Re: [Bioc-devel] rtracklayer

2017-02-03 Thread Shepherd, Lori
It appears that this issue has been resolved. Thank you. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

[Bioc-devel] Updates to Bioconductor Dockers

2017-02-22 Thread Shepherd, Lori
Hello Bioconductor Users: I would like you all to be aware of some changes to the Bioconductor dockers. The Bioconductor Core Team has decided to support and maintain the Bioconductor base and core dockers only. We have had some volunteers take over the metabolomics and proteomic dockers so they

[Bioc-devel] Single Package Builder

2017-02-27 Thread Shepherd, Lori
The Single Package Builder is currently offline. We are working on restoring and will update when it is back online. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email

Re: [Bioc-devel] Single Package Builder

2017-02-27 Thread Shepherd, Lori
el <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Monday, February 27, 2017 9:14:45 AM To: Martin Morgan Subject: [Bioc-devel] Single Package Builder The Single Package Builder is currently offline. We are working on restoring

Re: [Bioc-devel] Package submission

2016-09-29 Thread Shepherd, Lori
It was a problem with the single package builder. We are making the necessary adjustments and rerunning any packages that did not receive build reports; You should receive results later this morning. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

Re: [Bioc-devel] Change in the function getHPa( ) of the hpar package

2016-09-29 Thread Shepherd, Lori
Hi, Please do not write your own function. We encourage utilizing existing functionality. As long as you are using the development version of hpar, that will be the version that is used in the upcoming release. Over the next few weeks I would recommend checking that you are using/testing

Re: [Bioc-devel] package submission from bitbucket

2016-10-04 Thread Shepherd, Lori
Lauren, Thank you for your interest in submitting to Bioconductor. Currently we only support the use of github for package submission. After the package has been accepted through the review process, it does not have to remain in github. Lori Shepherd Bioconductor Core Team Roswell Park

Re: [Bioc-devel] warning on GenomeInfoDb::keepStandardChromosomes()

2016-10-05 Thread Shepherd, Lori
I just uploaded a fix. This should be corrected in version 1.9.14 Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

[Bioc-devel] new biocView

2016-09-21 Thread Shepherd, Lori
A new biocView has been added to the list of terms: SingleCell Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message may contain legally privileged and/or

Re: [Bioc-devel] Build warnings on moscato1

2016-09-28 Thread Shepherd, Lori
Hello, Thank you for bringing this to our attention. For now please ignore this WARNING. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From:

Re: [Bioc-devel] Build warnings on moscato1

2016-09-28 Thread Shepherd, Lori
I'm looking into this issue. Please do not be alarmed, I will be manually kicking off a new build for your package. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] Package submission

2016-09-29 Thread Shepherd, Lori
I will look into this and if need be start a new build for you. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

[Bioc-devel] spb updates

2016-11-22 Thread Shepherd, Lori
We are making some updates to the single package builder. It may be unavailable at times during the process. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 This email message

[Bioc-devel] single package builder

2016-11-15 Thread Shepherd, Lori
Hello We will be attempting to update the single package builder to bioc 3.5 with R 3.4 over the next few days. Please note that there may be some disruption and the builders may not be available for packages that make updates during this time. We hope this transition will go quickly and

Re: [Bioc-devel] philr recent build fail

2016-10-12 Thread Shepherd, Lori
This is a problem with ggtree not with your package. You should be okay. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

2016-12-15 Thread Shepherd, Lori
$error [1] "At least 80% of man pages documenting exported objects must have runnable examples. The following pages do not:" This ERROR occurs when man pages are included without runnable examples. You have examples in it looks like 5/12 of your man pages (~42%). We encourage 80% $warning [1]

Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

2016-12-16 Thread Shepherd, Lori
rk 14263 From: Jurat Shayidin <juratb...@gmail.com> Sent: Friday, December 16, 2016 6:06:41 AM To: Shepherd, Lori; bioc-devel@r-project.org Subject: Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck Dear Lori: Thanks for your

Re: [Bioc-devel] Quick question about result of R CMD check and R CMD BiocCheck

2016-12-16 Thread Shepherd, Lori
checks. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Jurat Shayidin <juratb...@gmail.com> Sent: Friday, December 16, 2016 8:51:43 A

Re: [Bioc-devel] New Package submission request to Bioconductor Project

2016-12-20 Thread Shepherd, Lori
We Thank you for taking the time and diligence to try and have a clean R CMD check and BiocCheck before submission. If these are your only issues and you feel the package is ready to be reviewed please submit http://bioconductor.org/developers/package-submission/ and your assigned reviewer

Re: [Bioc-devel] Question about status of new package submission

2016-12-23 Thread Shepherd, Lori
Are you sure you submitted the package to the right location? Normally we see new packages as issues on https://github.com/Bioconductor/Contributions/issues once they are submitted. Please ensure you use this link to submit your package:

Re: [Bioc-devel] How to get further assessment for newly submitted package?

