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

[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 '/Users/kevin/r/r-devel-sanitizers/library'
(as 'lib' is unspecified)
curl: (22) The requested URL returned error: 404 Not Found
Warning in gzfile(file, "rb") :
  cannot open compressed file
'/var/folders/tm/5dt8p5s50x58br1k6wpqnwx00000gn/T//RtmpyHUICQ/repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.5%2Fbioc%2Fsrc%2Fcontrib.rds',
probable reason 'No such file or directory'
curl: (22) The requested URL returned error: 404 Not Found
Warning in gzfile(file, "rb") :
  cannot open compressed file
'/var/folders/tm/5dt8p5s50x58br1k6wpqnwx00000gn/T//RtmpyHUICQ/repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.5%2Fdata%2Fannotation%2Fsrc%2Fcontrib.rds',
probable reason 'No such file or directory'
curl: (22) The requested URL returned error: 404 Not Found
Warning in gzfile(file, "rb") :
  cannot open compressed file
'/var/folders/tm/5dt8p5s50x58br1k6wpqnwx00000gn/T//RtmpyHUICQ/repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.5%2Fdata%2Fexperiment%2Fsrc%2Fcontrib.rds',
probable reason 'No such file or directory'
curl: (22) The requested URL returned error: 404 Not Found
Warning in gzfile(file, "rb") :
  cannot open compressed file
'/var/folders/tm/5dt8p5s50x58br1k6wpqnwx00000gn/T//RtmpyHUICQ/repos_https%3A%2F%2Fbioconductor.org%2Fpackages%2F3.5%2Fextra%2Fsrc%2Fcontrib.rds',
probable reason 'No such file or directory'


Bizarrely, I don't see this in a non-interactive session; that is, this
works fine:

R -e "install.packages('lazyeval', repos =
BiocInstaller:::biocinstallRepos())"


For reference, I'm using 'curl' for downloads:

> options("download.file.method", "download.file.extra")
$download.file.method
[1] "curl"

$download.file.extra
[1] "-L -f --stderr -"


And the version of R I'm using:

R Under development (unstable) (2017-01-24 r72026)
Platform: x86_64-apple-darwin16.3.0 (64-bit)
Running under: macOS Sierra 10.12.3


I don't see the aforementioned warnings with R 3.3.2.

Best,
Kevin

On Wed, Feb 1, 2017 at 4:26 AM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

> 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 1:15 AM, Levi Waldron <lwaldron.research at gmail.com>
> wrote:
>
> >
> > On Wed, Feb 1, 2017 at 12:51 AM, Martin Morgan <
> > martin.morgan at 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
> problem
> >> is likely to be in R (devel) per se. I'll try to get access to a Mac and
> >> investigate.
> >
> >
> > Yes, in fact, now I notice that it also happens with just
> > install.packages("lazyeval"), on the second invocation with the same repo
> > argument (although exiting and starting R again creates a new tmp
> directory
> > so gives another free invocation. Sorry for blaming it on biocLite().
> >
> > --
> > Levi Waldron
> > http://www.waldronlab.org
> > Assistant Professor of Biostatistics     CUNY School of Public Health
> > US: +1 646-364-9616 <(646)%20364-9616>
> >        Skype: levi.waldron
> >
>
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>
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