[Bioc-devel] Error in building vignette for previously stable version

Hi all, I am the developer of NormalyzerDE. A few days ago the release version of NormalyzerDE started getting errors in the vignette building (with no updates from my side). I saw in the mailing list that others also had encountered issues in the vignette. I don't know how widespread the

Re: [Bioc-devel] Bioconductor package twilight

Hi Lori, I just tried to clone to Github and understand I need BioC Git credentials to do so, however I was not able to activate my account and got the following message on https://git.bioconductor.org/BiocCredentials/account_activation/ stefanie.sch...@gmx.de is not associated with a

[Bioc-devel] Build error

Hello bioc-devel team, I recently came across an error when the automatic bot was trying to build my package. The error only happens on OSX systems. === R CMD BUILD === * checking for file CSSQ/DESCRIPTION ... OK * preparing CSSQ: *

Re: [Bioc-devel] RangedData objects deprecated

The RangedData objects are still viable with the software you are using, but trying to set colnames will trigger an error. In Bioc 3.11 you won't even be able to use the RangedData class at all. So an intervention is needed now. The RangedData objects that were serialized or created in your

[Bioc-devel] RangedData objects deprecated

Dear Bioc devel team, Can you advise how to amend the following code to update references to RangedData objects? I’m running the Broad ichorCNA, which had a similar issue described in the package internal code, which I gather has been addressed

Re: [Bioc-devel] Windows only vignette error - any ideas?

To me this issue doesn't seem to be directly linked to BiocStyle as the affected package does not depend on it. Might be still a problem with rmarkdown though. Cheers, Andrzej On Wed, Dec 4, 2019 at 10:12 PM Shepherd, Lori < lori.sheph...@roswellpark.org> wrote: > We are hoping it is related to

Re: [Bioc-devel] Windows only vignette error - any ideas?

We are hoping it is related to this: https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html so you should just sit tight. Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets

Re: [Bioc-devel] Fwd: TVTB problems reported in the Multiple platform build/check report for BioC 3.10

I think it is this https://stat.ethz.ch/pipermail/bioc-devel/2019-December/015870.html so you should just sit tight... On 12/5/19, 7:39 AM, "Bioc-devel on behalf of Kevin RUE" wrote: Hi, I've been getting a weird Latex-related error on the daily build recently, _although I

[Bioc-devel] Fwd: TVTB problems reported in the Multiple platform build/check report for BioC 3.10

Hi, I've been getting a weird Latex-related error on the daily build recently, _although I haven't updated the package in ages_. https://master.bioconductor.org/checkResults/3.10/bioc-LATEST/TVTB/malbec1-buildsrc.html I'm guessing some LaTeX package must have been updated recently and causes

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

Thanks -- the solution I used was to install the Simon-Urbanek-modified distribution clang 8.0 from the page noted in my reply. On Wed, Dec 4, 2019 at 3:10 PM Bunis, Daniel wrote: > I was running into the `clang: *error: *unsupported option '-fopenmp’` > yesterday myself. I’m not on Sierra,

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

I was running into the `clang: *error: *unsupported option '-fopenmp’` yesterday myself. I’m not on Sierra, but I fixed it with the top answer on this page:

Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

We will start the process and be in touch off the bioc mailing list. We would require you officially take over as maintainer as all bioconductor packages require an active maintainer. PathNet was failing and we reached out (several times) and deemed the package orphaned as we never heard back

Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

Yes, I could do that if needed. From: Shepherd, Lori Sent: Wednesday, December 4, 2019 1:28 PM To: Ludwig Geistlinger; bioc-devel@r-project.org Subject: Re: Final List of Deprecated Packages for Bioc3.10 ***ATTENTION: This email came from an external source. Do

Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

Are you volunteering to permanently take over as maintainer of this package? Lori Shepherd Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From:

Re: [Bioc-devel] Final List of Deprecated Packages for Bioc3.10

Hi Lori, Is it possible to undeprecate the "PathNet" package? I just checked, the problem is a failing unit test, causing the otherwise well working package to fail R CMD check. I fixed this here on a local clone of https://git.bioconductor.org/packages/PathNet and could push these minor

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,

[Bioc-devel] -fopenmp switch issue on mac

When installing packages from source, I frequently run into this error with %vjcair> clang --version Apple LLVM version 9.0.0 (clang-900.0.39.2) Target: x86_64-apple-darwin16.7.0 Thread model: posix InstalledDir:

Re: [Bioc-devel] Activating git credentials

It's possible your university is blocking emails. But either way, I've set a password for you and reset your account. You should receive a private email. Once you add your SSH keys, you'll have access to your package. Best, Nitesh > On Dec 4, 2019, at 10:10 AM, Turaga, Nitesh > wrote: >

Re: [Bioc-devel] Activating git credentials

You never activated the account earlier. This will be your first time, so you don't have a password. I see, it could be that the "username" section of your email is case-sensitive. I just sent you a test email, can you confirm if you've received it? If you have we can assume that the email is

Re: [Bioc-devel] Activating git credentials

Hi Nitesh, thanks for your help. I have checked the junk folder, but nothing there. In principle no e-mail is sent since the error says that there is maintainer associated with the email. Perhaps a stupid question, but could it be that the error comes because I have uppercase characters? The

Re: [Bioc-devel] Activating git credentials

Hi Marc, Your email address is associated with your package. "m.pagesgall...@umcutrecht.nl" You should be able to activate it from BiocCredentials. Have you tried checking in your spam folder or junk folder for the activation email? https://git.bioconductor.org/BiocCredentials It seems

Re: [Bioc-devel] Error in Vignette of package

Dear Package Developers, BiocStyle will be patched within the next couple of days to address the observed errors. Until then please refrain from making any changes to your package, the issue should resolve itself once BiocStyle is updated. Cheers, Andrzej On Mon, Dec 2, 2019 at 11:20 AM Andrzej

[Bioc-devel] jupyter installation on merida1

Dear BioConductor maintainers, The buildbots almost seem able to build my package’s vignettes again, but the jupyter installation on merida1 still [ http://bioconductor.org/checkResults/release/bioc-LATEST/destiny/merida1-buildsrc.html | doesn’t seem quite right ] : * creating vignettes

[Bioc-devel] Activating git credentials

Hi all, I am trying to activate my Bioconductor Git Credentials account. When trying it gives an error saying that the email address is not associated with a package maintainer. However, I am the maintainer of pulsedSilac