2016-12-28 Thread Shepherd, Lori
You will receive feedback soon. Reviewers are assigned multiple packages and will review them in the order they were received. There is also a delay because of the holidays season. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics &

Re: [Bioc-devel] TabixFileList() constructor broken in devel

2016-12-28 Thread Shepherd, Lori
Thank you for bringing this to our attention. There were some updates made a few weeks ago to the behavior and input of 'TabixFileList()' . Its current implementation will work with a character vector as input. I will investigate further into why this change was made and if it needs to be

Re: [Bioc-devel] Problem for Biostrings?

2017-03-29 Thread Shepherd, Lori
That is correct. When the Biostrings package is corrected this ERROR in your package should resolve automatically. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] Error loading rtracklayer

2017-03-29 Thread Shepherd, Lori
For the single package builder: Once the issue is resolved you could kick off a new build by bumping the version number; it is probably the fastest way. I will also try to check and manually build packages that encountered this error and haven't kicked off a new build. Lori Shepherd

Re: [Bioc-devel] Error loading rtracklayer

2017-03-29 Thread Shepherd, Lori
This is an ERROR with rtracklayer until the ERROR is resolved in rtracklayer you will continue to see this ERROR in your package. We are in the processes of resolving and should be correctly shortly. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

[Bioc-devel] new package submission deadline for Bioconductor 3.5

2017-03-17 Thread Shepherd, Lori
Hello, The new package submission deadline is March 31. This deadline will serve as the potential to be included in release 3.5 pending review; packages after this deadline will remain in Bioconductor devel pending proper review. Thank you. Lori Shepherd Bioconductor Core Team Roswell Park

Re: [Bioc-devel] Question on the build and biocheck of the package

2017-03-16 Thread Shepherd, Lori
Hello, 1. Please ignore the dependency ERROR on tokay2 for now. Some of this is on our end and we are in the process of correcting. 2. You have to make sure the webhook is set up for your package to automatically build on version bumps. If you have not set up the webhook, please do so

Re: [Bioc-devel] Build error on tokay2

2017-04-04 Thread Shepherd, Lori
This is an ERROR on our tokay2 builder and we are in the process of resolving. You do not need to take any actions at this time and when it is resolved this should clear up automatically on the next build. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

[Bioc-devel] ensembl 87 and 88 added to AnnotationHub

2017-04-04 Thread Shepherd, Lori
Hello all, The ensembl 87 and 88 gtfs (converted to GRanges on the fly) have been added to AnnotationHub and are currently available: > library(AnnotationHub) > hub = AnnotationHub() updating metadata: retrieving 1 resource

Re: [Bioc-devel] Check error on malbec2

2017-04-04 Thread Shepherd, Lori
Write and access your output to a temporary directory instead using tempdir(). Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

Re: [Bioc-devel] Check error on malbec2

2017-04-06 Thread Shepherd, Lori
of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Aimin Yan <aimin.at.w...@gmail.com> Sent: Wednesday, April 5, 2017 9:39:59 AM To: Shepherd, Lori Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Check erro

Re: [Bioc-devel] Installing EBImage with custom packages dir?

2017-04-11 Thread Shepherd, Lori
Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Guillaume MULLER <g...@presans.com> Sent: Tuesday, April 11, 2017 8:28:34 AM To: Shepherd, Lori; bioc-devel@r-project.org Subject: Re:

Re: [Bioc-devel] Installing EBImage with custom packages dir?

