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Question: Certificate problem with ExperimentHub / AnnotationHub
1
gravatar for morganx
11 months ago by
morganx10
morganx10 wrote:

Hi, I'd like to use curatedmetagenomicdata to download some experiments from ExperimentHub and am running into certificate error issues. I have previously searched this forum and tried the solutions I found, but they do not seem to work, as detailed in the following.  Immediately prior to R session, I tried deleting the corrupt cache from the command line and restarting R. I tried unlinking the cache during R, and I have verified that my bioconductor packages are current and valid.

The piece of code I am trying to execute successfully is:

library(ExperimentHub)

eh = ExperimentHub()

 

The errors and session info are detailed below. Any assistance is appreciated.

 

#Unix command prompt

$ rm -rf /Users/morxo28p/.ExperimentHub/

#From within R:

> file.exists('/Users/morxo28p/.ExperimentHub/experimenthub.sqlite3')

[1] FALSE

> library(ExperimentHub)

#library loaded successfully, terminal output of this trimmed

> eh = ExperimentHub()

updating metadata: retrieving 1 resource

Error: database is corrupt; remove it and try again

  database: ‘/Users/morxo28p//.ExperimentHub/experimenthub.sqlite3’

  reason: missing tables

In addition: Warning message:

download failed

  hub path: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’

  cache path: ‘/Users/morxo28p//.ExperimentHub/experimenthub.sqlite3’

  reason: Peer certificate cannot be authenticated with given CA certificates 

> traceback()

9: stop("database is corrupt; remove it and try again", "\n  database: ", 

       sQuote(path), "\n  reason: ", conditionMessage(err), call. = FALSE)

8: value[[3L]](cond)

7: tryCatchOne(expr, names, parentenv, handlers[[1L]])

6: tryCatchList(expr, classes, parentenv, handlers)

5: tryCatch({

       expected <- c("biocversions", "input_sources", "location_prefixes", 

           "rdatapaths", "recipes", "resources", "statuses", "tags", 

           "timestamp")

       if (!all(expected %in% dbListTables(conn))) 

           stop("missing tables")

       sql <- "SELECT COUNT(id) FROM resources"

       if (.db_query(conn, sql)[[1]] == 0L) 

           warning("empty 'resources' table; database may be corrupt")

   }, error = function(err) {

       stop("database is corrupt; remove it and try again", "\n  database: ", 

           sQuote(path), "\n  reason: ", conditionMessage(err), 

           call. = FALSE)

   })

4: .db_is_valid(db_path)

3: .db_get(db_path, url, proxy)

2: .Hub("ExperimentHub", hub, cache, proxy, ...)

1: ExperimentHub()

#Troubleshooting - unlink and try again

> unlink('/Users/morxo28p/.ExperimentHub/experimenthub.sqlite3')

> file.exists('/Users/morxo28p/.ExperimentHub/experimenthub.sqlite3')

[1] FALSE

> eh = ExperimentHub()

updating metadata: retrieving 1 resource

Error: database is corrupt; remove it and try again

  database: ‘/Users/morxo28p//.ExperimentHub/experimenthub.sqlite3’

  reason: missing tables

In addition: Warning message:

download failed

  hub path: ‘https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3’

  cache path: ‘/Users/morxo28p//.ExperimentHub/experimenthub.sqlite3’

  reason: Peer certificate cannot be authenticated with given CA certificates 

# R session information

> BiocInstaller::biocValid()

[1] TRUE

> sessionInfo()

R version 3.3.2 (2016-10-31)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X El Capitan 10.11.6

locale:

[1] en_NZ.UTF-8/en_NZ.UTF-8/en_NZ.UTF-8/C/en_NZ.UTF-8/en_NZ.UTF-8

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods  

[8] base     

other attached packages:

[1] ExperimentHub_1.0.0 AnnotationHub_2.6.4 BiocGenerics_0.20.0

loaded via a namespace (and not attached):

 [1] Rcpp_0.12.8                   IRanges_2.8.1                

 [3] digest_0.6.10                 mime_0.5                     

 [5] R6_2.2.0                      xtable_1.8-2                 

 [7] DBI_0.5-1                     stats4_3.3.2                 

 [9] RSQLite_1.1-1                 BiocInstaller_1.24.0         

[11] httr_1.2.1                    curl_2.3                     

[13] S4Vectors_0.12.1              tools_3.3.2                  

[15] Biobase_2.34.0                shiny_0.14.2                 

[17] yaml_2.1.14                   httpuv_1.3.3                 

[19] AnnotationDbi_1.36.0          memoise_1.0.0                

[21] htmltools_0.3.5               interactiveDisplayBase_1.12.0



 

ADD COMMENTlink modified 11 months ago by Levi Waldron380 • written 11 months ago by morganx10
2
gravatar for gregory.wargula
11 months ago by
gregory.wargula ♦♦ 30
gregory.wargula ♦♦ 30 wrote:

The certificate issue for 'https://experimenthub.bioconductor.org/' should now be resolved. Greg

ADD COMMENTlink written 11 months ago by gregory.wargula ♦♦ 30

Thank you. I am no longer getting this error and it is working properly.

ADD REPLYlink written 11 months ago by morganx10

After a few days without issue, I am seeing this issue again. CA certificate for AnnotationHub is fine but ExperimentHub is having issues.

ADD REPLYlink written 10 months ago by Lucas Schiffer160

Same here:

> curatedMetagenomicData::LomanNJ_2013_Hi.metaphlan_bugs_list.stool()
snapshotDate(): 2016-12-12
see ?curatedMetagenomicData and browseVignettes('curatedMetagenomicData') for documentation
loading from cache ‘/Users/lw391//.ExperimentHub/289’
ExpressionSet (storageMode: lockedEnvironment)
assayData: 736 features, 44 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: OBK1122 OBK1196 ... OBK5066 (44 total)
  varLabels: subjectID first ... number_reads (19 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 23571589 
Annotation:  
Warning message:
database may not be current
  database: ‘/Users/lw391//.ExperimentHub/experimenthub.sqlite3’
  reason: Peer certificate cannot be authenticated with given CA certificates 
> 
ADD REPLYlink written 10 months ago by Levi Waldron380
1
Should be fixed now. Greg From: "Levi Waldron [bioc]" <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> Reply-To: "reply+890df79f+code@bioconductor.org<mailto:reply+890df79f+code@bioconductor.org>" <reply+890df79f+code@bioconductor.org<mailto:reply+890df79f+code@bioconductor.org>> Date: Wednesday, December 28, 2016 at 12:07 PM To: Gregory Wargula <gregory.wargula@roswellpark.org<mailto:gregory.wargula@roswellpark.org>> Subject: [bioc] C: Certificate problem with ExperimentHub / AnnotationHub Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User Levi Waldron<https: support.bioconductor.org="" u="" 3429=""/> wrote Comment: Certificate problem with ExperimentHub / AnnotationHub<https: support.bioconductor.org="" p="" 90483="" #90641="">: Same here: > curatedMetagenomicData::LomanNJ_2013_Hi.metaphlan_bugs_list.stool() snapshotDate(): 2016-12-12 see ?curatedMetagenomicData and browseVignettes('curatedMetagenomicData') for documentation loading from cache '/Users/lw391//.ExperimentHub/289' ExpressionSet (storageMode: lockedEnvironment) assayData: 736 features, 44 samples element names: exprs protocolData: none phenoData sampleNames: OBK1122 OBK1196 ... OBK5066 (44 total) varLabels: subjectID first ... number_reads (19 total) varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' pubMedIds: 23571589 Annotation: Warning message: database may not be current database: '/Users/lw391//.ExperimentHub/experimenthub.sqlite3' reason: Peer certificate cannot be authenticated with given CA certificates > ________________________________ Post tags: software error, curatedmetagenomicdata, annotationhub, experimenthub You may reply via email or visit C: Certificate problem with ExperimentHub / AnnotationHub This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
ADD REPLYlink written 10 months ago by gregory.wargula ♦♦ 30

Thanks Greg, fix confirmed.

ADD REPLYlink written 10 months ago by Levi Waldron380
0
gravatar for Lucas Schiffer
11 months ago by
CUNY School of Public Health, New York, NY
Lucas Schiffer160 wrote:

I too see the issue when I call ExperimentHub – the CA certificates are related to Amazon S3, which is the storage mechanism on the backend. Although this should only trigger an warning and not a error. To fix the issue first do the following from the command line:

$ rm -rf /Users/morxo28p/.ExperimentHub

This should remove corrupt database and then you can do the following from R to download data from curatedMetagenomicData:

library(curatedMetagenomicData)
ZellerG_2014.metaphlan_bugs_list.stool()

It is also possible to bring up the names of datasets by typing:

curatedMetagenomicData::

And hitting tab for a list of autocompletion choices; although, that will only work in RStudio.

To be clear, this is not an issue related to curatedMetagenomicData, ExperimentHub, or AnnotationHub. CA certificates are an amazon problem and the corrupt database is a user issue. If further issues are encountered, try removing the database again and reinstalling packages.

UPDATE: Having followed my own advice, I too get the error and cannot fix the issue by the above steps. What I believe to be the issue is that Amazon S3 CA certificates have expired. If the download is absolutely essential at the moment you could cURL the sqlite file like this from command line:

$ mkdir /Users/morxo28p/.ExperimentHub
$ cd /Users/morxo28p/.ExperimentHub
$ curl -O -k  https://experimenthub.bioconductor.org/metadata/experimenthub.sqlite3

This will download the database, regardless of the expired CA certificates and then you should be able to download datasets from within R.

ADD COMMENTlink modified 11 months ago • written 11 months ago by Lucas Schiffer160
0
gravatar for Levi Waldron
11 months ago by
Levi Waldron380
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron380 wrote:

Lucas, it looks like the user has already followed your advice in their original post... I am having the same problem which seems to be an invalid certificate for https://experimenthub.bioconductor.org, an ExperimentHub issue. Val, do you know what the problem is?

ADD COMMENTlink written 11 months ago by Levi Waldron380
1

Looking at the certificate from GoDaddy:

Expired: Sunday, December 18, 2016 at 15:51:04 Eastern Standard Time

And that is for all bioconductor.org domains.

ADD REPLYlink written 11 months ago by Lucas Schiffer160

That would explain it! At least, I'm happy to see it was a curatedMetagenomicData user who found this first :).

ADD REPLYlink written 11 months ago by Levi Waldron380
0
gravatar for Levi Waldron
11 months ago by
Levi Waldron380
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron380 wrote:

Thank you Gregory, curatedMetagenomicData is working again for me!

ADD COMMENTlink written 11 months ago by Levi Waldron380
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