Re: [Bioc-devel] Web App for SSH keys

On 04/19/2018 06:29 PM, Leonardo Collado Torres wrote: Hi Valerie, Thanks for the reply and the doc changes ^^. I added a few short replies below. Best, Leo On Thu, Apr 19, 2018 at 4:49 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org><mailto:valerie.obench...@roswellpark.or

Re: [Bioc-devel] push access to adaptest

Nima has been added to adaptest. Valerie On 04/30/2018 02:05 PM, WILSON CAI wrote: i approve On Mon, Apr 30, 2018 at 11:13 AM Nima Hejazi wrote: Hello BioC team --- Wilson Cai (cc'd) and I are co-developers / co-authors of the adaptest

[Bioc-devel] Bioconductor 3.7 release: 3.7 branch created

The Bioconductor 3.7 branch is now ready. If all goes well over the next 24 hours we'll announce the official release tomorrow. You have access to 2 versions of your package in git: the "release" and "devel" versions. The �release� branch is for bug fixes and documentation improvements only. The

[Bioc-devel] Bioconductor 3.7 release: stop pushes to master

Developers, Today we will create the Bioconductor 3.7 branch from 10am - 1pm EST (2pm - 5pm UTC). At 10am EST, we will block pushes to the master branch. Please stop all pushes to master before this time and do not resume until further notice. Another email will be sent when it is OK to resume

Re: [Bioc-devel] bsseqData

remote: Please see Biocondcutor guidelines > > remote: https://bioconductor.org/developers/package-guidelines/ > > remote: > > To git.bioconductor.org:packages/bsseqData.git > > ! [remote rejected] master -> master (pre-receive hook declined) > > error:

Re: [Bioc-devel] bsseqData

I've just given you and Pete access. Please give it a try and let me know if you have problems. Val On 04/28/2018 10:50 AM, Kasper Daniel Hansen wrote: Could Pete and I get write access to bsseqData? Best, Kasper [[alternative HTML version deleted]]

[Bioc-devel] No Mac builds for 3.7 today

Just a heads up that tokay2 ran out of disk space in the last build so we don't have the Mac in the report today. Valerie 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

Re: [Bioc-devel] Remove from email list

Hi Sara, You can manage your account here: https://stat.ethz.ch/mailman/listinfo/bioc-devel Valerie On 04/24/2018 03:37 PM, Sara Linker wrote: Hi at Bioc-devel, Would it be possible to please remove me from the email list? Best, Sara ___

Re: [Bioc-devel] " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC)

I guess this is ChIC (from the title?) which is clean on today's report: https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Valerie On 04/24/2018 01:17 PM, Obenchain, Valerie wrote: Carmen, What is the name of your package? Valerie On 04/16/2018 11:42 AM, Carmen M. Livi wrote

Re: [Bioc-devel] Bioc 3.7 build failed for GenvisR package

GenVizR looks clean on the build report today: https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ Valerie On 04/20/2018 01:08 PM, Obenchain, Valerie wrote: Hi Zach, The build report for today is not helpful because GenVisR failed on all platforms due to a biomaRt failure. Because

Re: [Bioc-devel] " Error in serialize(data, node$con, xdr = FALSE)" during Vignette build (ChIC)

Carmen, What is the name of your package? Valerie On 04/16/2018 11:42 AM, Carmen M. Livi wrote: Hi all, my package recently got accepted and moved to the Bioconductor repository. Suddenly I get an error during the package build for Linux and OS (the INSTALL is working). The error occurs

Re: [Bioc-devel] Transition from Google Sheet to Web App

activate your account. An activation link will be sent to your email. Once your account is activated you can login. Trying to login without activation will lead to an error. Let us know if you have any questions or problems. Best Regards, > On Apr 18, 2018, at 8:56 AM, Oben

Re: [Bioc-devel] build errors

arl.st...@gmail.com>> wrote: Aha, the error is reproduced in R 3.5.0. I can take a look at it now. On Fri, Apr 20, 2018 at 3:37 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> wrote: I'm out for the next few days so will look

Re: [Bioc-devel] build errors

for testing? If not, it would be a good idea to update and see if you can reproduce the error. Valerie On 04/19/2018 03:38 PM, Obenchain, Valerie wrote: Hi Karl, I'll look into this. Valerie On 04/19/2018 02:00 PM, Karl Stamm wrote: How can I debug an error that occurs on the build server

Re: [Bioc-devel] Bioc 3.7 build failed for GenvisR package

Hi Zach, The build report for today is not helpful because GenVisR failed on all platforms due to a biomaRt failure. Because that failure is intermittent, I just tried to build the package again on tokay2 and there were no problems (vignette or otherwise). Let's give this another day or two.

