Re: [Bioc-devel] surfaltr build on Bioc 3.17 error advice

2023-03-21 Thread Hervé Pagès
On 21/03/2023 12:48, Pooja Gangras wrote: > Hi Herve, > > Thank you for the quick response. > > So what surprises me is that msa was compiling and building just fine > on the devel branch until now. As I said, the switch from C++14 to C++17 happened not too long ago in the devel version of R. An

Re: [Bioc-devel] Manifest and annotation packages for EPIC methylation array v2.0

2023-03-21 Thread Zuguang Gu
I am aware of the AnnotationHub package, but currently I think it is not possible to integrate with minfi. In the last several lines in https://github.com/hansenlab/minfi/blob/master/R/IlluminaMethylationAnnotation-class.R setMethod( "getManifest", signature(object = "IlluminaMethylationA

Re: [Bioc-devel] surfaltr build on Bioc 3.17 error advice

2023-03-21 Thread Pooja Gangras
Hi Herve, Thank you for the quick response. So what surprises me is that msa was compiling and building just fine on the devel branch until now. And hence so was surfaltr, without any errors. There was a warning in surfaltr which one can see on the 3.16 release, I had fixed it in the devel branch

Re: [Bioc-devel] surfaltr build on Bioc 3.17 error advice

2023-03-21 Thread Hervé Pagès
Hi Pooja, Generally speaking there are 3 things you can do when a dep breaks your package: 1. Consider getting rid of that dep. 2. Contact the author/maintainers of the dep to let them know about the problem. If you can suggest a fix (e.g. by sending a PR on GitHub), that's even better, as

Re: [Bioc-devel] Single Package Builder package dependency issue

2023-03-21 Thread Kern, Lori
This issue should now be resolved. Thank you for your patience Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc

Re: [Bioc-devel] download stats not accessible

2023-03-21 Thread Luo Weijun via Bioc-devel
Thanks for the clarification. I have a analytics plot, which receives the download stats from these pages and has not been updated for months. I thought this is the cause, but could be something else. Anyway, thanks for working on the problem. Weijun On Monday, March 20, 2023, 01:06:26

Re: [Bioc-devel] Reopen cfTools issue #2608

2023-03-21 Thread RAN HU
Thank you, Lori! I have successfully opened a new issue. Best, Ran On Tue, Mar 21, 2023 at 8:36 AM Kern, Lori wrote: > I modified the code and if you try to resubmit again it should work this > time. > > Lori Shepherd - Kern > > Bioconductor Core Team > > Roswell Park Comprehensive Cancer Cent

[Bioc-devel] surfaltr build on Bioc 3.17 error advice

2023-03-21 Thread Pooja Gangras
Hi, I got an email yesterday alerting me of the error in the build in the new BioC release. Upon looking into the error further I found out that the error is occurring because a dependency 'msa' package is not being built in the new release likely due to some issues with the C++ compiler (just gue

Re: [Bioc-devel] Reopen cfTools issue #2608

2023-03-21 Thread Kern, Lori
I modified the code and if you try to resubmit again it should work this time. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 Fr

Re: [Bioc-devel] Reopen cfTools issue #2608

2023-03-21 Thread RAN HU
Hi Lori, I submitted a new issue #2962. Since I cannot post to the same directory twice, this issue was also closed. Could you please open it? Thanks, Ran On Tue, Mar 21, 2023 at 04:31 Kern, Lori wrote: > With the recent updates to the branch renaming and given the large gap in > time, Could y

[Bioc-devel] Bioconductor 3.17 db0s, OrgDbs and TxDbs now available

2023-03-21 Thread Interdonato, Kayla
Hello Bioconductor Community! The newest db0s, OrgDbs, and TxDbs annotation packages for the upcoming Bioconductor 3.17 release are up and available for download in the devel version of Bioconductor. The deadline for submitting contributed annotations will be Wednesday April 12th. The new db0 p

Re: [Bioc-devel] Manifest and annotation packages for EPIC methylation array v2.0

2023-03-21 Thread Kern, Lori
The maintainer for these two packages IlluminaHumanMethylationEPICmanifest IlluminaHumanMethylationEPICanno.ilm10b4.hg19 Is actually Kasper Daniel Hansen as listed in the DESCRIPTION file not bioc core members. You could reach out to Kasper to see if there is any intention or efforts that have

Re: [Bioc-devel] Reopen cfTools issue #2608

2023-03-21 Thread Kern, Lori
With the recent updates to the branch renaming and given the large gap in time, Could you please resubmit as a new issue. Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New Yor