Contents

1 Overview

In spring 2019 the Hubs (AnnotationHub/ExperimentHub) upgraded their backend to utilize BiocFileCache. This upgrade changed how resources were downloaded and saved. While the Hub code itself ensures validity, it is possible to access the BiocFileCache of resources directly without the Hub front ends, which opens up the possibility of having caching problems. This document will touch on some troubleshooting for these issues as well as any other frequently asked issues. If the question or answer cannot be found here please ask on the Bioconductor Support Site or on the mailing list <bioc-devel@r-project.org>

2 Troubleshooting

2.1 Invalid Cache

An invalid cache ERROR results from a missing sqlite or index file in the Hub’s BiocFileCache. The Hub code needs these files in order to operate correctly. Rerun the Hub constructor (AnnotationHub() or ExperimentHub()) again. If you were trying to run the constructor with localHub=TRUE, you will have to run localHub=FALSE at least once to redownload the Hub sqlite file.

2.2 Corrupt Cache

A corrupt cache ERROR results from multiple entries in the BiocFileCache matching a query for a particular file. This will involve removing one, multiple, or all entries for a file. Please see specific section below although all follow the same principles.

2.2.1 sqlite file

If the sqlite file is the problematic file you should see something like the following (maybe be experimenthub.sqlite3 respectively)

> ah = AnnotationHub()
Error: Corrupt Cache: sqlite file
  See vignette section on corrupt cache
  cache: /home/lori/.cache/AnnotationHub
  filename: annotationhub.sqlite3

You will need to investigate the underlying BiocFileCache for the Hub and remove some or all of the files so that there is only a single entry for the filename. Call the BiocFileCache constructor with the path listed as cache in the ERROR message.

library(BiocFileCache)
bfc <- BiocFileCache("/home/lori/.cache/AnnotationHub")

Now we can query the BiocFileCache using the filename of the ERROR message. This shows the number of entries for the filename. There should only be one row

res <- bfcquery(bfc, "annotationhub.sqlite3", field="rname", exact=TRUE)
res
# A tibble: 2 x 10
  rid   rname create_time access_time rpath rtype fpath last_modified_t… etag
  <chr> <chr> <chr>       <chr>       <chr> <chr> <chr> <chr>            <chr>
1 BFC1  anno… 2019-03-05… 2019-03-06… /hom… web   http… 2019-02-19 19:1… NA
2 BFC13 anno… 2019-03-06… 2019-03-06… /hom… rela… /hom… NA               NA
# … with 1 more variable: expires <dbl>

You will need to deterime if you can validate which entry should remain by evaluating the entries in the cache; [dplyr package][] methods may be useful for parsing the tibble res object.

If you can identify which entry should be kept - remove the other entries in the cache or rename the rname by calling the BiocFileCache functions bfcremove or bfcupdate with the rid of the offending entries

library(dplyr)
res %>% select(rid, rname, rpath, fpath)

# example of rename the rname
bfcupdate(bfc, rids="BFC13", rname="What I am renaming the rname to")

# example remove
bfcremove(bfc, rids="BFC13")

If you cannot figure out which entry should be kept I recommend removing all entries so that a fresh redownload can occur. Then call the Hub constructor.

bfcremove(bfc, rids=res$rid)
ah = AnnotationHub()

2.2.1.1 redownload of sqlite file

A force redownload of the sqlite hub file can be achieved through the refreshHub function. To specify which of the Bioconductor Hubs to redownload use the hubClass argument with either AnnotationHub or ExperimentHub.

ah2 = refreshHub(hubClass="AnnotationHub")

2.2.2 index file

If the index file is the problematic file you should see something like the following (maybe be experimenthub.index.rds respectively)

> ah = AnnotationHub()
snapshotDate(): 2019-02-19
Error: Corrupt Cache: index file
  See vignette section on corrupt cache
  cache: /home/lori/.cache/AnnotationHub
  filename: annotationhub.index.rds

You will need to investigate the underlying BiocFileCache for the Hub and remove some or all of the files so that there is only a single entry for the filename. Call the BiocFileCache constructor with the path listed as cache in the ERROR message.

library(BiocFileCache)
bfc <- BiocFileCache("/home/lori/.cache/AnnotationHub")

Now we can query the BiocFileCache using the filename of the ERROR message. This shows the number of entries for the filename. There should only be one row

res <- bfcquery(bfc, "annotationhub.index.rds", field="rname", exact=TRUE)
res
# A tibble: 2 x 10
  rid   rname create_time access_time rpath rtype fpath last_modified_t… etag
  <chr> <chr> <chr>       <chr>       <chr> <chr> <chr> <chr>            <chr>
1 BFC2  anno… 2019-03-05… 2019-03-05… /hom… rela… 66d4…               NA NA
2 BFC14 anno… 2019-03-06… 2019-03-06… /hom… rela… /hom…               NA NA
# … with 1 more variable: expires <dbl>

You will need to deterime if you can validate which entry should remain by evaluating the entries in the cache; [dplyr package][] methods may be useful for parsing the tibble res object.

