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>
The ExperimentHub and AnnotationHub use CRAN package httr functions HEAD and
GET for accessing web resources. This can be problematic if operating behind a
proxy. The easiest solution is to set the httr::set_config with the proxy
information.
proxy <- httr::use_proxy("http://my_user:my_password@myproxy:8080")
## or
proxy <- httr::use_proxy(Sys.getenv('http_proxy'))
httr::set_config(proxy)
AnnotationHub::setAnnotationHubOption("PROXY", proxy)
## or
ExperimentHub::setExperimentHubOption("PROXY", proxy)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.
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.
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 AnnotationHub's TroubleshootingTheCache 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()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")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 AnnotationHub's TroubleshootingTheCache 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()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 AnnotationHub's TroubleshootingTheCache 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 AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
cache: /home/lori/.cache/AnnotationHub
potential duplicate files:
45b42ba7aaa1_38317
7a4726896632_38317But 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_38317Therefore we would want to move or rename the file 7a4726896632_38317.
> fl <- file.path(bfccache(bfc), "7a4726896632_38317")
> fl
[1] "/home/lori/.cache/AnnotationHub/7a4726896632_38317"
> unlink(fl)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 AnnotationHub's TroubleshootingTheCache 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.
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 AnnotationHub's TroubleshootingTheCache 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.
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 : 72911The 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.
There is a flag in the constructor localHub=TRUE to use only show previously
downloaded resources. If you are using this in an offline setting, please also
see the BiocManager vignette on offline
use. The
Hubs use BiocManager::version to filter resources appropriate for your current
version of R/Bioconductor; therefore the offline usage of BiocManager needs to
be established.
The error that occurs that likely needs offline set up will look similar to the
following:
ExperimentHub(localHub=TRUE)
Error: failed to connect to local data base
database: ‘/home/user/.cache/R/ExperimentHub/24dc84dbf615e_experimenthub.sqlite3’
reason: invalid version specification ‘Bioconductor version cannot be validated; no internet connection?’`
The situation may occur where a hub is desired to be shared across multiple
users on a system. This presents permissions errors. To allow access to
multiple users create a group that the users belong to and that the underlying
hub cache belongs too. Permissions of potentially two files need to be altered depending
on what you would like individuals to be able to accomplish with the hub. A
read-only hub will require manual manipulatios of the file
BiocFileCache.sqlite.LOCK so that the group permissions are g+rw. To allow
users to download files to the shared hub, both the
BiocFileCache.sqlite.LOCK file and the BiocFileCache.sqlite file will need group
permissions to g+rw. Please google how to create a user group for your system
of interest. To find the location of the hub cache to be able to change the group
and file permissions, you may run the following in R ah = AnnotationHub(); hubCache(ah). For quick reference in linux you will use chown currentuser:newgroup to change the group and chmod to change the file
permissions: chmod 660 or chmod g+rw should accomplish the correct
permissions.
Two issues have been commonly reported regarding the lock file.
There could be permission ERROR regarding group and public access. See the
previous Group Cache Access section.
This is an issue with filelock on particular systems. Particular partitions and non standard file systems may not support filelock. The solution is to use a different section of the system to create the cache. The easiest way to define a new cache location is by using environment variables.
In R:
Sys.setenv(BFC_CACHE=<new cache location>)
Alternatively, you can set an environment variable globally to avoid having to set uniquely in each R session. Please google for specific instructions for setting environment variables globally for your particular OS system.
Other common filelock implemented packages that have specific environment variables to control location are:
As of AnnotationHub version > 2.23.2, the default caching location has
changed. The default cache is now controlled by the function tools::R_user_dir
instead of rappdirs::user_cache_dir. Users who have utilized the default
AnnotationHub location, to continue using the created cache, must move the cache and its
files to the new default location, create a system environment variable to
point to the old location, or delete and start a new cache.
The following steps can be used to move the files to the new location:
Determine the old location by running the following in R
rappdirs::user_cache_dir(appname="AnnotationHub")
Determine the new location by running the following in R
tools::R_user_dir("AnnotationHub", which="cache")
Move the files to the new location. You can do this manually or do the following steps in R. Remember if you have a lot of cached files, this may take awhile.
# make sure you have permissions on the cache/files
# use at own risk
moveFiles<-function(package){
olddir <- path.expand(rappdirs::user_cache_dir(appname=package))
newdir <- tools::R_user_dir(package, which="cache")
dir.create(path=newdir, recursive=TRUE)
files <- list.files(olddir, full.names =TRUE)
moveres <- vapply(files,
FUN=function(fl){
filename = basename(fl)
newname = file.path(newdir, filename)
file.rename(fl, newname)
},
FUN.VALUE = logical(1))
if(all(moveres)) unlink(olddir, recursive=TRUE)
}
package="AnnotationHub"
moveFiles(package)A user may set the system environment variable ANNOTATION_HUB_CACHE to control
the default location of the cache. Setting system environment variables can vary
depending on the operating system; we suggest using google to find appropriate
instructures per your operating system.
You will want to set the variable to the results of running the following in R:
path.expand(rappdirs::user_cache_dir(appname="AnnotationHub"))NOTE: R has Sys.setenv however that will only set the variable for that R
session. It would not be available or recognized in future R sessions. It is
important to set the variable as a global user-wide or system-wide
environment variable so it persists in all future logins to your system.
Lastly, if a user does not care about the already existing default cache, the old location may be deleted to move forward with the new default location. This option should be used with caution. Once deleted, old cached resources will no longer be available and have to be re-downloaded.
One can do this manually by navigating to the location indicated in the ERROR
message as Problematic cache: and deleting the folder and all its content.
The following can be done to delete through R code:
CAUTION This will remove the old cache and all downloaded resources. All resources will have to be re-downloaded after executing this code.
library(AnnotationHub)
package = "AnnotationHub"
oldcache = path.expand(rappdirs::user_cache_dir(appname=package))
setAnnotationHubOption("CACHE", oldcache)
ah = AnnotationHub(localHub=TRUE)
## removes old location and all resources
removeCache(ah, ask=FALSE)
## create the new default caching location
newcache = tools::R_user_dir(package, which="cache")
setAnnotationHubOption("CACHE", newcache)
ah = AnnotationHub()