Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz

Thanks, super useful. So you're saying it was working with 2.51.1? Or is it working with the release version? Best, Kasper On Mon, Mar 24, 2025 at 12:28 PM Andrew McDavid wrote: > Dear Kasper and Robert, >> >> b) as I said in my original report, with Rgraphviz 2.51.1, I cannot >> reproduce the

Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz

G="integer"), > prototype=list(subG=as.integer(0)) > ) > > and the backtrace shown in some of the reports points out to > 'Rgraphviz::buildEdgeList()'. so, maybe this problem was unrelated with the > buffer overflow after all. > > I've look

Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz

ri, Mar 14, 2025 at 9:22 AM Robert Castelo wrote: > Thanks Kasper, let me know if there is anything I could help with. > > cheers, > > robert. > > On 13/3/25 22:54, Kasper Daniel Hansen wrote: > > I am actively working on Rgraphviz right now following some reports

Re: [Bioc-devel] failing with non-reproducible error "no slot of name "name" for this object of class "pEdge"" from Rgraphviz

I am actively working on Rgraphviz right now following some reports by CRAN about - issues with the package failing on the C23 standard - issues with the package failing on Windows using the new R toolset for the next R release - a switch from sprintf to snprintf Tomas and Brian have been sup

Re: [Bioc-devel] Problem with S4 method dispatch: method found for SummarizedExperiment, but not SingleCellExperiment

t; setGeneric("Umethod", function(x) standardGeneric("Umethod")) > setMethod("Umethod", signature="U", function(x) cat("Umethod!\n")) > o <- new("C") > Umethod(o) ## it works!! > > Thanks in advance for your support and su

Re: [Bioc-devel] Problem with S4 method dispatch: method found for SummarizedExperiment, but not SingleCellExperiment

In my experience, class unions are hard to work with and quickly get out of hand. I don't really understand what you actually want to do, beyond defining a class union. My impression is that your main goal is to write simplified code. I could be wrong, but I doubt class unions is the best way to so

Re: [Bioc-devel] New BioC 3.21 settings for R 4.5.0

Thanks for the clarification Herve. There is probably no doubt that we have packages with too many imports. However, like Kristian mentions, one of the original reasoning behind the creation of Bioconductor and our build system with release and devel branch, was the typical larger dependency graph

Re: [Bioc-devel] Important Bioconductor Release Deadlines

It's a bit late, but I'll point out that the use of R-devel dates back 20y to the inception of the Bioconductor project. So this is the way it has always been. Of course, this is an argument of conservatism which is always dangerous, But at least it illustrates that this is not a small change to ma

Re: [Bioc-devel] Check time on macOS (MIRit)

To be a bit more clear and vague at the same time: currently, some of our macOS builders exhibit weird slowdowns when the build system is run automatically compared to running builds "by hand". This is pretty weird, and hopefully we can figure out the cause and fix it. Specifically, builds on kjohn

Re: [Bioc-devel] build reports for apple silicon

eport. > > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ---------- > *From:

[Bioc-devel] build reports for apple silicon

We're clearly producing binary builds for Apple Silicon. Why do we not have a build report for this platform? Best, Kasper [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc

Re: [Bioc-devel] How to declare optional system requirement for package

To me, whether or not this is a good idea depends a bit on the degree to which these functions are generally useful. Best, Kasper On Wed, Nov 29, 2023 at 5:41 PM Hervé Pagès wrote: > Hi Alex, > > On 11/28/23 22:47, Alex Wong via Bioc-devel wrote: > > > Hi there, > > > > I am the author of Splic

Re: [Bioc-devel] Is my package suitable for Bioconductor?

