R Cannot connect to AnnotationHub server

[gxt13111560461]

BiocManager::version() [1] ‘3.17’ packageVersion("AnnotationHub") [1] ‘3.8.0’ hub <- AnnotationHub::AnnotationHub() Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE'

Who can help me? Thank you!

[lshep]

You need to have internet connection to run AnnotationHub. See also the troubleshooting section on "invalid cache" https://bioconductor.org/packages/3.17/bioc/vignettes/AnnotationHub/inst/doc/TroubleshootingTheCache.html#troubleshooting

[gxt13111560461]

Hello, thank you for your answer. After a few days of trying, I can be sure that there is no problem with my network. It seems that the problem is that the installation package is not installed completely. However, after I manually uninstall and install successfully, I still get the error after trying again:

library(AnnotationHub) hub <- AnnotationHub() Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE'

At 2023-08-21 20:11:53, "lshep" @.***> wrote:

You need to have internet connection to run AnnotationHub. See also the troubleshooting section on "invalid cache" https://bioconductor.org/packages/3.17/bioc/vignettes/AnnotationHub/inst/doc/TroubleshootingTheCache.html#troubleshooting

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: @.***>

[gxt13111560461]

Hello, thank you for your answer. After a few days of trying, I can be sure that there is no problem with my network. It seems that the problem is that the installation package is not installed completely. However, after I manually uninstall and install successfully, I still get the error after trying again:

library(AnnotationHub) hub <- AnnotationHub() Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE'

The problem seems to be on the file：splite file. After reading the guidance document, I still can't understand, can you help me?

You need to have internet connection to run AnnotationHub. See also the troubleshooting section on "invalid cache" https://bioconductor.org/packages/3.17/bioc/vignettes/AnnotationHub/inst/doc/TroubleshootingTheCache.html#troubleshooting

[lshep]

Are you online or behind a proxy?

[gxt13111560461]

I am online. ---- Replied Message ---- | From | @.> | | Date | 08/24/2023 22:21 | | To | @.> | | Cc | gxt13111560461 @.>, Comment @.> | | Subject | Re: [Bioconductor/AnnotationHub] R Cannot connect to AnnotationHub server (Issue #43) |

Are you online or behind a proxy?

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[lshep]

Are you behind a proxy? If you are behind a proxy on your network there is new documentation on how to operate behind a proxy. I forgot to version bump when I updated documentation for behind a proxy if should be live in the vignette soon. The AnnotationHub uses 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)

If you are not behind a proxy can you check the following

AnnotationHub::getAnnotationHubOption("LOCAL")

and see if you can access the AnnotationHub

hub=getAnnotationHubOption("URL")
readBin(hub, n=1L, what="raw")

[gxt13111560461]

require(AnnotationHub) hub <- AnnotationHub() Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE' proxy <- @.***:8080") proxy <- httr::use_proxy(Sys.getenv('http_proxy')) httr::set_config(proxy) AnnotationHub::setAnnotationHubOption("PROXY", proxy) AnnotationHub::getAnnotationHubOption("LOCAL") [1] FALSE hub <- AnnotationHub() Assuming valid proxy connection through ':1' If you experience connection issues consider using 'localHub=TRUE' |==============================================================| 100% snapshotDate(): 2023-04-24Oh! Thank you for your help! I successfully solved this problem! Thank you from the bottom of my heart! Hope you are doing well.

At 2023-08-24 22:41:05, "lshep" @.***> wrote:

Are you behind a proxy? If you are behind a proxy on your network there is new documentation on how to operate behind a proxy. I forgot to version bump when I updated documentation for behind a proxy if should be live in the vignette soon. The AnnotationHub uses 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 <- @.***:8080")

or

proxy <- httr::use_proxy(Sys.getenv('http_proxy')) httr::set_config(proxy) AnnotationHub::setAnnotationHubOption("PROXY", proxy)

If you are not behind a proxy can you check the following

AnnotationHub::getAnnotationHubOption("LOCAL")

and see if you can access the AnnotationHub

hub=getAnnotationHubOption("URL") readBin(hub, n=1L, what="raw")

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

[lshep]

Glad that worked. The documentation behind this should be more visible on the next push of the package. Sorry for the delay and inconvenience.

[Wull1994]

Hello, thank you for your answer. After a few days of trying, I can be sure that there is no problem with my network. It seems that the problem is that the installation package is not installed completely. However, after I manually uninstall and install successfully, I still get the error after trying again:

library(AnnotationHub) hub <- AnnotationHub() Cannot connect to AnnotationHub server, using 'localHub=TRUE' instead Using 'localHub=TRUE' If offline, please also see BiocManager vignette section on offline use Error in .updateHubDB(hub_bfc, .class, url, proxy, localHub) : Invalid Cache: sqlite file Hub has not been added to cache Run again with 'localHub=FALSE'

The problem seems to be on the file：splite file. After reading the guidance document, I still can't understand, can you help me?

You need to have internet connection to run AnnotationHub. See also the troubleshooting section on "invalid cache" https://bioconductor.org/packages/3.17/bioc/vignettes/AnnotationHub/inst/doc/TroubleshootingTheCache.html#troubleshooting

You can try to use VPN. I have the same problem, but when the VPN was used, the problem was solved.

[lshep]

See previous post about setting the proxy or if not behind a proxy see if AnnotationHub is accessible: https://github.com/Bioconductor/AnnotationHub/issues/43#issuecomment-1691815665