2017-04-11 Thread Shepherd, Lori
If you are able to set environment variables or have a .bash_aliases, you could set the R_LIBS or R_LIBS_USER environment variables to your desired path "~/.R/x86_64-pc-linux-gnu-library/3.1.2". When these are set it should become the default path in .libPaths() when you start R. Lori

Re: [Bioc-devel] Recent error in FamAgg with R-3.4rc

2017-04-19 Thread Shepherd, Lori
You can continue to commit changes and bug corrections until this Friday 21. After that date any change will remain in devel and if necessary would have to be corrected in release after the release is finished. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department

Re: [Bioc-devel] question on package build

2017-03-13 Thread Shepherd, Lori
I can investigate this and see what was going on however, you deleted the first comment when submitting packages that included the link to your github repository. Until you add the section agreeing to the Bioconductor terms of package review and include the link to your github repository we

Re: [Bioc-devel] Check error on malbec2

2017-04-05 Thread Shepherd, Lori
m: Aimin Yan <aimin.at.w...@gmail.com> Sent: Tuesday, April 4, 2017 3:41:02 PM To: Shepherd, Lori Cc: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Check error on malbec2 Thank you, I changed to use tempdir(), and it works now. One more question is how to locate those outputs in tempo

Re: [Bioc-devel] Catching SVN up to Github

2017-07-28 Thread Shepherd, Lori
It seems like you renamed your package after it was submitted based on the current version in svn and the current ERROR occurring on the build report. Could you check your git config -l and see if the svn-remote* in the config file are updated to reflect the naming change? Lori Shepherd

[Bioc-devel] Initial List of Deprecated Packages for Bioc3.6

2017-08-03 Thread Shepherd, Lori
The Bioconductor Team is starting to identify packages that will be deprecated in the next release to allow the Bioconductor community to respond accordingly. This list will be updated monthly leading up to the release. The initial list of deprecated packages is as follow:

Re: [Bioc-devel] unable to push local changes to bioconductor svn repository

2017-07-19 Thread Shepherd, Lori
You are correct that it is because this is a workflow package and not a software package. The workflow package location is /trunk/madman/workflows/ It should be updated there. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics &

Re: [Bioc-devel] saving and obtaining a list with BiocFileCache package

2017-07-03 Thread Shepherd, Lori
Hello Arman, I would be possible to save the list as an Rdata object. The process would be 1. create a new item in the cache and retrieve the path 2. use that path in a save( listObj, file="path") Then you could load the RData object in your next session and it would be available

[Bioc-devel] Common Bioconductor Methods and Classes

2017-08-08 Thread Shepherd, Lori
Hello all, Many have requested a page that helps identify common Bioconductor methods and classes that should try to be utilized in package development. We have created the following webpage in the developers resources section of the website and links are also include in the

Re: [Bioc-devel] ExperimentHub broken in bioc-devel?

2017-06-05 Thread Shepherd, Lori
It should be up in bioc-devel soon. It failed to build last night do to other package dependencies failing. All should be remedied by tomorrows build. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets

Re: [Bioc-devel] How to re-check the submitted package?

2017-06-07 Thread Shepherd, Lori
What package are you referring to? If you updated the Description and a new build did not occur make sure you have set up the webhook: https://github.com/Bioconductor/Contributions#adding-a-web-hook Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

[Bioc-devel] ensembl 89 gtfs and fasta twobits have been added to AnnotationHub

2017-06-07 Thread Shepherd, Lori
Hello all, The ensembl 89 gtf (converted to GRanges on the fly) and fasta (twobit files) been added to AnnotationHub and are currently available in Bioc3.6 (development) with AnnotationHub (<= 2.9.0): > library(AnnotationHub) > hub = AnnotationHub() updating metadata: retrieving 1 resource

[Bioc-devel] complete set of OrgDb packages have been added to AnnotationHub

2017-06-09 Thread Shepherd, Lori
Hello all, The complete set of OrgDb packages have been added to AnnotationHub and are now available in both release and devel versions of Bioconductor. The following example is for release: > library(AnnotationHub) > hub <- AnnotationHub() updating metadata: retrieving 1 resource

[Bioc-devel] Single Package Builder

2017-05-02 Thread Shepherd, Lori
Over the next week, we will be transitioning the Single Package Builder to the latest versions of R and Bioc 3.6. The single package builder is used when new packages are submitted to: https://github.com/Bioconductor/Contributions . Please be advised that there may be intermittent periods

Re: [Bioc-devel] Error in BUILD report (anamiR)

2017-05-05 Thread Shepherd, Lori
Thank you for your efforts. Since the windows ERROR is out of your control we will undeprecate your package. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

