Re: [Bioc-devel] NanoStringDiff package update

2018-01-26 Thread Shepherd, Lori
If you have successfully pushed to the git.bioconductor.org server (which I do see your changes) with a valid version bump (which the last was), the changes will become available to the user on the next build of the system. We do nightly builds so it should appear on the daily build report

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

2018-01-26 Thread Vincent Carey
On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/24/2018 03:38 PM, Wolfgang Huber wrote: > >> GenomicFeatures_1.31.3 imports RMySQL. >> >> I'm having great trouble installing RMySQL from source on a recent MacOS >> (10.13.3) with homebrew. >> >> The

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

2018-01-26 Thread Martin Morgan
On 01/24/2018 03:38 PM, Wolfgang Huber wrote: GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old implementation based on legacy code from

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

2018-01-26 Thread Tim Triche, Jr.
Moving it to Suggests: would certainly ease installation on clusters and such. --t On Fri, Jan 26, 2018 at 8:59 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/24/2018 03:38 PM, Wolfgang Huber wrote: > >> GenomicFeatures_1.31.3 imports RMySQL. >> >> I'm having great trouble

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

2018-01-26 Thread Hervé Pagès
Yep, moving RMySQL to Suggests makes sense. Will do. Also migrating to RMariaDB is on the TODO list. Note that the current problem of RMySQL being hard to install on Mac is only because CRAN doesn't provide an RMySQL binary for R 3.5 yet:

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

2018-01-26 Thread Simina Boca
Thank you Nitesh! Where should I use the private key? I only see the public key mentioned here: http://bioconductor.org/developers/how-to/git/maintain-github-bioc/ Sorry if I'm missing something very obvious! Best, Simina On Fri, Jan 26, 2018 at 12:23 PM, Turaga, Nitesh <

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

2018-01-26 Thread Turaga, Nitesh
Hi Simina, I’m assuming your keys are stored in the folder “.ssh”. If that is the case, try, ssh-keygen -y -e -f That command will print out a public key. If that public key is the same as the one I’ve sent you, they you can use that. (Remember that public keys, don’t have “.pub”

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

2018-01-26 Thread Simina Boca
Dear all, Thank you to Sean, Lori, and Nitesh for helping me out with a package update last year. I'm now trying to update another package, MultiMed. I have it set up on Github https://github.com/SiminaB/MultiMed - you can see that the contributors are Marc, Herve, and Dan Tenenbaum. However, I

Re: [Bioc-devel] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

2018-01-26 Thread Wolfgang Huber
26.1.18 14:59, Martin Morgan scripsit: On 01/24/2018 03:38 PM, Wolfgang Huber wrote: GenomicFeatures_1.31.3 imports RMySQL. I'm having great trouble installing RMySQL from source on a recent MacOS (10.13.3) with homebrew. The package's homepage says "The 'RMySQL' package contains an old