If you can identify which entry should be kept - remove the other entries in the cache or rename the rname by calling the BiocFileCache functions bfcremove or bfcupdate with the rid of the offending entries

library(dplyr)
res %>% select(rid, rname, rpath, fpath)

# example of rename the rname
bfcupdate(bfc, rids="BFC14", rname="What I am renaming the rname to")

# example remove
bfcremove(bfc, rids="BFC14")

If you cannot figure out which entry should be kept I recommend removing all entries so that a fresh redownload can occur. Then call the Hub constructor.

bfcremove(bfc, rids=res$rid)
ah = AnnotationHub()

2.2.3 resource path

If the resource path is a problem, this indicates that there may be duplicate files in the cache. There may only exist at any given time one downloaded file path per resource as indicated by the filename schema “. This ERROR indicates duplicate values`

The ERROR should look similar to

Error: Corrupt Cache: resource path
  See vignette section on corrupt cache
  cache: /home/lori/.cache/AnnotationHub
  potential duplicate files:
499d6769cf1d_5012
66d42a51a258_5012

You will need to investigate the underlying BiocFileCache for the Hub and remove some or all of the files so that there is only a single entry for the resource path. Call the BiocFileCache constructor with the path listed as cache in the ERROR message.

library(BiocFileCache)
bfc <- BiocFileCache("/home/lori/.cache/AnnotationHub")

Now we can query the BiocFileCache using the duplicate files of the ERROR message.

res <- bfcquery(bfc, "5012", field="rpath", exact=FALSE)
res
# A tibble: 2 x 10
  rid   rname create_time access_time rpath rtype fpath last_modified_t… etag
  <chr> <chr> <chr>       <chr>       <chr> <chr> <chr> <chr>            <chr>
1 BFC3  AH50… 2019-03-05… 2019-03-05… /hom… web   http… 2014-03-28 09:2… dd0c…
2 BFC19 dup … 2019-03-06… 2019-03-06… /hom… web   http… 2014-03-28 09:2… dd0c…
# … with 1 more variable: expires <dbl>

You will need to deterime if you can validate which entry should remain by evaluating the entries in the cache; [dplyr package][] methods may be useful for parsing the tibble res object.

If you can identify which entry should be kept - remove the other entries in the cache or rename the rname by calling the BiocFileCache functions bfcremove. If you cannot the best appropate is to remove the resource and redownload a new entry.

# remove single entry
bfcremove(bfc, rids="BFC19")

# remove all
bfcremove(bfc, rids=res$rid)

If the query resulted in only one entry, there is likely a file in your cache location that has the format similar to the entry in the cache and will have to be removed or renamed. An example

Error: Corrupt Cache: resource path
  See vignette section on corrupt cache
  cache: /home/lori/.cache/AnnotationHub
  potential duplicate files:
45b42ba7aaa1_38317
7a4726896632_38317

But when you do the query there is only one value

> res <- bfcquery(bfc, "38317", field="rpath", exact=FALSE)
> res
# A tibble: 1 x 10
  rid   rname create_time access_time rpath rtype fpath last_modified_t… etag
  <chr> <chr> <chr>       <chr>       <chr> <chr> <chr> <chr>            <chr>
1 BFC37 AH32… 2019-03-08… 2019-03-08… /hom… web   http… 2013-07-25 07:0… 11c3…
# … with 1 more variable: expires <dbl>

The file path of the valid entry is

> bfcinfo(bfc, rid="BFC37") %>% dplyr::select(rpath)
# A tibble: 1 x 1
  rpath
  <chr>
1 /home/lori/.cache/AnnotationHub/45b42ba7aaa1_38317

Therefore we would want to move or rename the file 7a4726896632_38317.

> fl <- file.path(hubCache(ah), "7a4726896632_38317")
> fl
[1] "/home/lori/.cache/AnnotationHub/7a4726896632_38317"

> unlink(fl)

2.2.4 resource id

If the resource id is problematic, it generally means that there are entries in the BiocFileCache with the same rname. You would see an ERROR similar to the following:

> cache(ah[1:4])
adding rname 'AH5015 : 5015'
Error: Corrupt Cache: resource id
  See vignette section on corrupt cache
  cache: /home/lori/.cache/AnnotationHub
  reason: not all 'rnames' found or unique.

You will need to investigate the underlying BiocFileCache for the Hub and remove or rename resources so there are no duplicate rnames in the cache.

library(BiocFileCache)
bfc <- BiocFileCache("/home/lori/.cache/AnnotationHub")
bfcinfo(bfc) %>% dplyr::select(rname)

You can remove with bfcremove and can rename with bfcupdate.

2.3 Corrupt Database

A corrupt hub database ERROR results from an invalid hub sqlite file. Perhaps the original download was interrupted or the file was overwritten.

You will have to remove the currently downloaded sqlite file so it can be redownloaded.

The output you received looked something similar to the following:

> ah = AnnotationHub()
Error: Corrupt Hub Database; See vignette section on corrupt database
  database: '/home/lori/.cache/AnnotationHub/66d467fcefa5_annotationhub.sqlite3'
  reason: missing tables

The simplest solution is to remove the file listed as the database: in the above output.

# from the example above
file.remove('/home/lori/.cache/AnnotationHub/66d467fcefa5_annotationhub.sqlite3')

Rerunning the constructor should now redownload a valid database object.

2.4 Cannot retrieve resource

This occurs when using a Hub object designated to only access locally downloaded files (ex. hub <- AnnotationHub(localHub=TRUE)) and a resource cannot be found in the current BiocFileCache database. The ERROR looks similar to

Error: Cannot retrieve resource
  Rerun constructor with 'localHub=FALSE' or exclude ID
  Requested resource not found in local cache:
    AH66165 : 72911

The options are to change the Hub object to isLocalHub=FALSE (isLocalHub(hub)<-FALSE) so the file can be downloaded. If this cannot be done because of internet access or other issues, the resource will not be available. If this was part of a subset to download, remove the resource id from the subset.