* of the CRAN policy, which AFAIK is intended to

Dear all, Is there an elegant way to add citations of packages when using Sweave? Ideally I'd like a function which creates a Bibtex-file with the packagenames as keys. The idea is to use \cite{packagename} or \cite{R} in LaTeX. I know you can get the Bibtex entry with toBibtex(citation("packagename")). But after updating R or a package one needs to update the bib-file too. When

So let me try to raise this issue once more, and perhaps be more clear about what I think the issue is.. In my opinion there is now a bug in make check in R-development (tested today with r79361). As I see it, I specify a reasonable TZ environment variable and this leads to make check emitting an error. Best, Kasper On Fri, Oct 2, 2020 at 11:28 AM Kasper Daniel Hansen < kasperdanielhansen

Simply advice: The former co-author contributed, so he is still author and probably copyright holder and has to be listed among the authors, otherwise it would be a CRAN policy violation since even if he does not develop further on, he developed parts of the so far existing package (if you talk about a CRAN package). I am not a lawyer, hence I cannot speak for copyright/license stuff in

For people reading this: I was installing bzip2 by hand. Two things to bear in mind (1) it only installs a shared library if you use a special Makefile (this is clearly stated in the installation docs) and (2) I had to symlink libbz2.so.1 to libbz2.so.1.0.6 (the included libbz2.so.1.0 was not being picked up). Best, Kasper On Fri, Mar 27, 2015 at 11:19 AM, Kasper Daniel Hansen <

Dear R developers, This is a rather peculiar question, but nevertheless I would still need an answer for. It is about an R package which I created (namely QCA), and from versions 1.0-0 to 1.1-4 I had a co-author. The co-author recently withdrawn from the package development, but still requires to be left in the authors list and be cited for the package in the CITATION file. Obviously, one could

As a fourth option, I wonder if the first author could fork the package? Presumably, appropriately cited, a fork is permitted by the license under which it was released. Then the original package, by both authors, still exists (and a final version could point to the new one) and the new package, citing the previous version appropriately, is by a single author. The page of CRAN's policies

Hi Kasper FWIW, the package development and maintenance support in 'mvbutils' makes it trivial to work with namespaced packages, even at the earliest stages of development. It's completely easy to add and remove functions to/from the namespace (and the exported visible bit) while the package is loaded. Debugging is seamless (via the 'debug' package, anyway). There is no need

I rebuilt R with export LC_CTYPE=en_US.UTF-8 and the test still fail. Surprisingly, when I run R from the bin directory and execute the test code, it runs without error: > oloc <- Sys.getlocale("LC_CTYPE") > mbyte.lc <- { + if(.Platform$OS.type == "windows") + "English_United States.28605" + else if(grepl("[.]UTF-8$", oloc,

As I see it, the display showing the first p << n PCs adding up to 100% of the variance is plainly wrong. I suspect it comes about via a mental short-circuit: If we try to control p using a tolerance, then that amounts to saying that the remaining PCs are effectively zero-variance, but that is (usually) not the intention at all. The common case is that the remainder terms have a roughly

Hi again, I have been playing around with the order of loading packages, and as far as I can tell, there's nothing specific with affycoretools that's causing my Rgui to crash (i.e., shuts down and the Microsoft 'please send error report' box pops up). Instead, it has something to do with the order & type of packages that are loaded that add items to the menu bar by

Kasper, I haven?t checked in depth, so just to clarify: you *are* setting CXX11=g++ so it is doing what you asked it to. Since the settings are inherited upwards, this implies that you are setting both CXX14 and CXX17 to g++. So I?m not quite sure I understand your concern. Cheers, Simon > On Sep 3, 2019, at 9:02 PM, Kasper Daniel Hansen <kasperdanielhansen at gmail.com> wrote: >

My subject line refers to a thread from June 2005 where I found explanations from Uwe Ligges and Friedrich Leisch as to what is intended by the R citation recommended within the software. Forgive me if I missed some points within the thread but when I found myself circling through messages I had already read, I stopped trying to follow it. I understand and mostly agree with how the R citation is

Sorry for the off-topic question, but I know there are some talented LaTeX users out there. Which bibliography style gives only the year in text citations (e.g "for further details, see Anderson (1992)" )? Thanks Jason -- Indigo Industrial Controls Ltd. http://www.indigoindustrial.co.nz 64-21-343-545 jasont at indigoindustrial.co.nz