I am happy to talk on Zoom about this, since I have some interest in this work. Best, Kasper On Tue, Oct 24, 2023 at 9:21 AM Vincent Carey wrote: > agreedthis discussion is best discussed in the open > > On Tue, Oct 24, 2023 at 8:57 AM Lluís Revilla > wrote: > > > Hi Tim, > > > > I think t

Re: [Bioc-devel] Python module "tensorflow_probability" not found

w and keras. It > > builds > > > and runs fine both on GitHub Actions (GitHub repo here: > > > https://github.com/fmicompbio/orthos) and on the Single Package > Builder. > > > We have also tested (locally) that it will use GPUs if available, and > > that >

Re: [Bioc-devel] Python module "tensorflow_probability" not found

So I think Kim is interfacing to tensorflow by using the keras package from CRAN (partly authored by the Rstudio people). This package leaves it to the user to install tensorflow, which is a highly non-trivial installation task. There is some partly helpful instructions for using conda together wit

Re: [Bioc-devel] BiocManager::install

t directly build upon BiocGenerics, IRanges etc. to > submit them to CRAN, to increase potential user base (b/c installation from > Bioconductor can be such a pain). And that’s really not the place I want to > be. > > Thanks and best wishes > Wolfgang > > > > > &

Re: [Bioc-devel] BiocManager::install

Could we get a list of use cases from Wolfgang? I am confused about what the issue is. Is the issue that it is painful to work with R-devel in the "off" 6-months? If so, I agree that it should be easier (even if we don't recommend it). But I am having a hard time parsing the email. I can recognize

Re: [Bioc-devel] Changing Maintainer Email Addresses

You should change the maintainer email in the DESCRIPTION file and commit it to Bioconductor git. Make sure you're subscribed to the devel email list on the new email. Best, Kasper On Mon, May 1, 2023 at 11:02 AM Augustin Luna wrote: > I am currently the maintainer of > > https://bioconductor.o

Re: [Bioc-devel] Question on tasks after successfully building a package

You need to increase your package version number to trigger a new build on the submission package. On Tue, Mar 29, 2022 at 7:03 AM Kern, Lori wrote: > You can modify your package at any time. Please remember to push to > git.bioconductor.org with any updates and fix any ERROR or Warnings that >

Re: [Bioc-devel] MAGMA executable

Ignoring the license issues (which may be significant), I strongly dislike this installation strategy. It (IMO) unreasonable that you potentially write in system locations on package load. You're looking in /usr/local/bin R.home/bin <- this makes not sense, this is the R home location, why shou

Re: [Bioc-devel] Use set.seed inside function

Martin's suggestion is the way to go. For display purposes, you basically never want random colors, you almost always want to select distinct colors and there are principled ways of doing that. Best, Kasper On Tue, Nov 30, 2021 at 6:59 AM Martin Morgan wrote: > Check out grDevices::hcl.pals (al

Re: [Bioc-devel] bpparam Non-deterministic Default

This should be solved by the vignette appropriately calling set.seed and explaining why they set the seed and why it is not done automatically. In a visible code chunk. On Sat, Nov 27, 2021 at 7:31 AM Spencer Nystrom wrote: > This GitHub issue, although lengthy, discusses some of the technical >

Re: [Bioc-devel] Issue with change in random sampling

The random number generator is tracked by a global state, which is a violation of functional programming. This is unavoidable. This is why we really don't want packages to EVER touch the random number state for example by setting the seed. You can also be affected by this if any function you depend

[Bioc-devel] lessons learned: negative experiences with git log

had changed. However, running git log --name-status I got this START git log == commit 955e30b3ae316265b4f5f130ab6f12c33081da54 Author: Kasper Daniel Hansen Date: Wed Aug 11 08:52:11 2021 -0400 Fixing length condition error :100644 100644 25e24de 3aee690 MDESCRIPTION

Re: [Bioc-devel] BiocCheck and version requirement

; > > > > Lori Shepherd > > > > Bioconductor Core Team > > > > Roswell Park Comprehensive Cancer Center > > > > Department of Biostatistics & Bioinformatics > > > > Elm & Carlton Streets > > > > Buffalo, New York 14263 > > > >

Re: [Bioc-devel] BiocCheck and version requirement

; Bioconductor Core Team > > Roswell Park Comprehensive Cancer Center > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > ------ > *From:* Bioc-devel on behalf of Kasper > Danie

Re: [Bioc-devel] Suppressing messages from Rprofile

You could also preprend your cat so it outputs something like INCLUDE_DIR=.. and then use grep and sed to trim it. Of course that can also end up being brittle. On Wed, Apr 7, 2021 at 10:48 PM Henrik Bengtsson wrote: > Correcting: the env var is R_LIBS_USER and nothing else. > > /Henrik > > On

[Bioc-devel] BiocCheck and version requirement

The latest BiocCheck (well, it may have been around for a bit) _requires_ the package to have a R >= 4.1 dependency. That seems new to me. Right now it's a bit irritating, because if you're submitting a package that works with latest stable release, you are now prohibited from installing it from G

Re: [Bioc-devel] Moving minfi classes definition to a lighter package

I am happy to engage in a discussion about this, although I'm not sure that I am ultimately interested in having two packages. But first I would like to look at some dependency graphs. I am wondering what makes the dependency tree this big (and my tree is smaller than yours, but still big: library

Re: [Bioc-devel] How to integrate code from a package not available on bioconductor

This question is actually pretty complicated and involves matters of copyright and academic credit, which are two different things. In general you cannot take code from the internet and republish it under your own name. It sounds like you want to include something substantial (as opposed to say a

Re: [Bioc-devel] Compiling a cpp source code while installing package

Alexandra, What you're proposing is possible, but it is definitely a non-trivial task, because you (as the package author) are now responsible for getting MAGMA compiled on Linux / Windows and OS X. If MAGMA is not designed as a library, that might be hard. Not impossible but hard. Best, Kasper

Re: [Bioc-devel] BiocManager and R-devel

gt; single version of R. Addressing the symptom is to remove the BiocVersion > package. I'd recommend the one-library-one-Bioconductor version approach to > for managing multiple versions outlined in the vignette. Your solution > means that you cannot switch back to your previously working

[Bioc-devel] BiocManager and R-devel

Installed R-devel as of today. I have a previous version of Bioconductor installed in site-library. I then do install.packages("BiocManager") # installs version 1.30.10 > library(BiocManager) Bioconductor version '3.11' is out-of-date; the current release version '3.12' is available with R ver

Re: [Bioc-devel] Package update before october 23rd deadline and build errors [duplicated, wrong email address previous]

Giula, Provided your package has been accepted by a reviewer, it will be released as part of Bioconductor 3.12, as long as it satisfies the other requirements, which includes some deadlines for when it is supposed to pass check without errors. In general, around release, there are a lot of change

Re: [Bioc-devel] VERSO issue #1689

I can't speak for the reviewer, but the package currently has 2 WARNINGS. If I were you, I would fix those warnings and push the fixes to Github, at which point the package will be re-built and re-checked. You're not supposed to have any ERRORS / WARNINGS when you submit. I would also look at the N

Re: [Bioc-devel] BSgenome changes

> Leonard > > > On Tue, Aug 18, 2020 at 10:06 AM Hervé Pagès wrote: > >> On 8/18/20 01:40, Kasper Daniel Hansen wrote: >> > In light of this, could we get a version of GRCh37 with only a single >> > mitochondrial genome? >> >> You mean a BSgen

Re: [Bioc-devel] BSgenome changes

In light of this, could we get a version of GRCh37 with only a single mitochondrial genome? On Fri, Aug 14, 2020 at 6:17 PM Hervé Pagès wrote: > Hi Felix, > > On 8/13/20 21:43, Felix Ernst wrote: > > Hi Leonard, Hi Herve, > > > > I followed your conversation, since I have noticed the same proble

Re: [Bioc-devel] LazyData in DESCRIPTION file

> > Dept. for Applied Bioinformatics > Inst. for Cell Biology and Neuroscience > Goethe University Frankfurt > > Biologicum, Room 3.209 > Phone +49 (0)69/798-42118 > > On 30. Apr 2020, at 16:02, Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > &g

Re: [Bioc-devel] LazyData in DESCRIPTION file

> > > Dr. Vinh Tran > > Dept. for Applied Bioinformatics > Inst. for Cell Biology and Neuroscience > Goethe University Frankfurt > > Biologicum, Room 3.209 > Phone +49 (0)69/798-42118 > > On 30. Apr 2020, at 14:55, Kasper Daniel

