Re: [Bioc-devel] Biostrings: substitution matrices disappeared?

Hi, Yesterday there was another email about Biostrings - https://stat.ethz.ch/pipermail/bioc-devel/2024-April/020395.html I thought it might be related to your problem. Regards, Martin On Thu, Apr 25, 2024 at 8:23 AM Ulrich Bodenhofer < ulrich.bodenho...@gmail.com> wrote: > Dear colleagues,

[Bioc-devel] Biostrings: substitution matrices disappeared?

Dear colleagues, dear BioC core team, One of my packages in the devel branch, the ‘msa’ package seems broken since yesterday. The vignette does not run anymore (therefore, the package does not build), and the reason is that the BLOSUM62 substitution matrix cannot be loaded form the ‘Biostrings’

Re: [Rd] [External] Re: Is ALTREP "non-API"?

On Wed, 24 Apr 2024, Hadley Wickham wrote: A few more thoughts based on a simple question: how do you determine the length of a vector? Rf_length() is used in example code in R-exts, but I don't think it's formally documented anywhere (although it's possible I missed it). Is using in an

Re: [Rd] View() segfaulting ...

As suggested by Josh Ulrich, here's what I get when running under valgrind. $ R -d valgrind ==218120== Memcheck, a memory error detector ==218120== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==218120== Using Valgrind-3.18.1 and LibVEX; rerun with -h for copyright info

[Rd] View() segfaulting ...

I'm using bleeding-edge R-devel, so maybe my build is weird. Can anyone else reproduce this? View() seems to crash on just about anything. View(1:3) *** stack smashing detected ***: terminated Aborted (core dumped) If I debug(View) I get to the last line of code with nothing obviously

Re: [Rd] [External] Re: Is ALTREP "non-API"?

On Wed, Apr 24, 2024 at 1:32 PM luke-tierney--- via R-devel wrote: > > On Wed, 24 Apr 2024, Hadley Wickham wrote: > > >> > >> > >> > > That is not true at all - the presence of header does not constitute > declaration of something as the R API. There are cases where internal >

Re: [Rd] Question regarding .make_numeric_version with non-character input

Hi Kurt, Is it intended that numeric_version() returns an error by default on non-character input in R 4.4.0? It seems that I can turn this into a warning by setting _R_CHECK_STOP_ON_INVALID_NUMERIC_VERSION_INPUTS_=false but I don't seem to be able to find any of this mentioned in the NEWS

Re: [Rd] [External] Re: Is ALTREP "non-API"?

On Wed, 24 Apr 2024, Hadley Wickham wrote: That is not true at all - the presence of header does not constitute declaration of something as the R API. There are cases where internal functions are in the headers for historical or other reasons since the headers are used both for the

Re: [Rd] Is ALTREP "non-API"?

> On Apr 25, 2024, at 12:55 AM, Hadley Wickham wrote: > > > > >>> That is not true at all - the presence of header does not constitute > >> declaration of something as the R API. There are cases where internal > >> functions are in the headers for historical or other reasons since the > >>

Re: [Rd] Is ALTREP "non-API"?

A few more thoughts based on a simple question: how do you determine the length of a vector? Rf_length() is used in example code in R-exts, but I don't think it's formally documented anywhere (although it's possible I missed it). Is using in an example sufficient to consider a function to be part

Re: [Bioc-devel] nebbiolo1 - build report

The new report is available:https://bioconductor.org/checkResults/3.19/bioc-LATEST/MSA2dist/. Jennifer Wokaty (they/them) Waldron Lab at CUNY SPH Bioconductor Core Team From: Bioc-devel on behalf of Herv� Pag�s Sent: Wednesday, April 24, 2024 12:27 PM To:

Re: [Bioc-devel] MIRit fails to build on palomino3

We will look into it. If there is anything that needs to be done on your end we will reach out. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] Build errors related to the new pwalign package

Hi developers, pairwiseAlignement() and stringDist() have recently moved from Biostrings to the new pwalign package. This is causing a number of failures today on the 3.19 report. Since yesterday I've been actively repairing packages affected by this by pushing fixes to git.bioconductor.org.