Re: [Bioc-devel] Transition from Google Sheet to Web App

, Llu�s On 18 April 2018 at 17:13, Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> wrote: The Web App for managing SSH keys is now available at https://git.bioconductor.org/BiocCredentials/ Accounts have been created for all package

Re: [Bioc-devel] Web App for SSH keys

e Best, Leo On Wed, Apr 18, 2018 at 12:53 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org><mailto:valerie.obench...@roswellpark.org> wrote: My last email didn't make it through to the list - trying again ... The Web App for managing SSH keys is now available at

Re: [Bioc-devel] build errors

Hi Karl, I'll look into this. Valerie On 04/19/2018 02:00 PM, Karl Stamm wrote: How can I debug an error that occurs on the build server and not on my PC ? I am having build errors on two of the three build servers with a line about vignette compilation and the latex error does not have enough

[Bioc-devel] Web App for SSH keys

My last email didn't make it through to the list - trying again ... The Web App for managing SSH keys is now available at https://git.bioconductor.org/BiocCredentials/ Accounts have been created for all package maintainers. Note the central identifier, i.e., how you login is your email.

Re: [Bioc-devel] Transition from Google Sheet to Web App

or problems. On 04/18/2018 05:56 AM, Obenchain, Valerie wrote: This transition will start at 9am EST today. We'll post back when it's done. Valerie On 04/17/2018 10:27 AM, Obenchain, Valerie wrote: Hi developers, Tomorrow we are bringing a web app online to help with the management of SSH keys

Re: [Bioc-devel] Transition from Google Sheet to Web App

This transition will start at 9am EST today. We'll post back when it's done. Valerie On 04/17/2018 10:27 AM, Obenchain, Valerie wrote: Hi developers, Tomorrow we are bringing a web app online to help with the management of SSH keys. The app will replace the Google Sheet currently used to add

[Bioc-devel] Transition from Google Sheet to Web App

Hi developers, Tomorrow we are bringing a web app online to help with the management of SSH keys. The app will replace the Google Sheet currently used to add keys. Through the web interface you'll be able to add keys and change your email or github username. There is also an option to see what

Re: [Bioc-devel] Setup for pushing changes in unifiedWMWqPCR to bioconductor git.

Hi, On 04/12/2018 03:02 AM, Joris Meys wrote: Hi all, For the package unifiedWMWqPCR I want to push some updates on the documentation, but apparently I don't have access to the bioconductor git any longer. I had to completely reinstall my system here, so probably either my key got lost, or I'm

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

Petr, Yesterday I installed R 3.5.0 beta on the devel Windows builder (tokay2). The report has not posted yet but I checked on the build of PharmacoGx and it is clean. It looks like the CRAN 'maps' package was updated on April 4. It's possible that during the nightly builds, the new version

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

Thanks for the report Petr. We'll look into it. Valerie On 04/10/2018 04:44 PM, petr smirnov wrote: 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

[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

[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

Re: [Bioc-devel] Permission denied to Bioconductor repository

We have 3 keys on file for you: ~/git.bioconductor.org/admin/gitolite-admin/keydir >cat key-1/g.merino.pub ssh-rsa

Re: [Bioc-devel] Problem getting updated checkResults

No problem. I'm glad you figured it out. Valerie On 04/02/2018 03:16 PM, Lorena Pantano wrote: Yep, silly mistake, it seems I was in the stable version. Dummy me. I�ll kick myself for make you waste your time. Thanks for your time. On Apr 2, 2018, at 5:30 PM, Obenchain, Valerie

Re: [Bioc-devel] Problem getting updated checkResults

Hi Lorena, You'll have to supply more information for us to help you. The build report shows version 1.7.3: https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ What version are you expecting? Have you pushed all local changes to git.bioconductor.org? What does `git log` say? How

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] new package deadline? 4/2 or 4/9

