Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

a chance that our (seqCAT and TVTB) VCF > files need to be updated to match any kind of new standard? I don't think it's related to the vcf standard but more with handling buffer overflow gracefully under different circumstances. Valerie > > Best, > Kevin > > On Wed, Jan 9

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

I need to update TVTB > or if it's something upstream. > > Best, > Kevin > > On Tue, Jan 8, 2019 at 5:05 PM Obenchain, Valerie > <mailto:valerie.obench...@roswellpark.org>> wrote: > > Hi Erik, > > There have been a few changes to VariantAnnotati

Re: [Bioc-devel] scanVCF: _DNAencode(): invalid DNAString input character: '1'

Hi Erik, There have been a few changes to VariantAnnotation lately. I'll take a look at seqCAT and get back to you. Valerie On 1/8/19 6:07 AM, Erik Fasterius wrote: > I recently started to get a weird error when building the vignette to my > seqCAT package, related to a VCF file I use as

Re: [Bioc-devel] SSH keys for the newly accepted package RCM

Hi Joris, This query was also sent to Bioconductor/Contributions on github. I've responded there. Valerie On 1/4/19 6:23 AM, Joris Meys wrote: > Dear, > > I'm the maintainer of the new package RCM, written by Stijn Hawinkel. In > the issue on github Stijn was asked to submit a SSH key to

[Bioc-devel] devel software builds

malbec2 stopped building last night around 9pm EST. I'm not sure yet what happened - looks like a network issue. Just a heads up that today's report will only include Mac and Windows. Valerie This email message may contain legally privileged and/or confidential information. If you are not

[Bioc-devel] package download stats

We've been having problems with the machine that runs the download stats so results haven't been posting regularly. This was fixed earlier this week and new results should all post today. Software is already done, annotation is in progress ... Valerie This email message may contain legally

Re: [Bioc-devel] "index" option of filterVcf in VariantAnnotation package

Hi, Thanks for reporting this. Now fixed in VariantAnnotaion 1.28.5 (release) and 1.29.11 (devel). These version are available immediately from the git server or tomorrow after 2pm EST with BiocManager::install(). Valerie On 12/27/18 10:49 AM, Jialin Ma wrote: > Dear all, > > The `index`

Re: [Bioc-devel] Compilation flags, CHECK errors and BiocNeighbors

. Thanks for being persistent on this issue and for bringing the conversation to bioc-devel. Val On 12/18/18 8:39 AM, Obenchain, Valerie wrote: > The devel build report hasn't posted yet but I took a look at the new > compiler flag output Herve implemented. The results show tokay2 is &g

Re: [Bioc-devel] NEWS not updated on devel site

Kristoffer, Thanks for the report. This has been fixed. Valerie On 12/14/18 4:09 AM, Shepherd, Lori wrote: > We will look into the issue. Thank you for making us aware. > > > Lori Shepherd > > Bioconductor Core Team > > Roswell Park Cancer Institute > > Department of Biostatistics &

Re: [Bioc-devel] Compilation flags, CHECK errors and BiocNeighbors

ackages > suggest that the correct flags (�-O2 -mtune=generic�) are used for C++98 > code. > > -A > >> On 17 Dec 2018, at 17:47, Obenchain, Valerie >> wrote: >> >> Hi Aaron, >> >> The only compilation flags that are different for tokay1 (release) and

[Bioc-devel] BioC 3.9 devel builds

Hi, Just a heads up that we won't have a build report for 3.9 today. Herve made some changes to the build report to display the C++14 compilation flags and I messed up the deployment. Tomorrow we should be back on track with the report and the new C++14 flags. Sorry for the inconvenience.

Re: [Bioc-devel] Cairo Error on MacOS on Bioc 3.9

Hi Christian, This is a known - there are no Mac binaries for El Capitan for R 3.6 at this point. We don't build Cairo from source on the Mac builder, we use the binary from CRAN. Once CRAN makes the binary available your package will build. Valerie On 12/14/18 4:37 AM, Christian Mertes

Re: [Bioc-devel] Compilation flags, CHECK errors and BiocNeighbors

Hi Aaron, The only compilation flags that are different for tokay1 (release) and tokay2 (devel) are C++14 flags. BiocNeighbors is not using C++14 but C++11 so I think the changes we discussed previously actually don't apply to your case. All compilation flags we use are listed at the top of

Re: [Bioc-devel] Unable to install GenVisR from bioc release

Zach, GenVisR is now clear on all platforms except devel Mac. That failure is expected since we don't have the El Capitan binaries for vdiffr and svglite. Valerie On 11/9/18 1:25 PM, Obenchain, Valerie wrote: > Hi Zach, > > GenVisR has not built on Linux so is not

Re: [Bioc-devel] merge the release and the dev version to eliminate errors

Hi Irene, I'll look into it. Valerie On 11/23/18 6:06 PM, Irene Zeng wrote: > Hi, > I am trying to fix the package on new dev 3.9. The errors appears to be > different from what it is in the release version 3.8. > The errors in 3.9 is in window system, while the errors in 3.8 are in the >

[Bioc-devel] Bioc 3.9 software builds Nov 23

The Linux builder for Bioc 3.9 was taking an unusually long time to complete the software builds today. Because of this, today's report will only include Windows and Mac results. Valerie This email message may contain legally privileged and/or confidential information. If you are not the

Re: [Bioc-devel] use bioc docker images to reproduce linux build error?

If you want to excluded trena from both 32-bit and 64-bit Windows the better .BBSoption is 'win' instead of both 'win32' and 'win64'. Right now it's skipping 32-bit but executing 64-bit. Val On 11/16/18 3:04 PM, Obenchain, Valerie wrote: > Hi Paul, > > I can reproduce the error on

Re: [Bioc-devel] use bioc docker images to reproduce linux build error?

Hi Paul, I can reproduce the error on my Linux system but not on the Mac and am not sure why this is. Haven't tried Windows yet but from the looks of the build report that one is fine too. R CMD check on Linux is failing on this line in getRegulatoryRegions,HumanDHSFilter-method: db <-

Re: [Bioc-devel] Unable to install GenVisR from bioc release

Hi Zach, GenVisR has not built on Linux so is not available on that platform. It has built on Windows and Mac so those binaries are available. The reason the package appears not available is because we purged the repos, explained here

Re: [Bioc-devel] submitting a tiny data package (GmapGenome.Hsapiens.rCRS)

Hi Tim, The options would be to make a data experiment package or put the data in ExperimentHub. Lori is our resident expert on these things but is out today. She'll be back next week and can provide more info. Valerie On 11/8/18 9:27 AM, Tim Triche, Jr. wrote: > What's the best/fastest way

Re: [Bioc-devel] What can I do if a depended package is not installed in Bioconductor build server

Hi Anh, We don't build CRAN packages from source on the Windows and Mac builders but instead install the binaries. Building all CRAN packages from source would require installation and maintenance of many more system dependencies. We may decide to support this in the future but currently it's

Re: [Bioc-devel] No curatedMetagenomicData build triggered

Hi Levi, We've had one experimental data build since the release, posted on Nov 1. Data experiment packages build on Tues, Thurs and Sun. Release should continue to follow this schedule. The devel builds are taking a very long time to complete and overlapping each other which means less

[Bioc-devel] Bioconductor 3.9 builds and R 3.6

Developers, We are experiencing much longer runtimes for the Bioconductor 3.9 (devel) builds which are running R 3.6. We are looking into a possible regression in R 3.6 or other causes. Because of the long run times, the sub-builds are overlapping which can saturate the machines and further

Re: [Bioc-devel] Ask help to install gs tokay2 build/check

Hi Jianhong, Ghostscript is already installed on the builders. On the Nov 1 build report for Bioc 3.9, motifStack is clean on tokay2 (Windows) but failed on malbec2 (Linux). There were other packages that depended on grImports with similar errors on Linux - dagLogo and motifbreakR. I went on