Re: [Bioc-devel] LazyData in DESCRIPTION file

If you don't have lazy data on, you should be able to load the data by using data(). Let us say you example data is called expData. With lazy data print(expData) Without lazy data you need explicit loading data(expData) print(expData) For the purpose of examples, there is also a user-leve

Re: [Bioc-devel] HDF5Array failure on windows

#x27; of the documentation > module. The solution (from my perspective) is usually to simply omit the [] > and let the R help system resolve the link dynamically (sometimes prompting > the user to choose, if there multiple man pages). > > > > Martin Morgan > > > > &

[Bioc-devel] HDF5Array failure on windows

We currently (and for a while) have had various errors in bsseq that seems to have come and go. We now have a failure on Windows which is related to HDF5. I see that HDF5Array also fails on Windows, which makes me believe the error could be upstream. There is also a warning about hep page links whi

Re: [Bioc-devel] Updates to SingleCellExperiment class structure - no action required

It sounds to me that the class definition / structure is updated. You should also have an associated updateObject() method to deal with this; that's tradition. Of course, you may already have addressed this and just not written about it in your email. On Sun, Feb 16, 2020 at 3:51 AM Aaron Lun < in

Re: [Bioc-devel] How to use RData files in Bioconductor data and software packages

Tobias, When you use the data() command on the data package, you need to do library(dummyData) first (and you therefore need to Suggest: dummyData) Here is an example from minfi/minfiData if (require(minfiData)) { dat <- preprocessIllumina(RGsetEx, bg.correct=FALSE, normalize="controls") }

Re: [Bioc-devel] proposal for additional seqlevelsStyle

If the chromosome name depends on the assembly, that makes GenomeInfoDb even more useful and necessary. Provided it is supported of course. On Fri, Dec 13, 2019 at 11:45 AM Vincent Carey wrote: > I tried an inline png but I think it was rejected by bioc-devel. Here's > another try. > > On Fri,

Re: [Bioc-devel] -fopenmp switch issue on mac

Are you using the clang 6 (R 3.5) / 7 (R 3.6) / 8 (R 4.0) which Simon supplies? This is for clang 6 with full path /usr/local/clang6/bin/clang --version clang version 6.0.0 (tags/RELEASE_600/final) Target: x86_64-apple-darwin18.7.0 Thread model: posix InstalledDir: /usr/local/clang6/bin On Wed,

Re: [Bioc-devel] CRAN packages depending on broken Bioc 3.11 packages may be archived

Or remove the graph dependency On Tue, Nov 26, 2019 at 3:16 PM James W. MacDonald wrote: > Hi Lori, > > Let me know if you don't hear from Benilton. It shouldn't be much work to > fix oligo - we could convert to using Gviz for the graphic that is > currently using GenomeGraphs. I can make the ch

Re: [Bioc-devel] How to move package from workflow to software

Without commenting on whether the move is appropriate, it should trigger a new review process. Best, Kasper On Fri, Nov 15, 2019 at 9:31 AM Julien Wollbrett wrote: > Hello Nitesh, > > Thank you for your answer. > > I added some functionalities to the BgeeCall package that are not > compatible t

Re: [Bioc-devel] Opinions on a meta-annotation package

>From your description it very much sounds like creating a new package is the way to go. On Thu, Oct 24, 2019 at 3:03 PM Pages, Herve wrote: > Hi Panagiotis, > > Avoiding code repetition is always a good idea. An alternative to the > creation of a 3rd package would be to have one of the 2 packag

Re: [Bioc-devel] check fails on arch 'i386'

I see these packages may have something to do with mini. There is a a (very old, nothing new) issue with the annotation objects in minfi where loading them uses a _lot_ of ram. For a long time I couldn't understand it, but now I get it. I should really fix this, and probably _very_soon. It won't ha

Re: [Bioc-devel] new package for accessing some chemical and biological databases

