can not download LunSpikeInData

[YinCY123]

the error returns

Error in value[3L] : failed to connect reason: Timeout was reached: [bioconductor.org] Operation timed out after 10002 milliseconds with 0 out of 0 bytes received Consider rerunning with 'localHub=TRUE'

does anybody know how to deal with?

[LTLA]

Depends on where you are. ExperimentHub uses AWS S3 to host its data, and, e.g., China has serious connectivity problems with AWS. Sometimes things work, sometimes they don't. In this case, if the error message is to be taken at face value, then it's actually a problem with the bioconductor.org interface rather than S3 itself. Perhaps @lshep can provide some more clarification.

[lshep]

I was running some computationally heavy scripts over the weekend trying to analyze some logs. perhaps it interfered. @YinCY123 can you try again and let us know if you are still having issues?

[YinCY123]

yes, I'm located in china, It seems that it still doesn't work.

I'm using the AnnotationHub()[['AH73905']] to retrieve, it doesn't work either

The verbose return as follows:

snapshotDate(): 2020-04-27 see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache snapshotDate(): 2020-04-27 loading from cache Error: failed to load resource name: AH73905 title: Ensembl 97 EnsDb for Mus musculus reason: database disk image is malformed In addition: Warning messages: 1: call dbDisconnect() when finished working with a connection 2: Couldn't set synchronous mode: database disk image is malformed Use synchronous = NULL to turn off this warning.

[lshep]

This is odd as I cannot reproduce ...

> ah = AnnotationHub()
snapshotDate(): 2021-03-15
ah[["AH7> ah[["AH73905"]]
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
require("ensembldb")
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.4
|Creation time: Sun Jul  7 08:07:59 2019
|ensembl_version: 97
|ensembl_host: localhost
|Organism: Mus musculus
|taxonomy_id: 10090
|genome_build: GRCm38
|DBSCHEMAVERSION: 2.1
| No. of genes: 56393.
| No. of transcripts: 144404.
|Protein data available.

Since it is saying the database is malformed, I'm wondering if it only partially downloaded the main sqlite database. can you try force redownloading the hub. And as long as that was successful then try again?

ah = refreshHub(hubClass="AnnotationHub")

[YinCY123]

after refreshHub(hubClass = 'AnnotationHub') ah[['AH73905']] can be download sucessfully, but the LunSpikeData still can not be downloaded

sce.416b <- LunSpikeInData(which = "416b") snapshotDate(): 2020-04-27 see ?scRNAseq and browseVignettes('scRNAseq') for documentation loading from cache Error: failed to load resource name: EH2674 title: Lun 416B plus spike-in counts reason: error reading from connection

[lshep]

Can you also try redownloading ExperimentHub since that is where the LunSpikeData is

refreshHub(hubClass = 'ExperimentHub')

I can download that data without issue as well

> temp = eh[["EH2674"]]
see ?scRNAseq and browseVignettes('scRNAseq') for documentation
downloading 1 resources
retrieving 1 resource
  |======================================================================| 100%

loading from cache
>

[YinCY123]

it looks like is the problem connection to be AWS S3 as @LTLA

[lshep]

perhaps this is the intermittent connectivity to China @LTLA was referring earlier?

[YinCY123]

yes, it seems like that

[YinCY123]

thanks for your help! @lshep