Question: R AnnotationHub download always fail
gravatar for young yu
2.8 years ago by
young yu0
young yu0 wrote:

I once loaded the AnnotationHub library and called the object by
ah <- AnnotationHub(cache = "E:/bioconductor_packages/") but it took much time, and keep in 1%. So, I had to interrupt it. Following is my code and error:


ah <- AnnotationHub(cache = "E:/bioconductor_packages/")

updating AnnotationHub metadata: retrieving 1 resource

|= | 1%

Warning message: In dir.create(cache, recursive = TRUE) : 'E:\bioconductor_packages' already exists Error: 'AnnotationHub' database corrupt; remove it and try again database: ‘E:/bioconductor_packages//annotationhub.sqlite3’ reason: missing tables In addition: Warning message: download failed hub path: ‘’ cache path: ‘E:/bioconductor_packages//annotationhub.sqlite3’ reason: Operation was aborted by an application callback

I tried many times but it never completed. I don't know how to solve this problem. My R version

version _
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
major 3
minor 2.2
year 2015
month 08
day 14
svn rev 69053
language R
version.string R version 3.2.2 (2015-08-14) nickname Fire Safety

I use in Rstudio in windows7, Rstudio version 0.99.903. Any idea what the problem could be? Thanks.

bioconductor R annotiationhub • 1.5k views
ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by young yu0

I've also had a similar issue in the past, with the annotationhub.sqlite3 file getting corrupted. Try updating biocLite(AnnotationHub), and possibly your R installation to 3.3.1

ADD REPLYlink written 2.8 years ago by Giovanni M Dall'Olio26k

thank you .but it still doesn't work. I updated R to 3.3.1, and removed biocinstaller, then update biocInstaller and AnnotationHub.

ADD REPLYlink written 2.8 years ago by young yu0

Did you try removing the AnnotationHub database (E:/bioconductor_packages//annotationhub.sqlite3) as suggested? How about the entire AH folder?

ADD REPLYlink written 2.8 years ago by keith.hughitt250

I did, but it didn't work.

ADD REPLYlink written 2.8 years ago by young yu0
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