We used to have (? or at least discussed the possibility of) occasional extensive checking so we could have tests long_tests (names made up). On Fri, Sep 13, 2019 at 9:50 AM Martin Morgan wrote: > Putting bioc-devel back in the loop. > > I think that the straight-forward answer to your origi

Re: [Bioc-devel] RGL warning

GLX is a module for X11. You need that module installed in whatever X11 installation you have. My understanding (which is weak) is that GLX is a standard module so it is weird it is missing. On Tue, Sep 10, 2019 at 12:39 PM Zhezhen Wang wrote: > Hi > > I am having the following warnings and not

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

t; On Tue, Sep 10, 2019 at 11:35 AM Christian Mertes > wrote: > > > >> Thanks a lot for the info! So from my understanding we dont use any > >> trimming or editing function from ImageMagick directly. I think this is > >> rather knitr based since we just include png fil

Re: [Bioc-devel] Failing to build vignette because of problems with ImageMagick

You don't declare any systems requirements for ImageMagick (doing so will probably not solve your problem, but you really should). Alternatively you could look into using the tools provided by the magick package, which wraps ImageMagick. But it looks like you're editing PNG files for your vignett

Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

There are importMethodsFrom(PACKAGE, NAME_OF_METHODS) importClassesFrom(PACKAGE, NAME_OF_METHODS) to help with selective importing S4 methods/classes. See section 1.5.6 of WRE. On Fri, Sep 6, 2019 at 9:24 AM Michael Lawrence via Bioc-devel < bioc-devel@r-project.org> wrote: > It sounds like

Re: [Bioc-devel] Fwd: Re: Build error due to TensorFlow installation

It might be true that the code is much easier on your end, but it comes with the complexity of using TensorFlow, which is a huge dependency. And that library can be easy or impossible to install depending on your box. I am not saying people shouldn't use TensorFlow, but I am saying it brings a lot

Re: [Bioc-devel] 'tokay1' error but passed other OS

that would be great. Please tag me when you do > so I can keep track of it also @lshep on GitHub > Cheers > > Get Outlook for Android <https://aka.ms/ghei36> > > -- > *From:* Venu Thatikonda > *Sent:* Wednesday, September 4, 2019 3:

Re: [Bioc-devel] 'tokay1' error but passed other OS

window until the issue is resolved. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics & Bioinformatics > > Elm & Carlton Streets > > Buffalo, New York 14263 > --

Re: [Bioc-devel] 'tokay1' error but passed other OS

Well, yes, its the status on the build system which matters. In your case it looks like you're doing BigWig parsing. Unfortunately, some of the tools we have for reading BigWig (tracklayer) does not work reliably on Windows - sometimes it works, sometimes it doesn't. My _guess_ is that you're runn

Re: [Bioc-devel] Resetting to previous commits

indeed a breaking change, and I thus > believed > > that it would have been counted as a bug-fix for the release branch. > > > > All the best, > > Erik > > > > On 14 Aug 2019, at 17:15, Kasper Daniel Hansen < > > kasperdanielhan...@gmail.com<mailto:

Re: [Bioc-devel] Resetting to previous commits

You cannot revert. By pushing those updates, you released a version into the wild. It is true that as long as it doesn't build on the build servers, it would have been hard to obtain for anyone, but it is still possible through git. You need to update the version. Best, Kasper On Wed, Aug 14, 201

Re: [Bioc-devel] Resetting to previous commits

to "copy" a snapshot of CRAN into release. Best, Kasper On Wed, Aug 14, 2019 at 11:13 AM Kasper Daniel Hansen < kasperdanielhan...@gmail.com> wrote: > You cannot revert. By pushing those updates, you released a version into > the wild. It is true that as long as it does

Re: [Bioc-devel] tokay1 C++14 compiler

based server. > > BTW: Recent updates from stan community suggest that the new rstan version > 2.20 will reduce the model compilation time from ~35sec to ~7sec, which > makes the decision of sticking with the run-time compilation setup not so > bad. > On 29.07.19 8:37 nachm., Kasper Dani

