Re: [Bioc-devel] build errors

2018-04-19 Thread Obenchain, Valerie
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] build errors

2018-04-19 Thread Karl Stamm
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 detail to find the source of the problem. I've recompiled the package on my machine

[Bioc-devel] Process to rename a bioconductor package

2018-04-19 Thread Adrian Altenhoff
Dear all, we would like to rename or own bioconductor package 'roma' --> 'oma' (as there exists another software tool with that name that could be misleading). So far the package is only in the development version. Is there a standard process how to proceed with such requests? Thanks! Adrian ___

Re: [Bioc-devel] EXTERNAL: Fwd: [Bioconductor/Contributions] GIGSEA (#720)

2018-04-19 Thread Marcel Ramos
Hi Shijia, I am assigned to the submission and will be reviewing your package soon. Please send further correspondence as comments to the issue on GitHub. Best regards, Marcel On 04/18/2018 08:31 PM, Shijia Zhu wrote: > Hi Everyone, > > My package just passed the check, without errors or wa

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

2018-04-19 Thread LluĂ­s Revilla
Hi all, I have a couple of doubts related to the new app. I've seen that one can update mail, and github id, and add new keys (Nice!). However I couldn't find if this account will be somehow linked to the user profile in the support site. Are there any plans in this direction? At the moment the e

Re: [Bioc-devel] Subsetting Multiple platform build/check report

2018-04-19 Thread Martin Morgan
It's not obvious or easy to test, and not meant cynically, but pull requests welcome https://github.com/Bioconductor/BBS/blob/master/3.8/report.js and FWIW there is the single package version https://bioconductor.org/checkResults/devel/bioc-LATEST/mzR Martin On 04/19/2018 08:53 AM, Neuma

[Bioc-devel] Subsetting Multiple platform build/check report

2018-04-19 Thread Neumann, Steffen
Hi, we currently can easily check for broken packages using: http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#show=timeout,error It would be great to also subset the packages: http://bioconductor.org/checkResults/devel/bioc-LATEST/index.html#package=mzR,MSnbase,xcms,CAMERA to ea

[Bioc-devel] ensembl 92 gtfs and fasta twobits have been added to AnnotationHub

2018-04-19 Thread Shepherd, Lori
Hello all, The ensembl 92 gtf (converted to GRanges on the fly) and fasta (twobit files) been added to AnnotationHub and are currently available in Bioc 3.7 Bioconductor version 3.7 (BiocInstaller 1.29.6), ?biocLite for help > library(AnnotationHub) > hub = AnnotationHub() snapshotDate(): 2018

Re: [Bioc-devel] GateFinder: Windows Server Error

2018-04-19 Thread Shepherd, Lori
I see the file there so the push was successful. I noticed you didn't include a version bump in the DESCRIPTION. Could you please change the version to 0.99.1 else the build system will not pick up on the change. Depending on when the version bump happens you will likely see the change on

Re: [Bioc-devel] BioC 3.7 Windows check warning "file link zz in package yy does not exist "

2018-04-19 Thread Ramon Diaz-Uriarte
On Wed, 18-April-2018, at 21:09:32, Martin Morgan wrote: > On 04/18/2018 02:45 PM, Vincent Carey wrote: >> >> >> On Mon, Apr 9, 2018 at 11:23 AM, Martin Morgan >> mailto:martin.mor...@roswellpark.org>> >> wrote: >> >> >> >> On 04/09/2018 10:51 AM, Ramon Diaz-Uriarte wrote: >> >> >>

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

2018-04-19 Thread Obenchain, Valerie
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. This email was taken from the DESCRIPTION of your package or the Google S

[Bioc-devel] Web App for SSH keys

2018-04-19 Thread Obenchain, Valerie
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. This

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

2018-04-19 Thread Turaga, Nitesh
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. This email was taken from the DESCRIPTION of your package or the Google S