Re: [Bioc-devel] GenomicFeatures

Historically we used to flush the repos before a release. At some point we stopped and I could not remember why. The situation you describe below is probably it. When preparing for 3.8, we ran into the case where we had quite a few stale packages in the repos. Their 'staleness' was due to

Re: [Bioc-devel] GenomicFeatures

Thanks Kasper. I'm looking into the error in GenomicFeatures. Martin or Marcel may have more to add but I think BiocManager::install() can only report what versions are in the repo. GenomicFeatures 1.34.0 has not built so doesn't yet exist in the repo. We archive all versions in release but

Re: [Bioc-devel] Warning in 'CHECK' report for Windows machine after release version bump

, network, strucchange, etc..) > are actually causing the same type of warnings on the BioC 3.9 build > report. 359 Bioconductor software packages are affected. > > We'll need to investigate. Safe to ignore for now. > > Cheers, > > H. > > On 11/1/18 05:05, Obenchain, Valerie wro

Re: [Bioc-devel] Warning in 'CHECK' report for Windows machine after release version bump

Hi, I noticed this before the release - many packages are affected with a similar error. Something this pervasive is likely due to a change (bug?) in base R and not something you need to fix. It may also be fixed in a later version of R version than what's on the build machines. Now that the

[Bioc-devel] Bioconductor 3.8 is released

Thank you developers for contributing to the project! Please see the full release announcement here: https://www.bioconductor.org/news/bioc_3_8_release/ The Bioconductor Team This email message may contain legally privileged and/or confidential information. If you are not the intended

[Bioc-devel] Bioconductor 3.8 branch created

The 3.8 branch has been created and commits can resume to git.bioconductor.org. If all goes as planned over the next 24 hours we'll announce the release tomorrow. You have access to 2 versions of your package in git: "release" and "devel". Release is for bug fixes and documentation

[Bioc-devel] Bioconductor 3.8 branching today

Bioc developers, Today we'll be creating the Bioconductor 3.8 branch starting at 11am EST. All commits to git.bioconductor.org will be blocked for about 2.5 hours. We'll post back when push access is restored and you can resume commits. Thanks. The Bioconductor team This email message may

[Bioc-devel] Creating Bioconductor 3.8 branch on Oct 30

Developers, Tomorrow we'll create the Bioc 3.8 branch starting at 11am EST. The process will take ~2.5 hours, maybe less. An email will go out about an hour before we branch asking that all commits stop during the branch process. We often see a delay in messages posting to bioc-devel so I

[Bioc-devel] Bioc 3.8 feature freeze

Developers, The release of Bioconductor 3.8 is one week out. Today marks the 'feature freeze' of 3.8 where we ask that all commits are limited to bug fixes and documentation (no more API changes). Thanks. Valerie This email message may contain legally privileged and/or confidential

Re: [Bioc-devel] Failing GenVisR package

Hi Zach, You should not have to add skip_on_bioc(). Confirming system dependencies, the vdiffr package requires FreeType >= 2.6.0 and the Bioconductor 3.8 builder has version 2.6.1. Do you know which font libraries are used? Did you start seeing these failures around the time of this commit

Re: [Bioc-devel] Need update access agaisnt package 'banocc'

Hi George, Thanks for letting us know - you should now have access. Valerie On 10/17/18 10:50 AM, George Weingart wrote: Hello, The package banocc has a build error - I was given the task to fix it and update the "Maintainer" information to include me and the head of our Lab, Prof. Curtis

Re: [Bioc-devel] Bioc 3.8 packages: if/while condition

,1.21.2 phyloseq,1.25.3 rHVDM,1.47.0 SEPA,1.11.0 seq2pathway,1.13.2 SPLINTER,1.7.2 SVAPLSseq,1.7.0 TFEA.ChIP,1.1.1 twilight,1.57.0 On 10/15/18 5:37 AM, Obenchain, Valerie wrote: Developers, The packages below execute an if() or while() statement on a condition with length greater than 1

[Bioc-devel] Last build of Bioconductor 3.7

Developers, Tonight is the last build of Bioconductor 3.7. After the report posts tomorrow we'll stop the 3.7 builds and the branch will be frozen. Any commits made today before 4:45pm EST will be included in the builds. Please run `R CMD build` and `R CMD check` before committing! Thanks.