Thanks for catching the typo - I'll fix that. The last day to submit packages is April 2. The API deadline (no new packages added to manifest) is the 16th so we moved the last day to submit from the 9th to the 2nd. This allows 2 weeks for the review instead of 1. Valerie On 03/27/2018 03:45

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

Hi, The only person with write permissions on the bnbc repo is Kasper, e.g, 'khansen'. If you want permissions to this repo please cc him so he can give us the ok. The only package user 'c.fletez-brant' has access to is flowClean. Valerie On 03/27/2018 08:25 AM, Kipper Fletez-Brant wrote:

[Bioc-devel] Bioconductor 3.7 release schedule

Developers and Community Members, The release of Bioconductor 3.7 will be on Tuesday, May 1, 2018. Please see the schedule for details: https://www.bioconductor.org/developers/release-schedule/ Over the next month, key deadlines will be announced on the bioc-devel mailing list:

Re: [Bioc-devel] Update existing packages and change name

checked). Does it take more time or additional steps are required? Thanks! Cheers, Sokratis On 12 March 2018 at 19:16, Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> wrote: Hi, There is a max file size restriction of <= 5MB for so

Re: [Bioc-devel] SVN to GIT

is bad (spaces). Either way, ssh-keygen -l -f does not validate. On Mar 13, 2018, at 8:48 AM, Obenchain, Valerie <valerie.obench...@roswellpark.org><mailto:valerie.obench...@roswellpark.org> wrote: Nitesh, Were the submitted keys invalid? Any idea why Nicolas didn't recei

Re: [Bioc-devel] SVN to GIT

can do ? Thank you Nicolas Le 09/03/2018 � 18:15, Obenchain, Valerie a �crit : Keys are processed once a day around 9am EST. You will get an email indicating if your submission was successful or not. Valerie On 03/09/2018 09:11 AM, Obenchain, Valerie wrote: Nicolas, You need to follow

Re: [Bioc-devel] Reset password

Hi Jose, You need to follow instructions here https://www.bioconductor.org/developers/how-to/git/ specifically fill out this form https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform Using j.muino as your user ID. You can either provide a

Re: [Bioc-devel] adding an additional maintainer - roma

Hi Klara, I've added alpae to the roma package. Your supervisor will need to complete this form and use alpae as the username: https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform Once the form is submitted we'll get the SSH key automatically from

Re: [Bioc-devel] Update existing packages and change name

an 5mb and the push hwas aborted. What can I do about this? Thanks in advance. Regards, Sokratis On 21 February 2018 at 20:37, Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> wrote: Hi Sokratis, Unfortunately you can'

Re: [Bioc-devel] SVN to GIT

Keys are processed once a day around 9am EST. You will get an email indicating if your submission was successful or not. Valerie On 03/09/2018 09:11 AM, Obenchain, Valerie wrote: Nicolas, You need to follow instructions to submit an SSH key: https://bioconductor.org/developers/how-to/git

Re: [Bioc-devel] SVN to GIT

Nicolas, You need to follow instructions to submit an SSH key: https://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Specifically, you need to fill out this form using n.servant as your username:

Re: [Bioc-devel] Daily build

/ChIPSeqSpike/NEWS), the file is not up to date. However, if you download ChIPSeqSpike_0.99.21.tar.gz and open the file NEWS, it is indeed the last one. So the modification is not reported on the landing page. 2018-03-09 10:40 GMT-05:00 Obenchain, Valerie <valerie.obench...@roswellpark.

Re: [Bioc-devel] SVN to GIT

Hi Nicolas, I understand you've been in contact with several people about this. Are you still having access problems? Valerie On 03/06/2018 01:04 AM, Servant Nicolas wrote: Dear all, I try a couple of weeks ago to move to git to maintain the HiTC package, but I did not succeed. I followed

Re: [Bioc-devel] Cleanup of Bioconductor organization on Github

Hi, Just a quick follow-on to this. Cleaning up the Bioconductor GitHub organization that Nitesh describes below is not related to SSH key errors when accessing packages on git.bioconductor.org. If you are having SSH key problems please post on bioc-devel and I can hep out. Previously Nitesh

Re: [Bioc-devel] Cleanup of Bioconductor organization on Github

Hi Keegan, This problem isn't related to the email Nitesh sent below. Instead it's a matter of us not having a ssh key on file for you. At least we don't have a key for the kdkorthauer user with permissions on the dmrseq package. Instructions are here

Re: [Bioc-devel] Daily build

Hi Nicolas, This is the last commit I see in the master branch for ChIPSeqSpike: commit abce855631cb5689bd345df41e71cfee356a1c6f (HEAD -> master, origin/master, origin/HEAD) Author: kitano902 Date: Fri Jan 26 14:29:26 2018

Re: [Bioc-devel] failing update Bioconductor package psygenet2r

nk I have updated correctly to Bioconductor know. Thanks for all your help, Best, Alba 2018-03-05 8:47 GMT-05:00 Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>>: Please remember to cc bioc-devel to keep the convers

Re: [Bioc-devel] failing update Bioconductor package psygenet2r

gain. Best, Alba 2018-03-03 17:03 GMT-05:00 Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>>: On 03/03/2018 01:41 PM, alba gutierrez wrote: Dear Valerie, I have one additional question. Although I appear as maintainer the package has

Re: [Bioc-devel] Access to package PGA

Hi, Please follow instructions here: https://bioconductor.org/developers/how-to/git/new-package-workflow/ And complete the google form here: https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform When completing the form, use s.xu as your ID and

Re: [Bioc-devel] Changing package maintainer: git credentials

Hi Liz, We still had n.harmston in a config file - I've removed him and and added liz-is. Please try again. Valerie On 02/25/2018 08:47 AM, Liz Ing-Simmons wrote: Hi there, I don't appear to have write access to the GenomicInteractions package, so I'm wondering if this went through

[Bioc-devel] Windows devel builds: NAs in BUILD BIN

Hi, You may have noticed occasional 'NA' values in the 'BUILD BIN' column on the the Windows (tokay2) build report. These NAs appear when the build products from the nodes (Windows and Mac) are not available to the postrun script on master (Linux). This 'unavailability' can be due to network

Re: [Bioc-devel] failing update Bioconductor package psygenet2r

Hi Alba, We have one key for a.gutierrez-sacristan: ssh-rsa B3NzaC1yc2EDAQABAAABAQCrqcl4CgcR0SfE1Q7J...VeLDzeJ4mlpPIzkBEH5gSyosZqAN5OtPuaZk6geSywTl6KM/ If this is the key you're using you should have access. What is the output of git remote -v Valerie On 02/23/2018 09:16 AM, alba

Re: [Bioc-devel] Anomaly in windows server (tokay2) build system

Hi Diego, Yes we are aware of the 'NA' values in the 'build bin' column. A package gets an NA when the build products were not sent back from the worker to the master builder. It's not always clear why this problem occurs - sometimes it's just a temporary connectivity problem. There are quite

Re: [Bioc-devel] Update existing packages and change name

Hi Sokratis, Unfortunately you can't rename a package ... and there is no such thing as a 'sub package'. Maybe you meant sub-package terms of dependencies. If you have new data to add that's independent of what's in pathprintGEOData you can create a new data package. I'm not sure what you

Re: [Bioc-devel] rsvg on mac

, Are there any estimates on how often CRAN OS X builds happen? There are still no builds for rsvg and other packages... Thanks, Alexey On Wed, Feb 7, 2018 at 8:09 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> wrote: Hi Kevin, CRAN bin

Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

. Valerie On 02/13/2018 07:53 AM, Jack Fu wrote: Thanks for checking Valerie. My github id is jmf47. Thanks! Jack On Feb 13, 2018, at 10:22 AM, Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> wrote: Hi, Jack, It doesn't l

Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

Hi, Jack, It doesn't look like you currently have access to other Bioconductor packages - is that correct? If you don't currently have access, I need to know your github username. Jeff, are we adding Jack to both polyester and ballgown? Valerie On 02/13/2018 02:57 AM, Jeff Leek wrote: HI

Re: [Bioc-devel] rsvg on mac

El Capitan. Also, rsvg is not installed on the release mac build machine either, which it should have a version for. Kevin On 02/07/2018 09:09 AM, Obenchain, Valerie wrote: Hi Kevin, CRAN binaries for El Capitan in devel aren't available. You can see this on the rsvg landing page: https://cr

Re: [Bioc-devel] Access to push to pacakges Polyester and Ballgown

Hi Jack, Have you gone through the steps outlined here? https://bioconductor.org/developers/how-to/git/ Specifically, have you added ssh keys? https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform If you have not added keys, you'll need to.

Re: [Bioc-devel] rsvg on mac

Hi Kevin, CRAN binaries for El Capitan in devel aren't available. You can see this on the rsvg landing page: https://cran.r-project.org/web/packages/rsvg/index.html Nothing we can do until CRAN makes them available. Valerie On 02/07/2018 08:29 AM, Kevin Horan wrote: The ChemmineR build is

Re: [Bioc-devel] cannot fetch upstream git

Bruno, It looks like some content in your message did not come through - please re-send. We need to see the commands you are running, specifically what package you're trying to access. Valerie On 01/30/2018 09:56 AM, bruno contrino via Bioc-devel wrote: Hello, I am having some issues

Re: [Bioc-devel] Linking up to polyester and ballgown

Hi Jack, User a.frazee has access to ballgown and j.leek has access to polyester. If neither one of these is you, the first step is to write bioc-devel and request access to the packages. Once you have access, you need to have an SSH Key on file. This is explained here:

Re: [Bioc-devel] Permission denied when fetching from BioC GitHub repository

Hi Federico, We don't have an ssh key on file for you. Please add one by following instructions at the link below and use the ID of 'f.comoglio': https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform You will get an email in the next 24 hours if

Re: [Bioc-devel] CINdex package build error in Linux

Hi Krithika, I believe this was related to a problem with getTable() in rtracklayer: https://github.com/lawremi/rtracklayer/issues/5 rtracklayer 1.39.5 built successfully today and the error in CINdex has cleared up: https://bioconductor.org/packages/3.7/bioc/html/CINdex.html Valerie

Re: [Bioc-devel] chipenrich bioc builds timeout not reproducible

Hi Raymond, Thanks for the report. I may have introduced a regression in nearest() when I patched a bug a few weeks ago. I'll look into it and get back to you. Valerie On 01/08/2018 05:17 AM, Raymond Cavalcante wrote: Hello, I�m getting release and devel build timeouts for chipenrich

Re: [Bioc-devel] Issue with dependencies on Windows (tokay2)

The missing Windows binaries for devel are a known issue and have been discussed several times on the list: https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012340.html https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012418.html The binaries have just become available in the past

Re: [Bioc-devel] RSS feed on bioconductor.org/developers/gitlog

Thanks Nitesh! Looks great. Val On 01/02/2018 12:56 PM, Turaga, Nitesh wrote: Hello Maintainers, Happy new year! The GIT logs are available as RSS feeds, or as markdown on the website at http://bioconductor.org/developers/gitlog/ This is across all the packages on the bioconductor

[Bioc-devel] no build reports today

Yesterday I killed both builds when I rebooted apache on git.bioconductor.org. I lost track of time and did this after the builds started. Sorry about that - we should be back to normal today. Valerie This email message may contain legally privileged and/or confidential information. If you

[Bioc-devel] release builds

We haven't had a release build report for the past few days due to a mess up with the manifest file. Sorry about that. Things should return to normal with tonight's builds and a fresh report should post tomorrow. Valerie This email message may contain legally privileged and/or confidential

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

Hi Karim, Thanks for looking into this. Yes, canceR is all green on today's build report. There was a problem accessing Tcl/Tk files during the canceR build on Dec 9th/10th which (I believe) caused the package to timeout and send you the warning email. I'm not sure why this happened but it

Re: [Bioc-devel] splitting simpleSingleCell into self-contained vignettes

Hi, On 12/11/2017 08:49 AM, Aaron Lun wrote: Following up on our earlier discussion: https://stat.ethz.ch/pipermail/bioc-devel/2017-October/011949.html I have split the simpleSingleCell workflow into three (four, if you include the introductory overview) self-contained Rmarkdown files. I am

Re: [Bioc-devel] packages modifying 'library' during R CMD check

On 12/02/2017 09:56 AM, Rainer Johannes wrote: Thanks Val I'll fix that for `xcms`. Is it enough to fix the devel version, or should we also fix the Bioc 3.6 release version? Let's fix them both. Thanks. Val cheers, jo On 29 Nov 2017, at 15:43, Obenchain, Valerie <valerie.obe