[Bioc-devel] fasta twobit for release 87 and 88 added to AnnotationHub

2017-05-08 Thread Shepherd, Lori
Hello all, The fasta (twobit files) for release-87 and release-88 have been added to AnnotationHub and are currently available in Bioc3.6 (development) with AnnotationHub (<= 2.9.0): > library(AnnotationHub) > hub = AnnotationHub() updating metadata: retrieving 1 resource

[Bioc-devel] Bioconductor Dockers have been updated

2017-05-04 Thread Shepherd, Lori
The bioconductor dockers have been updated for the release. The release versions now utilize R 3.4.0 and Bioc 3.5 while the devel versions now utilize R 3.4.0 and Bioc 3.6. Older versions are available using tags. For more information on Bioconductor dockers please see

Re: [Bioc-devel] VIGNETTES IN DEVEL

2017-09-19 Thread Shepherd, Lori
There were changes to BiocStyle in devel which might account for some of the different The changes can be found in the BiocStyle NEWS file https://github.com/Bioconductor/BiocStyle/blob/master/NEWS There also was some previous discussion in this thread:

[Bioc-devel] Deadline for Packages and Data Bioc3.6

2017-09-21 Thread Shepherd, Lori
Hi Bioconductor Community, The release of Bioconductor 3.6 will be Tuesday, October 31. Please see the schedule for details: http://bioconductor.org/developers/release-schedule/ Some important deadlines that are coming up: Friday October 6 is the deadline for new package submissions. Packages

Re: [Bioc-devel] Question about inclusion in upcoming bioconductor

2017-09-17 Thread Shepherd, Lori
1. Yes. If you package was accepted and is on g...@git.bioconductor.org then it is set to be included in the next release version of Bioconductor. You do not need to do anything; the Bioconductor team will handle making appropriate branches to the repository. 2. You can add changes to

[Bioc-devel] Workflows now building with Bioc3.6

2017-09-20 Thread Shepherd, Lori
Hello, The workflow builder has been updated to use Bioconductor 3.6 in preparation for the release. Please monitor any workflows you may maintain and debug accordingly. Also, new workflows will now be submitted to Bioconductor in the form of a package as documented:

[Bioc-devel] Bioconductor 3.6 release: new package deadline

2017-10-06 Thread Shepherd, Lori
Hello, Today Friday October 6 is the deadline for new package submissions for a chance to be included in Bioc 3.6. Packages submitted before this date, the core will try and work with to get the package through the acceptance process before the deadline. Packages submitted after this date will

Re: [Bioc-devel] BIOC devel 3.6 buid/check

2017-10-06 Thread Shepherd, Lori
rk 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Friday, October 6, 2017 11:01:57 AM To: Mª José Nueda; bioc-devel@r-project.org Subject: Re: [Bioc-devel] BIOC devel 3.6 buid/check Did you set the upstream r

Re: [Bioc-devel] BIOC devel 3.6 buid/check

2017-10-06 Thread Shepherd, Lori
Did you set the upstream remote? The upstream remote should be g...@git.bioconductor.org:packages/maSigPro.git git remote add g...@git.bioconductor.org:packages/maSigPro.git will set this. what do you see when you do remote -v? If that is set... Did you remember to git push upstream

Re: [Bioc-devel] new package submission (pcxn) Abnormal build result

2017-10-05 Thread Shepherd, Lori
Yes, this seems to be a problem on our side. We are looking into it. For now you can ignore this ERROR. There was a similar post here: https://stat.ethz.ch/pipermail/bioc-devel/2017-September/011773.html Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of

Re: [Bioc-devel] BioC 3.6: CHECK report

2017-10-05 Thread Shepherd, Lori
The development branch of bioconductor is a place for developers and maintainers of packages to implement changes or new features. Some of these changes could effect the expected output or behavior of functions, it is therefore possible to get new ERRORs if a package your package depends on

Re: [Bioc-devel] BioC 3.6: BUILD/CHECK reports are not updating.

2017-10-05 Thread Shepherd, Lori
Hi It can take up to 24 hours to see the changes pushed to the Bioconductor server and be reflected on the build report. There is normally a new build report generated daily. There was an issue on our end that prevent the build report from completing yesterday but there should be a new

Re: [Bioc-devel] EXTERNAL: Issues of package updating

2017-10-16 Thread Shepherd, Lori
The packages have moved from svn repository to git; And has been announced on the support site, mailing list, and website. Please follow the instructions for updating your package on the g...@git.bioconductor.org server : http://bioconductor.org/developers/how-to/git/ Lori Shepherd

Re: [Bioc-devel] EXTERNAL: Permission denied (publickey)

2017-10-12 Thread Shepherd, Lori
Once the package moves over to the daily build system, the builds are not triggered immediately on a version bump and the results will no longer post to the issue tracker. The package is considered part of the daily build system and the version bump and successful push to

[Bioc-devel] List of Deprecated Packages Bioc3.6

2017-09-08 Thread Shepherd, Lori
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly leading up to the release. The current list of deprecated packages is as follows:

Re: [Bioc-devel] updating Bioconductor package that is already on Github

2017-09-06 Thread Shepherd, Lori
Have you submitted your ssh key https://docs.google.com/forms/d/e/1FAIpQLSdlTbNjsQJDp0BA480vo4tNufs0ziNyNmexegNZgNieIovbAA/viewform

Re: [Bioc-devel] Package DMCHMM is not installed

2017-09-12 Thread Shepherd, Lori
Bioconductor has a release version and a devel version. Releases happen twice a year (The next occurring at the end of October). All new packages accepted will remain in the devel version of Bioconductor until the next schedule release. The package for that time, will only be available on

Re: [Bioc-devel] Resubmit package

2017-09-05 Thread Shepherd, Lori
If you go to the github issue (#375), I believe there is an option at the bottom to reopen issue. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263

Re: [Bioc-devel] Bioconductor-mirror permanently removed August 25th

2017-09-06 Thread Shepherd, Lori
Even before the bioconductor git server, when we still were using svn, users were confused at where to make updates and push changes. Now even more so we have seen several packages try and push to the bioconductor-mirror or change the remotes to point the the mirror locations. It has created

Re: [Bioc-devel] external dependencies

2017-10-02 Thread Shepherd, Lori
You can still submit to bioconductor despite this limitation. You could also do a os check in the examples and tests that fail on windows and make a comment that this is the case. If the program is not meant to run in windows there is options to handle that as well and the review assigned to

[Bioc-devel] Final List of Deprecated Packages for Bioc3.6

2017-09-29 Thread Shepherd, Lori
The Bioconductor Team had identified the following packages that will be deprecated in the next release Bioc3.6 Unresponsive/not-maintained packages: BioMedR ddgraph EWCE HCsnip stepwiseCM Maintainer requested deprecation: domainsignatures iontree oneChannelGUI RCytoscape

Re: [Bioc-devel] Something about time out errors

2017-09-29 Thread Shepherd, Lori
Thank you for your concern. There is some conflict on our system that we will look into further. For now, you can ignore this ERROR on mac - the reviewer of your package is aware. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics &

Re: [Bioc-devel] [Bioconductor/Contributions] DMCHMM (#430)

2017-08-28 Thread Shepherd, Lori
Please comment on the issue that the package is ready for another review so your reviewer knows you are finished making changes. It is also nice to include a summary of what has been changed on the github issue. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department

[Bioc-devel] ensembl 90 gtfs and fasta twobits have been added to AnnotationHub

2017-08-28 Thread Shepherd, Lori
The ensembl 90 gtf (converted to GRanges on the fly) and fasta (twobit files) been added to AnnotationHub and are currently available in Bioc3.6 (development) > hub = AnnotationHub() snapshotDate(): 2017-08-28 > length(query(hub, c("ensembl", "gtf", "release-90"))) [1] 248 > length(query(hub,

Re: [Bioc-devel] Question : GitHub-Commit changes to the released branch

2017-08-25 Thread Shepherd, Lori
The current release is RELEASE_3_5 Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel on behalf of

Re: [Bioc-devel] EXTERNAL: Can't push to git

2017-10-11 Thread Shepherd, Lori
When did you submit the new svnid and key? It can take up to 24 hours for the keys to be processed. The keys are currently processed once daily not upon submission. Perhaps try again this afternoon and then let us know if you are still having troubles. Lori Shepherd Bioconductor Core Team

Re: [Bioc-devel] EXTERNAL: Re: IMPCdata push permissions to git repo

2017-10-23 Thread Shepherd, Lori
What are the packages you are trying to access? Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel

Re: [Bioc-devel] EXTERNAL: Re: DOI for packages

2017-10-19 Thread Shepherd, Lori
___ From: Laurent Gatto <lg...@cam.ac.uk> Sent: Thursday, October 19, 2017 3:10:52 PM To: bioc-devel@r-project.org Cc: Shepherd, Lori Subject: EXTERNAL: Re: [Bioc-devel] DOI for packages On 19 October 2017 13:22, Shepherd, Lori wrote: > Hello Bioconductor, > > We have a

[Bioc-devel] Shields/Badges on Package landing pages

2017-10-24 Thread Shepherd, Lori
There have been a number of issues with the shields/badges on the package landing pages do to the Bioconductor git transition. We are in the process of updating the procedure to generate these shields to correct out-of-date or missing items. We are disabling the affected shields/badges so

[Bioc-devel] List of Deprecated Packages for Bioc3.8

2017-11-22 Thread Shepherd, Lori
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages is as follows: Maintainer requested deprecation:

Re: [Bioc-devel] List of Deprecated Packages for Bioc3.8

2017-11-22 Thread Shepherd, Lori
;bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Wednesday, November 22, 2017 8:07:30 AM To: Martin Morgan Subject: [Bioc-devel] List of Deprecated Packages for Bioc3.8 The Bioconductor Team is continuing to identify packages that

Re: [Bioc-devel] BiocFileCache for developers

2017-12-01 Thread Shepherd, Lori
l.com> Sent: Friday, December 1, 2017 11:23:39 AM To: Shepherd, Lori Cc: Michael Love; bioc-devel@r-project.org Subject: Re: [Bioc-devel] BiocFileCache for developers On Fri, Dec 1, 2017 at 11:16 AM, Shepherd, Lori <lori.sheph...@roswellpark.org<mailto:lori.sheph...@roswellpark.org>>

Re: [Bioc-devel] Single Package Builder Updates and Testing

2017-12-13 Thread Shepherd, Lori
oc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Monday, December 11, 2017 9:14:41 AM To: Martin Morgan Subject: [Bioc-devel] Single Package Builder Updates and Testing The Single Package Builder will be undergoing some updat

[Bioc-devel] workflow page reorganization

2017-12-15 Thread Shepherd, Lori
Hello all, There has been a request to reorganize the workflow page as workflows have grown past basic and advanced. http://bioconductor.org/help/workflows/ We wanted to check with the community what your thoughts were for categories. Thank you for your suggestions. Lori Shepherd

[Bioc-devel] Updated Deprecated Package List for Bioc 3.7

2017-12-15 Thread Shepherd, Lori
The Bioconductor Team is continuing to identify packages that will be deprecated in the next release to allow for the Bioconductor community to respond accordingly. The list will be updated monthly. The current list of deprecated packages is as follows: Maintainer requested deprecation:

Re: [Bioc-devel] workflow page reorganization

2017-12-15 Thread Shepherd, Lori
iant calling > - Nucleotide tallies > - eQTL > > - Resource querying: (needs a better name) > - recountWorkflow > - TCGAWorkflow > > - Other: > - everything else. > > I haven't looked at the Basic workflows, which are probably basic enough > to be l

Re: [Bioc-devel] GSE62944, empty EH164 and EH165

2017-12-15 Thread Shepherd, Lori
Thank you for bringing this to our attention. The resources were created with a previous version of SummarizedExperiment that were not compatible with the current version. New resources have been added and are visible in both release 3.6 and devel 3.7. Please note the new EH_id's: >

Re: [Bioc-devel] OrgDb in AnnotationHub

2017-11-17 Thread Shepherd, Lori
oc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lori <lori.sheph...@roswellpark.org> Sent: Thursday, November 16, 2017 2:36:05 PM To: Martin Morgan Subject: [Bioc-devel] OrgDb in AnnotationHub The OrgDb's that we normally offer in AnnotationHub that are not offered as

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

2017-11-17 Thread Shepherd, Lori
Streets Buffalo, New York 14263 From: James W. MacDonald <jmac...@uw.edu> Sent: Wednesday, November 15, 2017 11:11:07 AM To: Shepherd, Lori Cc: Van Twisk, Daniel; bioc-devel; Yu, Guangchuang Subject: Re: [Bioc-devel] annotation data not updated? On Wed, Nov

Re: [Bioc-devel] How much does it takes for a package to appear at Bioconductor.org after a push?

2017-11-14 Thread Shepherd, Lori
It normally can take up to 24 hrs to appear on the build report after pushing changes depending on when the changes were pushed. We pull changes once a day and propagate to the landing page only if there was a version bump and successful build. Lori Shepherd Bioconductor Core Team Roswell

[Bioc-devel] Single Package Builder / Package Submission

2017-11-14 Thread Shepherd, Lori
We will begin to update the single package builders used to build and check new package submission to R 3.5 Bioc 3.7 today. While this is occurring the single package builder will be off line and there will be no builds for newly submitted packages. Thank you for your patience and

Re: [Bioc-devel] Single Package Builder / Package Submission

2017-11-14 Thread Shepherd, Lori
Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263 From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Shepherd, Lor

Re: [Bioc-devel] DaMiRseq in ERROR in the stable release

2017-11-20 Thread Shepherd, Lori
It is quite possible that it could be because of a dependent package. Unfortunately the only way to tell would be to see if any of those packages are producing a similar ERROR on the build report or to investigate your code to see where and how this ERROR is occurring. It is possible that it

[Bioc-devel] OrgDb in AnnotationHub

2017-11-16 Thread Shepherd, Lori
The OrgDb's that we normally offer in AnnotationHub that are not offered as our Standard OrgDb packages are currently unavailable in Bioc 3.6. We are updating the files and will notify when they are back online. Thank you for your understanding. Lori Shepherd Bioconductor Core Team

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

2017-11-15 Thread Shepherd, Lori
When this issue was brought up I updated the files that were downloaded when using AnnotationHub so they should be updated as well. The files were updated but the rdatadateadded was not updated when I added the new files. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute

[Bioc-devel] GitHub Repo for reporting issues with Bioconductor.org Website

2017-11-10 Thread Shepherd, Lori
Hello All, We have made a github repository https://github.com/Bioconductor/bioconductor.org for reporting bugs or issues with http://bioconductor.org. Please feel free to open issues with concerns, suggestions, or bugs. https://github.com/Bioconductor/bioconductor.org/issues Thank you

[Bioc-devel] Dockers have been updated for Release and Devel

2017-11-03 Thread Shepherd, Lori
Hello everyone, The Bioconductor dockers (base and core) have been updated for http://bioconductor.org/help/docker/ Release R3.4.2 _ Bioc3.6 https://hub.docker.com/r/bioconductor/release_base2/ https://hub.docker.com/r/bioconductor/release_core2/ Devel R3.5.0 _ Bioc3.7

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

2017-11-03 Thread Shepherd, Lori
Buffalo, New York 14263 From: Sokratis Kariotis <s.kario...@sheffield.ac.uk> Sent: Friday, November 3, 2017 7:04:08 AM To: Herv� Pag�s Cc: Shepherd, Lori; bioc-devel Subject: Re: [Bioc-devel] Accepted packages can't find each other and fail build Hey a

Re: [Bioc-devel] Package update not showing on Bioc 3.6 webpage

2017-11-03 Thread Shepherd, Lori
It can take up to 24 hours for the results to show in the build report. Please check again today and let us know if it is not reflected in the Friday build report. Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton

Re: [Bioc-devel] I can't merge the changes by bioc team with my accepted package

2017-11-01 Thread Shepherd, Lori
Could you please provide the full output from the following: git remote -v git checkout master git fetch upstream git merge upstream/master Lori Shepherd Bioconductor Core Team Roswell Park Cancer Institute Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo,

[Bioc-devel] website

2017-11-09 Thread Shepherd, Lori
Hello everyone, We are making some updates that could affect the website. If the website is down please be patient it is intermittent and should be remedied quickly. We will try and get these updates done as soon as possible. Thank you Lori Shepherd Bioconductor Core Team Roswell Park

Re: [Bioc-devel] Is version 1.1.0 correct for a new released package?

2017-11-02 Thread Shepherd, Lori
ay, November 1, 2017 2:36:05 PM To: Shepherd, Lori; bioc-devel Subject: RE: [Bioc-devel] Is version 1.1.0 correct for a new released package? Thanks for your thorough answer. So, when I’m going to push the first devel change, the version must be 1.1.1 while bug fixes for the released package wi

Re: [Bioc-devel] Is version 1.1.0 correct for a new released package?

2017-11-01 Thread Shepherd, Lori
Yes this is correct - Pkg_version x.y.z We do a version bump on the devel version of the package to make the versioning consistent with release( y even in release) - hence the first version bump to 1.0.0 - this is now the current release version of your package The second version bump is

  1   2   3   >