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

[Shepherd, Lori]

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-bounces at r-project.org> on behalf of Levi Waldron <lwaldron.research at gmail.com>
Sent: Saturday, June 3, 2017 2:34:15 PM
To: Obenchain, Valerie
Cc: bioc-devel at 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.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
> >
>
>
>
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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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