[Bioc-devel] Bioc 3.8 packages: if/while condition

Developers, The packages below execute an if() or while() statement on a condition with length greater than 1. This is currently a warning in R but will soon become an error. Thanks to Tomas Kalibera for identifying packages that contain this error. If you maintain one of these please have a

Re: [Bioc-devel] Package simulatorZ timeout under Windows on the release but not the devel branch

Looks like this has cleared up in the Oct 10 report: https://www.bioconductor.org/checkResults/release/bioc-LATEST/ We send notifications about failures in release twice a week (Monday and Thursday). This could have been a transient problem but happened to occur on a day we send

Re: [Bioc-devel] Invalid Parameter - /figure-html

Hi, It looks like vignette in TCGAWorkflow hasn't changed except for updating to use BiocManager. This often points to a breaking change in an upstream dependency (244 in your case) or it could be a problem on the builder. The code chunk causing problems in devel is the call to

Re: [Bioc-devel] Invalid Parameter - /figure-html

Hi Tiago, I'm looking into this. Valerie On 9/27/18 7:43 AM, Tiago Chedraoui Silva wrote: Hello, The workflow I'm maintaining is giving this message "Invalid Parameter - /figure-html" in the devel and release windows environment.

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel mailto:bioc-devel-boun...@r-project.org>> on behalf of Obenchain, Valerie <mailto:valerie.obench...@roswellpark.org> Sent: Sunday, October 7, 2018 11:54:46 AM T

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

(Lori would know). If the SPB does require .BBSoptions we should document that in https://github.com/Bioconductor/Contributions/blob/master/CONTRIBUTING.md Valerie On 10/7/18 8:39 AM, Obenchain, Valerie wrote: Hi Tim, As Michael said, the usual case is the data package 'Suggests' the software

Re: [Bioc-devel] avoiding circular dependencies between a Data package and a Software package

Hi Tim, As Michael said, the usual case is the data package 'Suggests' the software and the software 'Depends' or 'Imports' the data but this dependency could be reversed. When submitting a combo of packages to the SPB for review, the package that 'Suggests' is submitted first followed by the

[Bioc-devel] Packages with 'Bad DESCRIPTION' on build report

In the past, packages with a malformed DESCRIPTION file were skipped in the nightly builds and not posted on the build report. This was a little confusing for both the maintainer (what happened to my package?) and maintainers of packages that depended on it. These packages are now reported as

[Bioc-devel] BioC 3.8 release schedule

Hi all, The release of Bioconductor 3.8 will be on October 31: https://www.bioconductor.org/developers/release-schedule/ Over the next weeks we'll announce key dates on the on bioc-devel@r-project.org mailing list. Thanks in advance for cleaning up packages

Re: [Bioc-devel] push upstream master denied

Hi Eric, Thanks for the descriptive error report. The e.kort is your username from svn days. When slinky was added instead of linking the package to your existing username we accidentally linked it to your github id. This bug has since been fixed. Ultimately it doesn't matter what the

Re: [Bioc-devel] Fw: permission denied

Minoo, You can manage your credentials for the Bioconductor git server here: https://git.bioconductor.org/BiocCredentials/ Activate your account with your email and you'll be logged in. Once in, you can see what SSH keys we have on file for you. If you still have problems, the docs at

Re: [Bioc-devel] Access permissions for DMRcate

.au>' has access to the following packages: DMRcatedata consensus Cheers, Tim On 14/09/18 15:38, Tim Peters wrote: Thanks Valerie, much obliged. Cheers, Tim On 14/09/18 06:06, Obenchain, Valerie wrote: Hi Tim, We had 2 accounts for you, one under tim.pet...@csiro.au<mailt

Re: [Bioc-devel] Problems accessing BiocCredentials

Hi Jakob, This was a bug on our end. It's been resolved and your account has been added. Please try again to activate at https://git.bioconductor.org/BiocCredentials/ Once you're in you should see the SSH keys automatically added from your github account. Valerie On 09/14/2018 12:52

