Re: [Bioc-devel] vignette problems

Hi Martin, Thank you very much, I am a bit concerned about the option of: Last�Changed�Date: 2018-04-05�09:37:37�-0400�(Thu,�05�Apr�2018) I did a change yesterday and push it, why isn't it visible? Best, Rafa On 09.04.2018 16:44, Martin Morgan wrote: > I'll try to provide you with a pull

Re: [Bioc-devel] vignette problems

On 04/10/2018 05:27 AM, campos wrote: Hi Martin, Thank you very much, I am a bit concerned about the option of: Last Changed Date: 2018-04-05 09:37:37 -0400 (Thu, 05 Apr 2018) I did a change yesterday and push it, why isn't it visible? Notice that at the top of the build report it says

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

Everything seems to be fine and the 3_6 release is online. Thanks for the help! Cheers, Sokratis On 5 April 2018 at 18:41, Shepherd, Lori wrote: > We are taking care of this on our end. Sorry for the confusion. > > > Lori Shepherd > > Bioconductor Core Team > >

Re: [Bioc-devel] Update of miRBaseVersions.db annotation package

Thanks very much, I appreciate! On Mon, Apr 9, 2018 at 7:45 PM Van Twisk, Daniel < daniel.vantw...@roswellpark.org> wrote: > The package looks okay now. I've moved the package onto our devel builder > and it should propagate within a day or two. > -- > *From:* Stefan

[Bioc-devel] Unable to access repository

Hi all, I am the maintainer for DrugVsDisease package and am trying to push new changes. However, I am getting the following error: Permission denied (publickey). fatal: Could not read from remote repository. Please make sure you have the correct access rights and the repository exists. I

Re: [Bioc-devel] new package IGV needs web browsers on the build machines to pass build & check

Many thanks, Vince! I will fix the printf and markdown errors. With release date now not far off, I propose (Bioc policymakers please weigh in if this is inadequate) to - remove web browser communication from vignette, examples and unit tests - evaluate stubs and/or "mocks" for possible use in

[Bioc-devel] New db0 annotation packages

Hello all! The new db0 packages were recently pushed to 3.7 and will be available tomorrow. This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to

Re: [Bioc-devel] Bioc-devel changes and SummarizedExperiment class

Hi Leonard, This should be fixed in SGSeq 1.13.6 (see commit 5dc16968f7ea1a4b59595ebaabacca9a76699b80). Cheers, H. On 04/04/2018 09:23 AM, Leonard Goldstein wrote: Hi Hervé, Some recent changes in bioc-devel are causing trouble with SummarizedExperiment objects if the rowRanges slot inherits

Re: [Bioc-devel] vignette problems

Hi Martin, it seems like mac is ok now. What has changed?? Thank you very much, Rafael On 10.04.2018 11:33, Martin Morgan wrote: On 04/10/2018 05:27 AM, campos wrote: Hi Martin, Thank you very much, I am a bit concerned about the option of: Last Changed Date: 2018-04-05 09:37:37 -0400 

[Bioc-devel] single-package build, from git trigger: new linux build report missing

Maybe this is already known. As recently as April 4th, a single-package build initiated from a git push trigger produced reports for all three architectures: merida2 (OS X), malbec2 (linux), and tokay2 (windows). Since then, and still today, I only get reports from tokay2 and merida2. The

Re: [Bioc-devel] vignette problems

Hi -- I'm not sure what you mean; the 'devel' builld report does not include mac (the build system experienced problems with disk space last night, so the build did not complete) https://bioconductor.org/checkResults/devel/bioc-LATEST/STAN/ and STAN failed in Release

[Bioc-devel] single-package build, from git trigger: new linux build report missing

Maybe this is already known. Maybe it’s my error. As recently as April 4th, a single-package build, initiated from a git push trigger, produced reports for all three architectures: merida2 (OS X), malbec2 (linux), and tokay2 (windows). Since then, and still today, I only get reports from

Re: [Bioc-devel] BiocCheck error

Hi Aimin -- the problem is that your vignette has two VignetteEngine commands in it PathwaySplice/vignettes master$ grep VignetteEngine * tutorial.Rmd: %\VignetteEngine{knitr::rmarkdown} tutorial.Rmd: %\VignetteEngine{knitr::knitr} Also, please avoid writing to files in the user system,

Re: [Bioc-devel] single-package build, from git trigger: new linux build report missing

Thanks, Martin. It is indeed back up. - Paul > On Apr 10, 2018, at 4:09 PM, Martin Morgan > wrote: > > I *think* this is back up; you could do a version bump or resubmit the web > hook (go to your repository --> settings --> webhooks -> edit -> 'Redeliver' >

Re: [Bioc-devel] single-package build, from git trigger: new linux build report missing

I *think* this is back up; you could do a version bump or resubmit the web hook (go to your repository --> settings --> webhooks -> edit -> 'Redeliver' the event with 'X-GitHub-event: push'). Thanks for the heads-up Martin On 04/10/2018 06:09 PM, Paul Shannon wrote: Maybe this is already

[Bioc-devel] right version "masked" by wrong version - not sure what "masked means"

I am trying to build IGV (a new submission) on windows (tokay2) after linux and macOS build clean. IGV needs its base class package, BrowserViz, at version >= 2.0, whose build report is OK for install, build, and build bin. BrowserViz 2.0.11 fails check, probably because now web browser is

[Bioc-devel] iGraph depending packages failing on Windows build machines

I noticed that our Bioconductor package (PharmacoGx) is failing to build on Windows development, with the error: error: DLL 'maps' not found: maybe not installed for this architecture? A google search brings up the package 'sincell', which has experienced this error before. The only dependency

[Bioc-devel] RELEASE_3_6 branch frozen at 3:00pm EST tomorrow

Hello Maintainers, We are going to block pushes to the RELEASE_3_6 branch tomorrow at 15:00 EST. Maintainers who were planning to commit have until tomorrow 15:00 EST (3pm EST) to fix any outstanding issues they have. NOTE: Once the builds are done, the Bioconductor RELEASE_3_6 branch will be

[Bioc-devel] BiocCheck error

I used "R CMD check PathwaySplice_1.3.0.tar.gz", and get it passed without errors and warnings. However I get the following error when I use "R CMD BiocCheck PathwaySplice_1.3.0.tar.gz" R CMD BiocCheck PathwaySplice_1.3.0.tar.gz This is BiocCheck version 1.15.8. BiocCheck is a work in progress.

[Bioc-devel] Bioconductor 3.7 release: update NEWS

Hi, Remember to update your NEWS files by Wednesday, April 25. Content from these is collated and included in the release announcement. Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or

[Bioc-devel] Mac builds in devel

We've been having some space issues with our devel Mac builder that has caused the builds to fail the past 2 days. Tomorrow the machine will be down briefly for some maintenance but should be back up in time to build at 5pm EST. If all goes well merida2 will be back in the report on Thursday