Re: [Bioc-devel] tokay1 C++14 compiler

'Unsupported on Windows' (thereby losing 1/2 your > user base). > > > > The expert on this (Hervé) will not be back for several days. > > > > Martin > > > > On 7/25/19, 6:33 PM, "Bioc-devel on behalf of Kasper Daniel Hansen" < > bioc

Re: [Bioc-devel] tokay1 C++14 compiler

What's weird here is that you supposedly depend on rstan which also requires a C++14. How can the build system have that package installed without having a compliant compiler? On Thu, Jul 25, 2019 at 12:05 PM Simo Kitanovski wrote: > Hello Bioconductor community, > > I maintain the Bioconductor

Re: [Bioc-devel] use -Wa, -mbig-obj -O3 when building package under Windows

[ This is a crazy bug where you have to increase optimization. ] I some to add here. I am involved in at least two packages which requires overriding the optimization switch to downgrade optimization. You have an additional problem where you need to add additional flags. The solution in affxparse

Re: [Bioc-devel] loading database package changes random number

ot transparent to the user, as a dependency-of-a-dependency-of-an > annotation package. > > > > I guess an acceptable solution would be for DelayedArray to remember and > restore the random number seed before creating a BiocParallel param, with > an edge case being that .Random.

Re: [Bioc-devel] loading database package changes random number

Why don't you let this be under the user's control and not do this at all. People should know that reproducibility of random numbers requires setting the seed, but that is best done by the user and not a package author. On Wed, May 22, 2019 at 9:30 AM Steffi Grote wrote: > Hi all, > > I tried to

Re: [Bioc-devel] InteractionSet for structural variants

ur SV > calling pipeline in your new coordinate system. A lot more effort, but I'd > have at least some confidence in the results. > > On Wed, May 22, 2019 at 12:07 AM Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > >> I know little about SV and the

Re: [Bioc-devel] InteractionSet for structural variants

I know little about SV and the associated software, but it is clear to me that we will see a lot of "personal" genomes in the future and having the ability to move between different reference genomes (coordinate systems) will be something I think we should think about having good/great support for.

Re: [Bioc-devel] SummarizedExperiments not equal after serialisation

Interesting detective work. This is nasty. Best, Kasper On Thu, May 16, 2019 at 2:19 AM Pages, Herve wrote: > Let's try to go to the bottom of this. But let's leave > SummarizedExperiment objects out of the picture for now and focus on what > happens with a very simple reference object. > > Whe

Re: [Bioc-devel] When to use generics?

This is a common situation. Most packages might have a need for something that looks like a generic, but it really only has a usage inside your own package(s). In many ways, the pseudo-generic you define using if() statements is often easier to work with, debugging wise and code-reading wise. Howe

Re: [Bioc-devel] package RBGL requires CRAN dependency on devel branch

On Wed, Mar 27, 2019 at 1:06 AM Aaron Lun < infinite.monkeys.with.keyboa...@gmail.com> wrote: > > well, we can't fix this in old branches of Bioc. > > Sure, but one could say that about breaking changes to any CRAN package. > Nothing particularly special about BH on that point. > Indeed, and this

Re: [Bioc-devel] package RBGL requires CRAN dependency on devel branch

library, so breaking changes will most likely > cause compilation errors that are obvious and easy to fix. Well, easy > enough if you were able to write C++ code in the first place. > > -A > > > On 25/03/2019 08:39, Vincent Carey wrote: > > On Mon, Mar 25, 2019 at 10:57

Re: [Bioc-devel] package RBGL requires CRAN dependency on devel branch

t; On Mon, Mar 25, 2019 at 10:57 AM Kasper Daniel Hansen < > kasperdanielhan...@gmail.com> wrote: > >> There are no issues with depending on CRAN packages. >> >> But I would advise caution. On one hand it is great that boost gets >> updated regularly. On the othe

Re: [Bioc-devel] package RBGL requires CRAN dependency on devel branch

There are no issues with depending on CRAN packages. But I would advise caution. On one hand it is great that boost gets updated regularly. On the other hand, it could lead to incompatibilities with RBGL and then you have to update that package rapidly. Also - and this is something we could consid

Re: [Bioc-devel] Call for collaborators/advice

Why is this not "just" a function which transforms one GI into another GI? Thats what it seems to me. On Fri, Mar 22, 2019 at 12:31 PM Luke Klein wrote: > I am writing a package that will extend the GenomicInteractions class. I > am a statistician, so I may not know best practices when it comes

Re: [Bioc-devel] set.seed and BiocParallel

But why do you want the same seed for the different features? That is not the right way to use stochastic methods. Best, Kasper On Tue, Mar 12, 2019 at 5:20 PM Bemis, Kylie wrote: > Hi all, > > I remember similar questions coming up before, but couldn’t track any down > that directly pertain to

Re: [Bioc-devel] How critical is package style for bioconductor?

lintr can be configured to use camelCase. On Tue, Feb 26, 2019 at 11:12 AM Turaga, Nitesh < nitesh.tur...@roswellpark.org> wrote: > As long as it’s consistent, you can use another style. Consistency helps > reviewers read the code easily. > > Most people generally use “camelCase" or “snake_case"

Re: [Bioc-devel] Error package build

According to the GitHub repos, the current maintainer is Valentin Dinu Which is not the email you have sent this message from. Do you have multiple email addresses and this is causing this? On Mon, Feb 25, 2019 at 8:44 PM margaret linan wrote: > Hi - > > I have submitted my package PoTRA usin

Re: [Bioc-devel] Using SerialParam() as the registered back-end for all platforms

To add to Henrik's comments, it is also worthwhile to recognize that mclapply() does not deliver statistically sound random numbers even within the apply "loop" unless you use RNGkind("L'Ecuyer-CMRG") which is not set as default. This is because mclapply will initialize random streams with differen

Re: [Bioc-devel] Compilation flags, CHECK errors and BiocNeighbors

I would hope we do not distribute binaries compiled with -march=native That seems very wrong. On Sun, Dec 16, 2018 at 1:56 AM Aaron Lun < infinite.monkeys.with.keyboa...@gmail.com> wrote: > Sometime between 6-18 November, BiocNeighbors’ BioC-devel builds began > failing on Windows 64-bit, and

Re: [Bioc-devel] Questions about some checks in the latest BiocCheck

First, the issue with using class() is that the return is a vector possibly with >1 element. This _does_ happen. This is why is() etc is much better,. Second, why do you need case insensitivity when testing for class. That makes NO sense to me. You should be testing for a specific (collection) of

Re: [Bioc-devel] Error : object 'lengths' is not exported by 'namespace:BiocGenerics'

It seems the short answer is: yes, base::lengths() works and should be fast If it either doesn't work or is slow, you should report it. On Tue, Nov 13, 2018 at 3:33 PM Pages, Herve wrote: > I'm going to try to provide some details, at the risk to confuse you even > more. > > > In BioC 3.8 / R

Re: [Bioc-devel] A little confuse about how to update accepted package

Wenhao, The night before the release your package was at 0.99.x in the devel branch At release, two things happened: the package was added to the release branch with version 1.0.0 the package in the devel branch was updated to version 1.1.0 So basically version 0.99.19 == 1.0.0 == 1.1.0. And

Re: [Bioc-devel] About the reproducibility of BioC server environment

In my experience, if I aggressively update my development installation of Bioconductor (including occasional updates of R-devel when appropriate) I can usually replicate most-all failures on the build server which has the same OS as my local machine. It does require aggressive updating though. On

Re: [Bioc-devel] macOS Mojave and R 3.6: issue with building some packages from source

You seem to install the Beta version of the Command Line tools. That's not right. Look at the top of apple.com/developer/downloads (First try with xcode-select --install on the command line, which I could not get to work). Following installation of these tools you need to run the following com

Re: [Bioc-devel] GenomicFeatures

gt; that was in neither CRAN nor Bioconductor. > > Though of course we'd like GenomicFeatures to be available in 3.8 > > Martin > > On 11/2/18, 1:05 PM, "Bioc-devel on behalf of Kasper Daniel Hansen" < > bioc-devel-boun...@r-project.org on behalf of kasperdanielhan

