Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-02-01 Thread Martin Morgan
On 02/01/2017 01:11 PM, Kevin Ushey wrote: Although installation succeeds for me (macOS Sierra with recent R-devel), I see the following output in an interactive session when I try to install the lazyeval package: install.packages('lazyeval', repos = BiocInstaller:::biocinstallRepos())

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-02-01 Thread Kevin Ushey
Although installation succeeds for me (macOS Sierra with recent R-devel), I see the following output in an interactive session when I try to install the lazyeval package: > install.packages('lazyeval', repos = BiocInstaller:::biocinstallRepos()) Installing package into

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-02-01 Thread Vincent Carey
i did not mean to implicate biocLite ... i am being too terse. i mention it because, after so many years of biocLite being spectacularly reliable ... persistence of a problem with its performance implies a serious upstream problem that would be very nice to eradicate ... On Wed, Feb 1, 2017 at

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-31 Thread Levi Waldron
On Wed, Feb 1, 2017 at 12:51 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > Levi triggered the problem with install.packages("lazyeval", > repos=biocinstallRepos(), which is an R-only command. Also, there have not > been any changes to the logic of biocLite() in this regard, so the

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-31 Thread Martin Morgan
On 01/31/2017 11:41 AM, Vincent Carey wrote: On Mon, Jan 30, 2017 at 11:14 PM, Martin Morgan > wrote: On 01/30/2017 09:52 AM, Levi Waldron wrote: On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-31 Thread Vincent Carey
On Mon, Jan 30, 2017 at 11:14 PM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > On 01/30/2017 09:52 AM, Levi Waldron wrote: > >> On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan >> wrote: >> >>> It seems like this is a local cache of the rstudio file that

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-30 Thread Martin Morgan
On 01/30/2017 09:52 AM, Levi Waldron wrote: On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan wrote: It seems like this is a local cache of the rstudio file that describes the mac repository. Maybe your vanilla execution of install.packages() does not use the

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-30 Thread Levi Waldron
On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote: > It seems like this is a local cache of the rstudio file that describes the > mac repository. Maybe your vanilla execution of install.packages() does not > use the repository that BiocInstaller does. So maybe

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-30 Thread Vincent Carey
For what it is worth I ran into the same situation with a new employee about two weeks ago. We got around it by doing manual installs of required packages but did not obtain a systematic solution. We did not have time to trace the situation sufficiently for a report. On Mon, Jan 30, 2017 at 9:52

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-30 Thread Levi Waldron
On Mon, Jan 30, 2017 at 12:23 AM, Martin Morgan wrote: > It seems like this is a local cache of the rstudio file that describes the > mac repository. Maybe your vanilla execution of install.packages() does not > use the repository that BiocInstaller does. So maybe >

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-29 Thread Martin Morgan
On 01/29/2017 11:57 PM, Levi Waldron wrote: On Sun, Jan 29, 2017 at 11:36 PM, Martin Morgan wrote: can you try to find out what file it is trying to read and what function call, e.g., options(error=recover) biocLite("lazyeval") That should get the call

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-29 Thread Levi Waldron
On Sun, Jan 29, 2017 at 11:36 PM, Martin Morgan wrote: > > > can you try to find out what file it is trying to read and what function > call, e.g., > > options(error=recover) > biocLite("lazyeval") > > That should get the call stack; choose readRDS and look for

Re: [Bioc-devel] error from biocLite on OSX with R-devel / Bioc-devel

2017-01-29 Thread Martin Morgan
On 01/29/2017 11:25 PM, Levi Waldron wrote: Not sure anyone will be able to help with this, but I can no longer install packages from bioc-devel using a current R-devel and biocLite() on my OSX Yosemite 10.10.5. I can still install from the command line `R CMD INSTALL` and `install.packages()`.