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

[Obenchain, Valerie]

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]]
>
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>



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