[Bioc-devel] GenomicFeatures

Seem broken in release. And btw., because it is broken, when I run BiocManager::valid() it doesn't report GenomicFeatures as out of date, despite the fact that I have version 1.33.2 installed, and there are newer versions in the 1.33.x hierarchy and the "right" (but broken) version in Bioc 3.8 i

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

Perhaps explain why On Fri, Nov 2, 2018 at 8:19 AM Jianhong Ou, Ph.D. wrote: > Hi, > > Is it possible to install ghostscript in tokay2 for development package > build? > > Yours Sincerely, > > Jianhong Ou > > Email: jianhong...@duke.edu > Bioinformatician II > Depart

Re: [Bioc-devel] Dependency to PEER

It is a major weakness of PEER that it has not been submitted to a standard repository. Of course, that is up to the PEER developers, but the community should put pressure on them. On Tue, Sep 25, 2018 at 12:40 PM Christian Mertes wrote: > Hi all, > > Im the developer of OUTRIDER. Our package no

Re: [Bioc-devel] package c++ optimization flag

This should be done extremely sparingly, but it is sometimes necessary if you know that higher optimization breaks the code. But that is the only use case. Otherwise you should trust the setting of the user who compiles R, ie. you should for example never force a higher optimization level IMO. We

Re: [Bioc-devel] Logolas package broken for R (3.4) users

I think the "correct" answer to this, is that it is impossible. Old releases are locked. The way to discover such things is to have appropriate test functions which will signal an error if things break. Best, Kasper On Tue, Aug 28, 2018 at 2:17 PM Obenchain, Valerie < valerie.obench...@roswellpa

Re: [Bioc-devel] Block bootstrap for GenomicRanges

I agree this is super important. I think there may be multiple ways of thinking about a decent bootstrapping or permutation of ranges, in genomics. I am quite interested in the topic. I think it might belong in a new package. I would be interesting in extending the conversation and have a couple o

Re: [Bioc-devel] updating maintainer

You update the maintainer field in devel. I don't know what to do about release. I don't understand the question about github. There is no "github email", there is a github username. And that username does not have to be the same as a maintainer email, because they really have nothing to do with

Re: [Bioc-devel] Including a submodule in the main package repository

My opinion: maintain two repos and pull/push between them. You would want the ability to have them out of sync anyway. Best, Kasper On Thu, Jun 14, 2018 at 1:16 AM, Thomas Sherman wrote: > Hi all, > > I'm a developer for the CoGAPS package (https://github.com/FertigLab/ > CoGAPS). I'm looking i

Re: [Bioc-devel] Package size note

Kenneth, You should _always_ run R CMD check (and R CMD BiocCheck) on the tarball generated by R CMD build. The build step essentially cleans the code. If your vignette takes a bit to generate (the vignette gets generated with R CMD build), just do R CMD build --no-build-vignettes Best, Kasper

Re: [Bioc-devel] Switch to SSH protocol for git clone instructions on package landing pages?

s, which I find very useful. Best, Kasper On Mon, May 7, 2018 at 12:22 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > > > On 04/30/2018 08:17 AM, Kasper Daniel Hansen wrote: > >> Still, it is convenient for some of us to have copy+paste code on the >>

Re: [Bioc-devel] Virtual class for `matrix` and `DelayedArray`? (or better strategy for dealing with them both)

We did this recently in minfi and getting acceptable performance was not trivial. We are still sorting out issues; we will eventually write about our experiences. Pete is working on some blog posts on this and we hope to do something more formal later. We would all love experience from more people

Re: [Bioc-devel] Switch to SSH protocol for git clone instructions on package landing pages?

Still, it is convenient for some of us to have copy+paste code on the landing page. How about having both https and ssh? On Sun, Apr 29, 2018 at 8:57 AM, Peter Hickey wrote: > Ah, thanks both Joris and Nitesh. I didn't appreciate that SSH access is > limited to those with a public key registere

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