[Bioc-devel] Updated OrgDb packages

Hello Bioconductor Community, Some missing evidence values have been identified in our orgDb packages. For this reason we are releasing a 3.8.3 version that fixes this issue. I apologize for any inconvenience this causes. This email message may contain legally privileged and/or confidential

Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

the effect on tomorrow's build report, only on Saturday's report. Cheers, H. On Thu, Apr 25, 2019 at 9:17 AM Vincent Carey <mailto:st...@channing.harvard.edu> wrote: Has this situation been rectified? On Tue, Apr 23, 2019 at 11:40 AM Van Twisk, Daniel < daniel.vantw...@roswel

[Bioc-devel] Fixes to db0s and org.db's + rebuild annotations depending on these

Hello Bioconductor Community We experienced some problems with our most recent annotations. The following updated orb.dbs and db0s should correct the issue. These is an existing problem with the UCSC's mouse knownGene resource the will be corrected on Monday next week. Please rebuild any

Re: [Bioc-devel] Weird monkey identifiers in org.Hs.eg.db

We've made some changes to our annotation generation scripts this release and it seems these may have introduced some errors. Thank you for identifying this issue and I will try to have some fixes out asap. From: Bioc-devel on behalf of James W. MacDonald

[Bioc-devel] Community generated annotation deadline is April 24th

Hello Bioconductor Community, Just a reminder that the community generated annotation package deadline is April 24th. Please submit these packages to me by then. Thank you! This email message may contain legally privileged and/or confidential information. If you are not the intended

[Bioc-devel] Bioconductor 3.9 Orgdbs and TxDbs available

Hello Bioconductor Community! The new OrgDb and TxDbs for the Bioconductor 3.9 release are now available. The new Orgdbs are: GO.db_3.8.0.tar.gz org.Ag.eg.db_3.8.0.tar.gz org.At.tair.db_3.8.0.tar.gz org.Bt.eg.db_3.8.0.tar.gz org.Ce.eg.db_3.8.0.tar.gz org.Cf.eg.db_3.8.0.tar.gz

[Bioc-devel] Bioconductor 3.9 db0s are available

Hello Bioconductor Community! The newest db0s for the upcoming Bioconductor 3.9 release are up and should propagate within a day or so. They are: anopheles.db0_3.8.0.tar.gz arabidopsis.db0_3.8.0.tar.gz bovine.db0_3.8.0.tar.gz canine.db0_3.8.0.tar.gz chicken.db0_3.8.0.tar.gz

[Bioc-devel] Bioconductor 3.9 contributed annotation package deadline

Hello Biocondcutor Community! This is just a friendly reminder that our contributed package deadline for the upcoming Bioconductor 3.9 release is April 24th. Also, we plan to have our db0 packages completed by April 8th. This email message may contain legally privileged and/or confidential

[Bioc-devel] Bioconductor 3.8 OrgDb and TxDb packages now availiable

Hello, all! The OrgDbs and TxDbs for Biocondcutor 3.8 have been built and will propagate to Bioconductor 3.8 within a day. The following packages are available: GO.db_3.7.0.tar.gz PFAM.db_3.7.0.tar.gz org.Ag.eg.db_3.7.0.tar.gz org.At.tair.db_3.7.0.tar.gz org.Bt.eg.db_3.7.0.tar.gz

[Bioc-devel] Updated db0 packages available

An error involving incorrect UniProt IPIs was detected in the most recent db0 packages. This error has been corrected and the newer 3.7.1 db0s are now available. If you are contributing an annotation package and rely on UniProt IPIs, we would recommend that you rebuild your package. We ask that

[Bioc-devel] Bioconductor 3.8 db0 annotation packages availiable; new deadline for contributed annotations Oct 22nd

The Biocondcutor 3.8 db0 annotation packages are now available. The packages were released late on our end and since some contributed annotations depend on these new db0 packages, we are pushing back the contributed annotations deadline. The new contributed annotations deadline is Oct 22nd.

[Bioc-devel] Contiributed annotations deadline

Hello all! Just a reminder that the contributed annotations deadline for the upcoming 3.8 bioconductor release is October 24th. Updated db0 packages will be available by October 8th. Thank you! This email message may contain legally privileged and/or confidential information. If you are

[Bioc-devel] TxDbs, OrgDbs, GO.db, and PFAM.db packages available

Hello all! The newest TxDbs, OrgDbs, GO.db, and PFAM.db packages have been pushed to Bioconductor 3.7 devel and should propagate by tomorrow. The following packages have been updated/added: Updated GO.db: GO.db_3.6.0.tar.gz Updated PFAM.db: PFAM.db_3.6.0.tar.gz Updated org dbs:

[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] Update of miRBaseVersions.db annotation package

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 Haunsberger <stefan.haunsber...@gmail.com> Sent: Saturday, April 7, 2018 9:36:02 AM To: Van Twisk, Daniel Cc: bioc-d

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

I'd be happy to update your annotation package. The package, however, appears to have multiple warnings and errors occurring on check and BiocCheck. There appear to be some documentation issues and a test failure in check. For BiocCheck, just be sure the BiocViews you are using are from one

[Bioc-devel] Bioconductor 3.7 annotation deadlines

Hello all! The deadline for contributed annotations for the upcoming Bioconductor 3.7 release is April 16th. db0 packages will be available by April 9th. This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the

Re: [Bioc-devel] annotation data not updated?

It appears that your org.Hs.eg.db and GO.db packages are still v3.4.2. Please run the command BiocInstaller::biocLite() to update your packages to the new version (v3.5.0). From: Bioc-devel on behalf of Yu, Guangchuang

Re: [Bioc-devel] annotation data not updated?

Thanks for looking into this. New versions of the OrgDbs and Db0s (v3.5.0) are now available that have up-to-date resources. Here is the output of the new org.Hs.eg.db: > x <- org.Hs.eg.db > x OrgDb object: | DBSCHEMAVERSION: 2.1 | Db type: OrgDb | Supporting package: AnnotationDbi |

[Bioc-devel] Bioconductor 3.6 release: OrgDb and TxDb annotations

Hello everyone, The new OrgDb and TxDb packages are now available on the devel branch, e.g., https://bioconductor.org/packages/devel/data/annotation/html/org.Rn.eg.db.html https://bioconductor.org/packages/devel/data/annotation/html/TxDb.Rnorvegicus.UCSC.rn5.refGene.html Updated OrgDb packages:

[Bioc-devel] Fw: EXTERNAL: Re: MSnID failing on release and devel

From: Vladislav Petyuk <pet...@gmail.com> Sent: Tuesday, October 10, 2017 2:56 PM To: Van Twisk, Daniel Subject: EXTERNAL: Re: MSnID failing on release and devel I submitted my SSH RSA key back on Friday evening. made sure that I have upstream in .git/

Re: [Bioc-devel] Organism.dplyr::supportedFilters warning

behalf of Van Twisk, Daniel <daniel.vantw...@roswellpark.org> Sent: Tuesday, October 3, 2017 3:08:36 PM To: Lucas Schiffer; Ludwig Geistlinger Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Organism.dplyr::supportedFilters warning A recent change that was made to GSEABase seems to b

Re: [Bioc-devel] Organism.dplyr::supportedFilters warning

A recent change that was made to GSEABase seems to be the source of the problem. We're looking at it now. From: Bioc-devel on behalf of Lucas Schiffer Sent: Tuesday, October 3, 2017 2:29:51 PM To: