Re: [Rd] bugzilla issues

Thanks, fixed. Simon > On Jan 26, 2018, at 3:40 AM, Uwe Ligges > wrote: > > Simon, > > can you take a look, please? > > Best, > Uwe > > > > On 26.01.2018 01:41, Ben Bolker wrote: >> tl;dr is the R bug tracker down or am I being an idiot? Help please ...

Re: [Rd] Why R should never move to git

In case it's useful: A) Git Cheatsheet: ADVANCED (GitHub) https://www.google.es/url?sa=t=web=j=https://services.github.com/on-demand/downloads/github-git-cheat-sheet.pdf=2ahUKEwjkhYmdt_bYAhXIwBQKHXWdBfoQFjAAegQIERAB=AOvVaw3RoN21aynhcDHqKncV31el B) Git Cheatsheet: BASICS (GitHub)

Re: [Rd] utils::install.packages with quiet=TRUE fails for source packages on Windows

I have filed a bug report here: https://github.com/rstudio/rstudio/issues/2070 Original Message From: peter dalgaard [mailto:pda...@gmail.com] Sent: Friday, Jan 26, 2018 10:15 AM GMT To: Andreas Kersting Cc: r-devel@r-project.org Subject: [Rd] utils::install.packages with

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

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

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

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

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] Should GenomicFeatures really depend pn RMySQL ? Is it time to migrate to RMariaDB ?

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

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

[R-pkg-devel] apparent S3 methods exported but not registered

I'm preparing a new release of PerformanceAnalytics, and as usual this brings the host of CRAN checks. I get this note: * checking S3 generic/method consistency ... NOTE Found the following apparent S3 methods exported but not registered:   mean.LCL mean.UCL mean.geometric mean.stderr See

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

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: [Rd] Fortran programs not writing stdout on windows

For reference, this has been fixed in R-devel, 74168. The problem only exists on Windows with RGui. As a workaround for older versions of R, one can unset environment variables "GFORTRAN_STDOUT_UNIT" and "GFORTRAN_STDERR_UNIT" for the duration of system/system2 calls that invoke external

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

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 ?

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] NanoStringDiff package update

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: [Rd] utils::install.packages with quiet=TRUE fails for source packages on Windows

The obvious guess would be that Rstudio is attempting something like redirecting output and getting itself confused. However, it is pretty clearly Their Problem, no? Rstudio has their own support infrastructure. -pd > On 26 Jan 2018, at 09:17 , Andreas Kersting wrote: >

Re: [Rd] bugzilla issues

Simon, can you take a look, please? Best, Uwe On 26.01.2018 01:41, Ben Bolker wrote: tl;dr is the R bug tracker down or am I being an idiot? Help please ... I decided I would follow up on https://stat.ethz.ch/pipermail/r-devel/2018-January/075410.html (reporting/suggesting a

Re: [Rd] utils::install.packages with quiet=TRUE fails for source packages on Windows

Just noticed that this problem only occurs from within RStudio (v1.1.414). Any ideas why? Am 26.01.2018 um 08:56 schrieb Andreas Kersting: Hi, Installing a source package on Windows using utils::install.packages() with quiet=TRUE fails, while it works with the default quiet = FALSE. The