Re: [Bioc-devel] iClusterPlus/iChip/iSeq packages

Hi Quincy, Your email has been updated. Please visit https://git.bioconductor.org/BiocCredentials and activate your account with the qianxing...@moffitt.org address. Once activated you can login and see the SSH keys we have on file for you. Valerie On

Re: [Bioc-devel] Bioconductor Git Credentials

Hi John, Your account was associated with email 'john.gag...@gmail.com'. Assuming this was an old email, I've updated to 'john.gagnon...@gmail.com'. You should now be able to activate your account with this current email. Valerie

Re: [Bioc-devel] Access permissions for DMRcate

Hi Tim, We had 2 accounts for you, one under tim.pet...@csiro.au and one under t.pet...@garvan.org.au. I've removed the @csiro.au account and your information (i.e., package permissions) should by synced up. Valerie On

Re: [Bioc-devel] Activation failure

Hi Lang, Thanks for letting us know. There was a bug in the code that checked the github username against other usernames (confirming "uniqueness"). This has been fixed and I've added your account. One SSH key was added automatically from your langholee github account. Please try again to

Re: [Bioc-devel] Activating Account failed

Hi, There was a bug in the code that added new accounts. The bug was fixed and your account has been added. Please try again to activate and log in. I see that 2 SSH keys were automatically from your ipumin github account. Once you login you'll be able to see these. Valerie On 09/12/2018

Re: [Bioc-devel] Request the change of the email of the maintainer

Hi Sohrab, If you still have access to the old email you can change this yourself. Activate your account here with the old email: https://git.bioconductor.org/BiocCredentials Once activated you can login. Then got to --> user profile --> update email. If you don't have access to

Re: [Bioc-devel] proteoQC

Bo, It looks like you have access to proteoQC, customproDB and PGA. Git credentials are managed through the new app here https://git.bioconductor.org/BiocCredentials/ We have an account for both wenbos...@gmail.com and we...@genomics.cn.

Re: [Bioc-devel] DMCHMM package new dev release

The builds start ~5pm EST daily. Commits made before that time will be included in the nightly builds. The build report posts the following day (see time at top of page): https://www.bioconductor.org/checkResults/release/bioc-LATEST/ https://www.bioconductor.org/checkResults/devel/bioc-LATEST/

Re: [Bioc-devel] No Mac builds Aug 29

Obenchain, Valerie wrote: We've been having problems with the release Mac builder (merida2) after the migration. It may be in and (mostly) out of the build report until we can resolve this. Valerie On 08/29/2018 09:06 AM, Obenchain, Valerie wrote: The migration is done. The Macs should be back in

Re: [Bioc-devel] No Mac builds Aug 29

We've been having problems with the release Mac builder (merida2) after the migration. It may be in and (mostly) out of the build report until we can resolve this. Valerie On 08/29/2018 09:06 AM, Obenchain, Valerie wrote: The migration is done. The Macs should be back in the build report

Re: [Bioc-devel] Logolas package broken for R (3.4) users

uch things is to have appropriate test functions which will signal an error if things break. Best, Kasper On Tue, Aug 28, 2018 at 2:17 PM Obenchain, Valerie mailto:valerie.obench...@roswellpark.org>> wrote: You could use an AMI with R 3.4 installed. See the 'AMI IDs' section: https://www.bioco

Re: [Bioc-devel] No Mac builds Aug 29

The migration is done. The Macs should be back in the build report tomorrow. Valerie On 08/24/2018 05:57 AM, Obenchain, Valerie wrote: MacStadium is moving to new server space next week, Tuesday August 28, 9-11pm EST. The downtime is during our software builds so the Macs (merida1, merida2

Re: [Bioc-devel] Logolas package broken for R (3.4) users

You could use an AMI with R 3.4 installed. See the 'AMI IDs' section: https://www.bioconductor.org/help/bioconductor-cloud-ami/#ami_ids Valerie On 08/27/2018 11:48 AM, kushal kumar dey wrote: Hi, I just found based on user reports that the old version of my package Logolas for R 3.4 and Bioc

Re: [Bioc-devel] Don't have access to new package

Hi John, The error was on our end. I've cleaned this up and you should now have access to multiHiCcompare and HiCcompare. Valerie On 08/27/2018 11:13 PM, John Stansfield wrote: I recently had a new package accepted to Bioconductor, however when I try to push changes upstream I get the

[Bioc-devel] No Mac builds Aug 29

MacStadium is moving to new server space next week, Tuesday August 28, 9-11pm EST. The downtime is during our software builds so the Macs (merida1, merida2) won't build that night and won't be in the Aug 29th report. They should be back in the report on the 30th. Valerie This email message

Re: [Bioc-devel] Multiple Bioconductor Maintainers?

Hi Charles, We want just one person in the 'Maintainer' field in DESCRIPTION so there is a single point of contact. You can give multiple people commit access to the package on the git.bioconductor.org server. To do this, write this list (bioc-devel) and provide the emails and github

Re: [Bioc-devel] update AnnotationHub and ExperimentHub server

The update is done and all hub-related services appear normal. Let us know on bioc-devel@r-project.org<mailto:bioc-devel@r-project.org> if you notice any problems. Thanks. Valerie On 08/16/2018 02:18 PM, Obenchain, Valerie wrote: I ran in to a few snags when I tried this update las

Re: [Bioc-devel] update AnnotationHub and ExperimentHub server

I ran in to a few snags when I tried this update last week. Just a heads up, I'm going to try again tomorrow, Friday Aug 17, from 9-noon EST. Valerie On 08/08/2018 02:51 PM, Obenchain, Valerie wrote: Tomorrow (Thursday, August 7) we'll be doing some updates to the server that host

Re: [Bioc-devel] tokay2 internet connectivity

Just to close the loop on this - the conversation went off-line and was resolved. When the omabrowser server OS was changed from Ubuntu to CentOS the problems on the Windows builders went away. Valerie On 07/23/2018 08:14 AM, Obenchain, Valerie wrote: Hi Klara, Unfortunately I still don't

Re: [Bioc-devel] EXTERNAL: sessionInfo() breaks the 5000-character limit on support.bioconductor.org

I see you've posted the ExpermentHub problem on the Support site. I'll take a look / respond there. Valerie On 08/12/2018 08:53 PM, Obenchain, Valerie wrote: Tim, Regarding the ExperimentHub problem, please post your issue here - code you tried, what error you saw. Last Thursday from ~9

Re: [Bioc-devel] EXTERNAL: sessionInfo() breaks the 5000-character limit on support.bioconductor.org

Tim, Regarding the ExperimentHub problem, please post your issue here - code you tried, what error you saw. Last Thursday from ~9-noon EST I did some work on the server that hosts the hubs. I briefly had the new server live, saw some problem and reverted to the old server. I want to make sure

Re: [Bioc-devel] [bcbmail] Re: EXTERNAL: Password Reset Help

from the SVN. I need to spend some time trying to figure out if I can commit. Thanks, Augustin Luna On Wed, Aug 8, 2018 at 8:57 AM, Obenchain, Valerie [Valerie.Obenchain AT RoswellPark.org] <mailto:can...@gmail.com> wrote: External Email - Use Caution Hi Augustin, Your a

[Bioc-devel] update AnnotationHub and ExperimentHub server

Tomorrow (Thursday, August 7) we'll be doing some updates to the server that host AnnotationHub and ExperimentHub. The work will take place from 9-noon EST. We don't anticipate any noticeable downtime (if all goes well) so this is just an fyi. Thanks. Valerie This email message may contain

Re: [Bioc-devel] EXTERNAL: Password Reset Help

Hi Augustin, Your account is under lu...@cbio.mskcc.org and it looks like this has not been activated. Do you still have access to this email? When I tried to enter a bogus email for a password reset at https://git.bioconductor.org/BiocCredentials/password_reset/

Re: [Bioc-devel] EXTERNAL: RSA key format

aq/ If you still have problems, please post the exact command you're trying and the error message. Valerie Best wishes, Jelle From: Obenchain, Valerie [mailto:valerie.obench...@roswellpark.org] Sent: maandag 6 augustus 2018 16:11 To: Goeman, J.J. (MSTAT); bioc-devel@r-project.org<mailto

Re: [Bioc-devel] EXTERNAL: Updating SSH keys without previous email account

Hi, There is an account for email anth...@achiu.me with github username 'idno0001'. Visit this page and activate (not login to) your account: https://git.bioconductor.org/BiocCredentials Once you're in you can see the keys we have for you. We scrape keys every 12

Re: [Bioc-devel] tokay2 internet connectivity

please ignore the Windows error for OmaDB. Thanks. Valerie On 07/06/2018 10:38 AM, Obenchain, Valerie wrote: Thanks for your patience on this. I belive it's related to the Internet Explorer settings on the builders. Hope to have this resolved soon. Valerie On 07/05/2018 10:35 AM, Obe

Re: [Bioc-devel] EXTERNAL: Adding one more maintainer - Mergeomics package

Hi, I don't see a github account under the name of liuwenting ... is this correct? Valerie On 07/20/2018 12:55 AM, Zeyneb Kurt wrote: Dear Bioc team, I am maintaining the �Mergeomics� package and would like to add one of my colleagues as an *additional* maintainer. Her github username is

Re: [Bioc-devel] EXTERNAL: MEDIPS

Hi Lukas, Your account was associated with cha...@molgen.mpg.de and I've changed this to lukascha...@ucsd.edu. You'll first need to 'activate' your account (vs 'login') at https://git.bioconductor.org/BiocCredentials/ Once you're in,

Re: [Bioc-devel] Date for the next release

Hi, We don't have a date yet but it will probably be in October (not necessarily the 31st). Valerie On 07/09/2018 11:34 PM, Samuel Wieczorek wrote: Hi I am the developer of the packages DAPAR and Prostar. I have to plan in advance some work and I would like to synchronise this with the

Re: [Bioc-devel] tokay2 internet connectivity

Thanks for the report. I'll look into it. Valerie On 07/02/2018 06:00 AM, Klara Kaleb wrote: Hi Bioc team, I am one of the maintainers for the OmaDB package, now in 3.7 release. The package is passing build and check on both mac and linux, however I am still experiencing an error on windows

Re: [Bioc-devel] updating maintainer

Sorry - my email was out of sync and I didn't see your earlier response. I'll take of this today. Valerie On 07/05/2018 06:57 AM, Obenchain, Valerie wrote: Sam, I haven't heard back from you. Do you still want to make this change? Valerie On 06/27/2018 05:24 AM, Obenchain, Valerie wrote

Re: [Bioc-devel] updating maintainer

Sam, I haven't heard back from you. Do you still want to make this change? Valerie On 06/27/2018 05:24 AM, Obenchain, Valerie wrote: Hi Sam, As Kasper mentioned, you should update the maintainer field in the DESCRIPTION file of your packages. We'll also need this information: - What

Re: [Bioc-devel] updating maintainer

Hi Sam, As Kasper mentioned, you should update the maintainer field in the DESCRIPTION file of your packages. We'll also need this information: - What packages to you currently maintain - What is your PI's github account and email - List of Bioconductor packages you PI currently maintains, if

[Bioc-devel] New DESCRIPTION fields in build products

This is an FYI on some changes made to the build products and VIEWS files. The build system code was recently modified to add 5 new fields to the DESCRIPTION file of the build products. These fields only appear in the built tarball or binary (not source code) and are parsed into the VIEWS

[Bioc-devel] rJava on Windows builders

Just a heads up that the new version of rJava that came out 5/29/2018 failed to install on the Windows builders yesterday. Because of this we see an increased number of failures in both release and devel. Unfortunately I didn't notice this before the builds started today so we'll see the same

