Re: [Bioc-devel] Git upstream/access issues

Sorry, this went off-list. Closing the loop to say permission was given and package maintainers were updated. Valerie On 03/27/2018 09:10 AM, Kipper Fletez-Brant wrote: Thanks Valerie. Kasper, would you sign off here so I can fix this? On Tue, Mar 27, 2018 at 3:54 PM, Obenchain, Valerie

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

Nitesh, Force push worked! Thanks! Best regards, Julie On 3/29/18, 2:12 PM, "Turaga, Nitesh" wrote: Hi Julie, It doesn’t matter if it is the RELEASE_3_6 branch. If the problem is duplicate commits, just force your Github RELEASE_3_6 to

Re: [Bioc-devel] How to access git repository as a new maintainer

In addition to changing the maintainer field in the DESCRIPTION and submitting a key (which I see was already done) - we would need an email sent to bioc-devel@r-project.org or maintai...@bioconductor.org from the original maintainer (Ravi Shankar in this case) requesting transfer or

Re: [Bioc-devel] appveyor CI failing with biocparam

Hi Martin Thanks for the quick reply. I think that would have been the real issue most probably. I fixed it, though the build still failed, but this time it might be due to build cache or other issues with appveyor? A unit test that was fixed earlier also keeps failing on appveyor. My travis

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

Hi Julie, It doesn’t matter if it is the RELEASE_3_6 branch. If the problem is duplicate commits, just force your Github RELEASE_3_6 to Bioconductor’s RELEASE_3_6. Best, Nitesh > On Mar 29, 2018, at 2:10 PM, Zhu, Lihua (Julie) > wrote: > > Nitesh, > > I will try

[Bioc-devel] Call for papers for Bioconductor F1000Research Gateway

Bioconductor is again working with F1000Research to coordinate the submission of papers for publication prior to the Bioc2018 conference. The official announcement and details are available at the Bioconductor support site: http://bit.ly/2J5X9kH Please share broadly and consider submitting your

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

Hi Julie, Did you try #8 from the documentation pointed out by the error message? Take a look at the documentation to fix this, https://bioconductor.org/developers/how-to/git/sync-existing-repositories/, particularly, point #8 (force Bioconductor master to Github master). The idea is to force

Re: [Bioc-devel] GUIDEseq problems reported in the Multiple platform build/check report for BioC 3.6

Thanks, Nitesh! Since it is a released version, I thought I will get input from you first. I will try #8 and let you know if it does not work. Best regards, Julie > On Mar 29, 2018, at 1:59 PM, Turaga, Nitesh > wrote: > > Hi Julie, > > Did you try #8 from

Re: [Bioc-devel] new package deadline? 4/2 or 4/9

Thanks, Val. Sorry to be pesky, but could you specify the deadline by time of day? Are submissions accepted anytime Monday, my local time? Or perhaps Roswell Park’s local time, 5pm? - Paul > On Mar 27, 2018, at 5:05 PM, Obenchain, Valerie > wrote: >

Re: [Bioc-devel] Tensorflow support for bioconductor packages

The problem with requiring explicit tensor flow installation is that it is tantamount to a system dependency in many ways, and those are annoying. Herve points out the problems with installing at load time. My suggestion was to install the package the first time someone tries to e.g. load an R

Re: [Bioc-devel] vignette problems

Dear bioc-devel team, I have made some changes in the package STAN and although it seems to install correctly, I have problems with timeout and error in windows... Could someone help me to improve the time? https://bioconductor.org/checkResults/3.7/bioc-LATEST/STAN/ Best, Rafael On

Re: [Bioc-devel] Tensorflow support for bioconductor packages

Hi Hervé, Michael, Thanks for your feedback. I will add in the reticulate check to ensure tensorflow is installed prior to running and appropriate sections in the vignettes. We have one package essentially ready for submission to bioc, so is the best route forward to submit now or wait until

Re: [Bioc-devel] appveyor CI failing with biocparam

Hi Vivek... On 03/29/2018 08:39 AM, Vivek Bhardwaj wrote: Dear All I have travis and appveyor CI running for my upcoming package in development. I find that the appveyor CI fails for the function `GenomicAlignments::summarizeOverlaps`, which is called by one of the functions in my package. It

Re: [Bioc-devel] Update data in data package, pcxnData

Hey all, The packages' changes went through to the 3_6 branch, but since pcxn and pcxnData depend on each other, there are errors when they get built as they see the old version of the other package. In the current example: