It should be up in bioc-devel soon. It failed to build last night do to other
package dependencies failing. All should be remedied by tomorrows build.
Lori Shepherd
Bioconductor Core Team
Roswell Park Cancer Institute
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buffalo, New York 14263
________________________________
From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Levi Waldron
<lwaldron.resea...@gmail.com>
Sent: Saturday, June 3, 2017 2:34:15 PM
To: Obenchain, Valerie
Cc: bioc-devel@r-project.org
Subject: Re: [Bioc-devel] ExperimentHub broken in bioc-devel?
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.obench...@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@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
>
>
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--
Levi Waldron
http://www.waldronlab.org
Assistant Professor of Biostatistics CUNY School of Public Health
US: +1 646-364-9616 Skype:
levi.waldron
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