Re: [Bioc-devel] a possible bug in development version of GenomicAlignments

Hi, I believe this regression was fixed with the most recent commit to S4Vectors: commit beacd33e43592c67c9e97517a58bf201ec0b4887 (HEAD -> master, origin/master, origin/HEAD) Author: Herv� Pag�s Date: Thu Nov 30 16:00:50 2017 -0800 Fix

[Bioc-devel] BioC 3.7 devel builds

Hi all, You may have noticed the devel builds have a lot of red. Part of the problem is that we currently have no CRAN binaries for Windows or OS X El Capitan built against R 3.5. In the BBS code, we are attempting to install CRAN dependencies from "source" where possible but some packages

Re: [Bioc-devel] Accepted packages can't find each other and fail build

Hi Sokratis, I added the .BBSoptions file to pcxn when it should have been added to pcxnData. The .BBSoptions file should be put in the package that 'Suggests' (not 'Depends') on the other. In this case it's pcxnData that needs the .BBSoptions. Sorry for the mix up, this has been fixed. The

Re: [Bioc-devel] EXTERNAL: FW: attract problems reported by the "Build/check report" for BioC 3.5

Yes, if all is green on the build report you can ignore it. Thanks. Valerie On 10/17/2017 11:46 AM, Samuel E Zimmerman wrote: Hi all, The below email was sent to me regarding an error in my package attract. I haven't updated the package in several months but this is the first time I am seeing

Re: [Bioc-devel] EXTERNAL: Re: Bioconductor 3.6 release: update NEWS

Sorry, didn't see Martin's response before sending. Valerie On 10/15/2017 07:17 AM, Obenchain, Valerie wrote: Hi, You have a couple of options described on the ?news man page. The most common is to have a NEWS plain text file at the same level as DESCRIPTION, NAMESPACE, R etc. For examples

Re: [Bioc-devel] EXTERNAL: Re: Bioconductor 3.6 release: update NEWS

, What should the NEWS file look like? Are there guidelines somewhere? Also, where should it be located? This page<https://www.bioconductor.org/developers/package-submission/> says `inst/NEWS`, but I see many packages has the file at root level. On Fri, Oct 13, 2017 at 5:16 PM, Obenchain, V

[Bioc-devel] Bioconductor 3.6 release: update NEWS

Package maintainers, If you haven't already, please update the NEWS files in your packages. This information will be included in the release announcement. The deadline for updating NEWS files is Tuesday, October 24: http://www.bioconductor.org/developers/release-schedule/ Thanks. Valerie

Re: [Bioc-devel] EXTERNAL: Landing page not updating version number

Hi Erik, Thanks for noticing this. The landing pages update every 20 minutes but because the builds only occur once a day the package version on the page only change once a day. Yesterday the build script that generates the list of packages to be propagated (i.e., versions have been bumped)

[Bioc-devel] Bioconductor 3.6 release: db0 annotations

Hi, The new db0 packages, version 3.4.3, are now available in the devel branch, e.g., http://www.bioconductor.org/packages/devel/data/annotation/html/human.db0.html Let us know if you run into problems. The plan is to make the new OrgDbs available next Friday, October 13, so feedback about

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

ry(scran) library(scater) ``` etc. This way the users can see the library() calls in the vignette. Best, Nitesh On Oct 4, 2017, at 4:14 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org><mailto:valerie.obench...@roswellpark.org> wrote: Hi guys, A little backgrou

Re: [Bioc-devel] library() calls removed in simpleSingleCell workflow

Hi guys, A little background on this vignette -> package conversion. The workflows were converted to package form because we want to integrate them into the nightly build system instead of supporting separate machines as we're now doing. As part of this conversion, packages loaded in workflow

[Bioc-devel] Bioconductor 3.6 release: deadline for new packages

Hi, This Friday, October 6, is the last day to submit new packages for inclusion in BioC 3.6. Packages submitted by Friday still need to complete the review process before the release but we'll do our best to get them in. Packages submitted after the deadline will be included in the new devel,

[Bioc-devel] Mac Workflow builds

Just a heads up that we've retired the Mac workflow builder. The Mac was a VM running at Fred Hutch. Disk space was full and hardware was old. Instead of trying to resurrect this machine, we're going without Mac workflow builds until after the October release. The plan is to incorporate the