Re: [Bioc-devel] onLoad failed for rJava in nigthly 'devel' build

Hi Lulu, Thanks for keeping an eye on the build report! It looks like something went wrong when the new version of rJava was installed on the Windows builders yesterday. Unfortunately today's builds started before we realized this so your package will likely have the same error on tomorrow's

Re: [Bioc-devel] Windows, normalizePath(), and non-ASCII characters

Hi Mike, Is this still an issue or has it been resolved? Val On 05/22/2018 02:19 PM, Mike Smith wrote: In trying to diagnose this issue at https://support.bioconductor.org/p/108548/ I've found some weird behaviour with Windows, normalizePath(), and non-ASCII characters. Essentially, if I run

Re: [Bioc-devel] merge two maintainer accounts

Hi Rhonda, Thanks for letting us know. We can definitely merge maintainers and would prefer just one account per person. I've removed the account for rbac...@ufl.edu. You now have the single account for rhonda.bac...@gmail.com which is

Re: [Bioc-devel] About MLSeq Package

Hi Gokmen, An account exits for you with email "gokmenzarar...@erciyes.edu.tr". This was the email associated with the svn user when the package was first accepted. I have changed the email to gokmenzarar...@hotmail.com

Re: [Bioc-devel] rsvg on mac

the release. They were new functions anyway. Kevin On 05/09/2018 03:25 PM, Obenchain, Valerie wrote: Kevin, I feel like we're not on the same page. We've had this discussion and both Herve and I tried to explain the situation: https://stat.ethz.ch/pipermail/bioc-devel/2018-February/012812.html We

Re: [Bioc-devel] rsvg on mac

at 9:05 PM, Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> wrote: Hi, There has been some discussion of the devel Mac binaries on the R-SIG-Mac mailing list. That list would be the best place to ask this question. https://stat.ethz.ch/pi

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

but it may be considered in the future. Valerie On 04/19/2018 07:59 AM, Obenchain, Valerie wrote: Hi Lluis, We (or at least I) had not considered linking the profile in the credentials app with the profile in the Support Site and currently they are not aware of each other. The email in DESCRIPTION

Re: [Bioc-devel] Package download when using functions from affy and oligo

Joris, Sorry I don't have much to offer here. I've cc'd the authors of oligo and affy who may have some insight. Valerie On 05/02/2018 11:35 AM, Joris Meys wrote: Dear, I've noticed that using certain functions in affy and oligo (eg oligo::read.celfiles and affy::bg.correct) start with

Re: [Bioc-devel] errors on Windows 3.7 builds

was left behind and the package was left in a broken state. stringi has been re-installed on tokay2 and things look ok now. There was a new source tarball for stringi on May 2 and this may be part of the problem. Valerie On 05/03/2018 10:21 AM, Obenchain, Valerie wrote: Please ignore the errors

[Bioc-devel] errors on Windows 3.7 builds

Please ignore the errors on the3.7 Windows builds today. Something obviously went wrong as there are 933 build failures. We're looking into it. Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the

[Bioc-devel] no Mac in devel build report today

We had a reachability problem with the devel Mac builder yesterday. We're getting things sorted out and merida1 should be back in the builds tomorrow. Valerie This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the

Re: [Bioc-devel] Email no longer active

<mailto:maria.ke...@gmail.com> . Thanks! Maria On Thu, 3 May 2018 at 14:10, Obenchain, Valerie <valerie.obench...@roswellpark.org<mailto:valerie.obench...@roswellpark.org>> wrote: Hi Maria, I can help you with this. I need the email you want the account under and your github

Re: [Bioc-devel] Email no longer active

Hi Maria, I can help you with this. I need the email you want the account under and your github username. Valerie On 05/03/2018 04:20 AM, Maria Keays wrote: Hello, I�m not sure if this is the right place for this so apologies if not, but: my Bioconductor developer account is associated

[Bioc-devel] Bioconductor 3.7 is released

Thanks to all the developers for contributing to the project! Full release announcement here: http://bioconductor.org/news/bioc_3_7_release/ The Bioconductor Team This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s),

  1   2   3   4   >