Re: [Bioc-devel] EBImage/cytomapper check error on tokay2 i386

I can confirm that I can reproduce this error on my own Windows machine. My first thought is that it's related to the new Windows toolchain. I'll try to take a look today and see if there's a simple fix in the code. On Mon, 20 Apr 2020 at 11:12, Nils Eling wrote: > Hi all, > > the checks for my

Re: [Bioc-devel] EBImage/cytomapper check error on tokay2 i386

It looks like this is upstream of EBImage, and is an issue in the tiff package, which is also currently failing on the 32-bit CRAN builder ( https://www.r-project.org/nosvn/R.check/r-devel-windows-ix86+x86_64/tiff-00check.html). The tiff::readTIFF() function is what's being used internally by EBIma

Re: [Bioc-devel] EBImage/cytomapper check error on tokay2 i386

Perfect, thanks a lot! Let me know if I can be of any help. Cheers, Nils > On 22 Apr 2020, at 09:57, Mike Smith wrote: > > I can confirm that I can reproduce this error on my own Windows machine. My > first thought is that it's related to the new Windows toolchain. I'll try to > take a look

Re: [Bioc-devel] Need help figuring out GeometryDoesNotContainImage-error on machv2-build for chimeraviz

I'm still unable to reproduce this error on my end. If anyone with a mac could try building locally I would be very grateful. Thanks. On Sat, Apr 18, 2020 at 4:06 PM Stian Lågstad wrote: > Hi, > > I'm haven't been able to figure out this error for the latest machv2 build > for chimeraviz: > > ``

[Bioc-devel] ReactomeGSA - Windows SSL error on tokay2

Hi, I'm getting a strange build error for the ReactomeGSA package. The package accesses our API through an https connection. I couldn't find any issue with our certificate. Builds on Linux and Mac are working fine. Therefore, it seems to be related to the certificate management on tokay2. I'd be

Re: [Bioc-devel] R-devel for Windows: Rtools3.5 vs Rtools4.0

Hi Herve, > Are you saying that 'R CMD config CC' returns > /mingw64/bin/x86_64-w64-mingw32-gcc-8.3.0 with the latest > Windows build of R 4.1.0? No, it doesn't. I was just trying to interpret the note "This build of R-Devel uses the gcc gcc 8.3.0 toolchain from rtools40." that is attached to R-

[Bioc-devel] Bioc 3.11 Feature Freeze

Developers, The release of Bioconductor 3.11 is one week out. Today marks the 'feature freeze' of 3.11 where we ask that all commits are limited to bug fixes and documentation (no more API changes). Thanks you for your cooperation. Lori Shepherd Bioconductor Core Team Roswell Park Comprehe

Re: [Bioc-devel] credentials/authors for MTseeker, biscuiteer, and data packages corresponding to each

Hi, Right now, both you and Tim are on the package as people with access to the package on the Bioconductor git repository. I would refrain from setting up a generic email. Mostly because, it doesn�t come with the same amount of accountability as a user�s email address. Nitesh From: "Morri

[Bioc-devel] Windows Development Build Error Message for COHCAP

Hi, I noticed that I received a few error messages in the Windows build for COHCAP: http://bioconductor.org/checkResults/devel/bioc-LATEST/COHCAP/tokay2-buildsrc.html I changed the default settings to avoid an earlier error message (again, just on Windows), but I am currently getting an error m

[Bioc-devel] Author name displayed incorrectly in package landing page

Dear Bioconductor team, I have recently realized the first author name in my rfaRm package is not displayed as intended in its landing page (https://bioconductor.org/packages/rfaRm). In short, I put my name as “Lara Selles Vidal” in the Author: field of the DESCRIPTION file. My first name is j

Re: [Bioc-devel] EXTERNAL: Author name displayed incorrectly in package landing page

Hi Lara, I often recommend the use of the `Authors@R` field in the DESCRIPTION file which will give you more control: ``` Authors@R: c(     person(given = "Lara", family = "Selles Vidal", ...),     ...     ) ``` Best, Marcel On 4/22/20 4:00 PM, Selles Vidal, Lara wrote: > Dear Bioconductor te

Re: [Bioc-devel] Author name displayed incorrectly in package landing page

You might have better luck updating the Author and Maintainer fields in the DESCRIPTION to Authors@R syntax. It should also be noted there should only be one maintainer for the package. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics

Re: [Bioc-devel] Author name displayed incorrectly in package landing page

An alternative that might also work is to add a CITATION file, which might make it easier to define first and last names. https://cran.r-project.org/doc/manuals/r-release/R-exts.html#CITATION-files On Wed, Apr 22, 2020 at 4:42 PM Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > You might

Re: [Bioc-devel] Package CNVPanelizer needs my attention

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Re: [Bioc-devel] Package CNVPanelizer needs my attention

I'm sorry I don't see any question or response to this? Was there something you had a question about? The package CNVPanelizer is failing on the builders across all platforms and needs attention. http://bioconductor.org/checkResults/devel/bioc-LATEST/CNVPanelizer/ The ERROR has to do with c

Re: [Bioc-devel] Package CNVPanelizer needs my attention

Hi, First, it seems that your question was stripped because it was in HTML and the mailing list doesn't support that. (Martin can chime in if any additional details are needed here) Second, for people wondering, this is the question, " Dear Martin, thanks for your reply, The CNVpanelizer (De

[Bioc-devel] Resubmitting additional packages as separate issues

Hello Bioc-devel, I recently submitted three packages to Bioconductor Contributions (CoreGx, RadioGx and ToxicoGx). After consulting my reviewer I now wish to resubmit the two dependent packages (RadioGx and ToxicoGx) on separate issues. I deleted the comments from #1445 where I submitted the ‘

Re: [Bioc-devel] Resubmitting additional packages as separate issues

I will assist you with this tomorrow and contact you in a private email when you can resubmit. Get Outlook for Android From: Bioc-devel on behalf of Chris Eeles Sent: Wednesday, April 22, 2020 7:23:17 PM To: Bioc-devel@r-project.org Sub