[Bioc-devel] Bioconductor 3.6 release

The release of Bioconductor 3.6 will be Tuesday, October 31. Please see the schedule for details: http://www.bioconductor.org/developers/release-schedule/ Over the next month we'll announce key deadlines on the bioc-devel mailing list: https://stat.ethz.ch/pipermail/bioc-devel/ Part of

[Bioc-devel] build reports

We're having a few problems smoothing out the git-based builds. Unfortunately there will be no build report for either release or devel today ... we hope to have this back on track for tomorrow. Thanks for your patience. Valerie This email message may contain legally privileged and/or

Re: [Bioc-devel] git server maintenance

This is done. The machine is up and functioning normally. Valerie On 08/28/2017 05:20 AM, Obenchain, Valerie wrote: git.bioconductor.org will be rebooted for routine maintenance on Tuesday, August 29 at 8am EST. This should only take a few minutes and in general should not be noticed

[Bioc-devel] git server maintenance

git.bioconductor.org will be rebooted for routine maintenance on Tuesday, August 29 at 8am EST. This should only take a few minutes and in general should not be noticed. If you push or pull to the git server at this exact time the action may fail and you'll have to retry. I'll post back when

[Bioc-devel] Mac devel builds

Hi, You may have noticed that veracruz1 has been pulled out of the devel build report for the past few days. The machine has been taking longer than usual to run R CMD build and check and doesn't complete in time to post to the build report. We're working on this - hope to have it sorted soon.

Re: [Bioc-devel] CRAN dependency missing

Hi Siddhartha, I've installed RProtoBuf on malbec1. As you can see from the clean Windows build, tokays1 already has the necessary system dependencies. There is no El Capitan Mac binary for RProtoBuf https://cran.r-project.org/web/packages/RProtoBuf/index.html so we may be installing this

[Bioc-devel] IP blocking on web site

Hi, We're increasing security on the web site, www.bioconductor.org, to prevent http flooding and other attacks. Over the past week I've been monitoring a rule that identifies IPs making > 400 requests per minute. It looks like this is catching just rogue IPs

Re: [Bioc-devel] Search on www.bioconductor.org fails

into this deeper. We hope to improve this installation or choose a more robust one in the future. Valerie On 08/21/2017 08:51 AM, Obenchain, Valerie wrote: Thanks for the report. I'll look into it. Valerie On 08/21/2017 08:07 AM, Kevin RUE wrote: Hi, I got the same issue yesterday if that can

Re: [Bioc-devel] Search on www.bioconductor.org fails

Thanks for the report. I'll look into it. Valerie On 08/21/2017 08:07 AM, Kevin RUE wrote: Hi, I got the same issue yesterday if that can help track down the origin; it wasn't just today. I thought it was a transient glitch and didn't report it immediately. I hadn't checked today yet. Best

[Bioc-devel] web site testing

Hi all, I'm doing some testing with the firewall rules on www.bioconductor.org through CloudFront. I may have inadvertently blocked a few requests between 3:30-4:30pm EST. Candidates for blockage would have been scripts hitting the web site >100 times per minute.

Re: [Bioc-devel] EOW agenda: Aug 11

Oops. Sent to wrong address - sorry for the noise. Valerie On 08/11/2017 08:41 AM, Obenchain, Valerie wrote: # Sprint update # Builds - no Mac builds for devel today # SPB # Package Reviews # Mailing lists ## Support Site: Martin looking at this one: Rgraphviz installation fails

[Bioc-devel] converting devel builds to https

I'm converting the build system code to use https for all communications. I ran into a couple of problems today and expect it will take a few tries to straighten everything out. The devel build report will be hit and miss over the next few days. Thanks for your patience. Valerie This email

[Bioc-devel] download stats

Download stats have not updated for some time. I'm looking into this and hope to have it sorted out soon. Valerie 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

Re: [Bioc-devel] updates on support.bioconductor.org

Updates are complete. The support site is up and functioning normally. Valerie On 08/03/2017 08:58 AM, Obenchain, Valerie wrote: Updates are scheduled for support.bioconductor.org today August 3, at 5pm EST. If all goes as expected this should take < 15 minutes. The support site may be s

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