Re: [Bioc-devel] nebbiolo1 - build report

As for the error you will see when today's report gets published it's caused by the recent move of the pairwiseAlignment stuff from Biostrings to the new pwalign package. I fixed it in MSA2dist 1.7.6 so it will go away in tomorrow's report. Please resync your GitHub repo with

Re: [Bioc-devel] nebbiolo1 - build report

Hi Kristian, I believe that this is because the new report didn't get published yet so the links in the email you received still points to yesterday's report. We're investigating. Best, H. On 4/24/24 09:10, Kristian Ullrich wrote: > Hi, > > I just got an email from bbs: > > Hi MSA2dist

Re: [Bioc-devel] New annotation hub package?

I can assist you with this request. In the future there is the email h...@bioconductor.org for these types of requests instead of the developer mailing list as mentioned in the documentation. I'll contact you off mailing list for further details and instruction. Cheers, Lori Shepherd -

[Bioc-devel] nebbiolo1 - build report

Hi, I just got an email from bbs: Hi MSA2dist maintainer, According to the Multiple platform build/check report for BioC 3.19, the MSA2dist package has the following problem(s): o ERROR for 'R CMD INSTALL' on nebbiolo1. See the details here:

Re: [Rd] Is ALTREP "non-API"?

> And in general, I'd urge R Core to make an explicit list of functions that you consider to be part of the exported API While I believe R Core is in the process of such clarification, I'd also vote for this. Now that WRE has "experimental" category, and if we take the current definition of

Re: [Bioc-devel] Package passing checks on Linux and macOS but failing on Windows

Okay thanks. However, I won't be able to fix my package until the dependencies are fixed. Is that okay? Cheers, Richard On Wed, 24 Apr 2024 at 15:45, Kern, Lori wrote: > Yes your package will still be included in the release. Even if a > package is failing, you would receive notifications

Re: [Bioc-devel] Package passing checks on Linux and macOS but failing on Windows

Yes your package will still be included in the release. Even if a package is failing, you would receive notifications and a deprecation cycle before the package would be officially removed. We like to see package fixed before a release so they can be made available to end users as soon as

[Bioc-devel] Package passing checks on Linux and macOS but failing on Windows

Hi all, My new package on the devel version of Bioconductor is passing the build/check report on Linux and macOS, but failing on Windows (Palomino3). It seems some other packages that my one depends on are also failing on Windows (e.g. rtracklayer) so I am wondering will my package still be added

[Bioc-devel] Final Reminder: EuroBioC2024 Abstract Deadline April 26th

Hi everyone, This is the last call to submit your abstracts for the EuroBioC2024 conference. The submission window closes this Friday, April 26th, at 5 PM BST. Ensure your research is showcased at EuroBioC2024 by submitting your abstract

[Bioc-devel] New annotation hub package?

Dear developers community, We are currently developing a package for which we are quite sure we will need a supporting AnnotationHub or ExperimentHub package to go with it. We are using a set of gene annotations (GENCODE version 40 hg38) and enhancer annotations (ENCODE registry of cCREs v3),

Re: [Rd] Is ALTREP "non-API"?

> > > > >>> That is not true at all - the presence of header does not constitute > >> declaration of something as the R API. There are cases where internal > >> functions are in the headers for historical or other reasons since the > >> headers are used both for the internal implementation and

Re: [Bioc-devel] Additional commit access for the BindingSiteFinder package

Could you please have the current maintainer Mirko Br�ggemann confirm this request? Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] Additional commit access for the BindingSiteFinder package

Hello, I recently joined the development of the Bioconductor BindingSiteFinder package and would like to get commit access to git.bioconductor.org for this package. The package was developed Mirko Brüggemann (in cc) and we are working on it together now. Could you

[Bioc-devel] MIRit fails to build on palomino3

Dear developers, My package (MIRit) can be successfully installed and built on nebbiolo1, iconway and kunpeng2. Moreover, it successfully passes R CMD check on all these platforms. However, it started failing the build process only on palomino3, due to a call to "bfcadd()" during vignette

Re: [R-pkg-devel] [External] Re: Package submission to CRAN not passing incoming checks

В Wed, 24 Apr 2024 00:17:28 + "Petersen, Isaac T" пишет: > I included the packages (including the raw package folders and their > .tar.gz files) in the /inst/extdata folder. Would you prefer your test to install them from the source directories (as you currently do, in which case the