Re: [Bioc-devel] Vignette package error

- Original Message - > From: "Jason Ross" > To: "bioc-devel" > Sent: Tuesday, February 2, 2016 11:39:51 PM > Subject: [Bioc-devel] Vignette package error > Hi, > > My recently submitted package is failing with this error: > "Error: processing vignette 'IntroductionToHarman.Rmd' failed

[Bioc-devel] Vignette package error

Hi, My recently submitted package is failing with this error: "Error: processing vignette 'IntroductionToHarman.Rmd' failed with diagnostics: there is no package called 'missMethyl' Execution halted" Build report here: http://bioconductor.org/spb_reports/Harman_0.99.1_buildreport_201602022337

Re: [Bioc-devel] Git-svn issue with release version of XBSeq

Fresh clone solved my problem! Thanks! Regards Yuanhang Liu PhD Candidate Bioinformatics and Computational Biology laboratory Cellular & Structural Biology UT Health Science Center at San Antonio email: liu...@uthscsa.educel: 210-784-082​8 From: Dan Te

Re: [Bioc-devel] Git-svn issue with release version of XBSeq

Try doing a fresh clone of the github repository in a new directory and start over from http://bioconductor.org/developers/how-to/git-mirrors/#scenario-2-set-up-your-own-github-repository Please paste all commands you type AND the output of each command, into an email and send it to us. Da

Re: [Bioc-devel] Git-svn issue with release version of XBSeq

Hi, Dan, Thanks for your prompt response. As I mentioned, I have no problem when committing changes to development version SVN source. But I got that error when I try to make changes to the release version and update the changes to SVN source (I have never made changes to release version svn b

Re: [Bioc-devel] Git-svn issue with release version of XBSeq

See https://bioconductor.org/developers/how-to/git-mirrors/#unable-to-determine-upstream-svn-information Dan - Original Message - > From: "Liu, Yuanhang" > To: "bioc-devel" > Sent: Tuesday, February 2, 2016 11:12:21 AM > Subject: [Bioc-devel] Git-svn issue with release version of XBSe

[Bioc-devel] Git-svn issue with release version of XBSeq

Previously, I successfully commit my changes to the development version of my package, XBSeq, through git-svn by following the steps described in https://www.bioconductor.org/developers/how-to/git-mirrors/. I recently want to make some changes to my package in the release version. However, after

Re: [Bioc-devel] question about citation file

Bump the release version to 1.0.1. See http://bioconductor.org/developers/how-to/version-numbering/ Dan - Original Message - > From: "Samuel E Zimmerman" > To: "bioc-devel" > Sent: Tuesday, February 2, 2016 7:37:20 AM > Subject: Re: [Bioc-devel] question about citation file > That is

Re: [Bioc-devel] question about citation file

That is exactly what I forgot to do. Thanks! One more question. Since I am doing a bug fix, I want to put the changes into my development version. If my devel version is 1.1.4 should my release version become 1.2.0? Thank you very much for all your help. Best, Sam __

Re: [Bioc-devel] topGO and cat() and print() statements in program code

I can't speak to the issue of changing somebody else's code without forking (which you are free to do), or getting their OK. But do note that there are usually ways around this. First, you can use include = FALSE in your chunk options statement, which will run all the code, but silence everything.

[Bioc-devel] topGO and cat() and print() statements in program code

Hi, I am using the very usefull package topGO to generate a report (R markdown). There is not much to complain about topGO (on the contrary) except that the package uses cat instead of message to display progress information. which ruins the report. Also the bioconductor package guidelines state: