[Bioc-devel] ExperimentHub broken in bioc-devel?

[Levi Waldron]

Thanks Val! 2.9.4 isn't in bioc-devel yet, but I got it through Subversion
and am up and running again.

On Sat, Jun 3, 2017 at 11:26 AM, Obenchain, Valerie <
Valerie.Obenchain at roswellpark.org> wrote:

> Hi Levi,
>
> Lori fixed this bug last week. You'll need AnnotationHub >= 2.9.4.
>
> Val
>
>
> On 06/03/2017 05:55 AM, Levi Waldron wrote:
> > It works for me when I have an existing cache, but not after removing the
> > cache:
> >
> >> unlink("~/.ExperimentHub", recursive=TRUE)
> >> suppressPackageStartupMessages(library(curatedMetagenomicData))
> >> ExperimentHub()
> > updating metadata: retrieving 1 resource
> >
> > |===========================================================
> ==============|
> > 100%
> > snapshotDate(): 2016-12-12
> > *Error in gzfile(file, "rb") : cannot open the connection*
> > In addition: Warning message:
> > In gzfile(file, "rb") :
> >   cannot open compressed file '/Users/lwaldron//.
> ExperimentHub/index.rds',
> > probable reason 'No such file or directory'
> >> sessionInfo()
> > R version 3.4.0 Patched (2017-06-02 r72758)
> > Platform: x86_64-apple-darwin15.6.0 (64-bit)
> > Running under: macOS Sierra 10.12.4
> >
> > Matrix products: default
> > BLAS:
> > /System/Library/Frameworks/Accelerate.framework/Versions/
> A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
> > LAPACK:
> > /Library/Frameworks/R.framework/Versions/3.4/
> Resources/lib/libRlapack.dylib
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] parallel  stats     graphics  grDevices utils     datasets  methods
> > base
> >
> > other attached packages:
> > [1] ExperimentHub_1.3.0 AnnotationHub_2.9.3 BiocGenerics_0.23.0
> >
> > loaded via a namespace (and not attached):
> >  [1] Rcpp_0.12.11                  IRanges_2.11.3
> >  [3] digest_0.6.12                 mime_0.5
> >  [5] R6_2.2.1                      xtable_1.8-2
> >  [7] DBI_0.6-1                     stats4_3.4.0
> >  [9] RSQLite_1.1-2                 BiocInstaller_1.27.2
> > [11] httr_1.2.1                    curl_2.6
> > [13] S4Vectors_0.15.2              tools_3.4.0
> > [15] Biobase_2.37.2                shiny_1.0.3
> > [17] httpuv_1.3.3                  yaml_2.1.14
> > [19] compiler_3.4.0                AnnotationDbi_1.39.1
> > [21] memoise_1.1.0                 htmltools_0.3.6
> > [23] interactiveDisplayBase_1.15.0
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
> This email message may contain legally privileged and/or confidential
> information.  If you are not the intended recipient(s), or the employee or
> agent responsible for the delivery of this message to the intended
> recipient(s), you are hereby notified that any disclosure, copying,
> distribution, or use of this email message is prohibited.  If you have
> received this message in error, please notify the sender immediately by
> e-mail and delete this email message from your computer. Thank you.
>



-- 
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics     CUNY School of Public Health
US: +1 646-364-9616                                           Skype:
levi.waldron

	[[alternative HTML version deleted]]