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

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
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