similar to: wishlist: ObjectFiles

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 -

>>>>> 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 <-

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:

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

Hi all, I am trying to compile Rgraphiz on Windows 7 64bit with R-2.13.0. I have installed Rtools213.exe from [1]. The 64bit packages in [2] provided me with the 64 bit version of graphviz. After intalling the binary version Rgraphviz 1.30 (in 32bit) it complains (as expected) that: > library(Rgraphviz) Error: package 'Rgraphviz' is not installed for 'arch=x64' I

I am considering a package with a namespace (Rgraphviz from Bioc). I essentially want to have some error handling for loading the dll, something like wrapping it into tryCatch or similar (reason: see below). Right now I am loading the dynamic libraries by useDynLib in my NAMESPACE file. When I look at the code from loadNamespace, I have the impression that what I want is impossible

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 suppose taste is learned as well. It does feel quite odd that the best way to define a long string without a note or text wrapping is by being creative with functions. This is valid in Python, Julia, and Rust (if you add `let` and a terminating semi-colon): my_str = "part1\ part2\ part2" I don't think it is abnormal to expect or desire this type of functionality in our favorite

(xposted to bioc-devel and r-devel as I feel it is relevant to both communities) As someone whose body of work is likely to consist mostly of infrastructural packages and research directly in computing I wholeheartedly agree with Kasper's suggestion that we as a community should work to provide and use package citations. I borrow heavily from existing work in terms of both concept and

R-devel now gives a warning for a non-standard license (this may have happened for a while). In Rgraphviz we include the Graphviz source code, which is under Eclipse. But the rest of the R package is under Artistic-2.0 or at least contains code from past contributors which were licensed under Artistic-2.0. The standard licenses does not really give an option for this situation, apart from using

One could also argue that paste0("a", "b", "c") is a function call that needs to be evaluated at runtime, whereas "abc" is a string constant understood by the parser, and often also language agnostic. I'd assume compilers and code- and text-search tools do a better job with the latter. /Henrik On Mon, Jun 2, 2025 at 2:18?PM Josiah Parry

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 <

Hi - since Rgraphviz was officially moved over to Bioconductor, this might be a misguided post, but it's worth a shot: I'm plotting a graph using Rgraphviz and in an attempt to force the edges to be behind the nodes (on a fairly complex graph), I set the "outputorder" graph attribute to "edgesfirst" (as is described in the graphviz docs here ->

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

Yes, the potential issue I see is that make check fails when I explicitly set TZ. However, I set it to be the same as what the system reports when I login. Details: The system (RHEL) I am working on has $ strings /etc/localtime | tail -n 1 EST5EDT,M3.2.0,M11.1.0 $ date +%Z EDT $ echo $TZ US/Eastern On Fri, Oct 2, 2020 at 9:48 AM Sebastian Meyer <seb.meyer at fau.de> wrote: > Thank

> On 3 Jun 2025, at 09:34, Henrik Bengtsson <henrik.bengtsson at gmail.com> wrote: > > One could also argue that paste0("a", "b", "c") is a function call that needs to be evaluated at runtime, whereas "abc" is a string constant understood by the parser, and often also language agnostic. I'd assume compilers and code- and text-search tools

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

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: >

Hello, after many failed attempts to correctly write BinaryFiles file "R CMD check will warn about them unless they are listed (one filepath per line) in a file BinaryFiles at the top level of the package." - CRAN docs would somebody kindly provide an example of BinaryFiles file? thank you Theo -- View this message in context: