Problem with AnnotationHub()
1
1
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rex.burger ▴ 10
@rexburger-11187
Last seen 3.9 years ago

Hi,

 i get the following error message when i execute AnnotationHub()

updating metadata: retrieving 1 resource Error: database is corrupt; remove it and try again database: ?/home/asan/.AnnotationHub/annotationhub.sqlite3? reason: missing tables In addition: Warning message: download failed hub path: ?https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3? cache path: ?/home/asan/.AnnotationHub/annotationhub.sqlite3? reason: Problem with the SSL CA cert (path? access rights?)

I checked this link

AnnotationHub corrupt database

the first solution by Martin Morgan did not work and i used BiocInstaller::biocValid(). It showed 86 packages are out of date. I then ran BiocInstaller::biocLite(). But the issue still persists

I have attached the output from sessionInfo() and hubCache()

sessionInfo()

R version 3.3.0 beta (2016-03-30 r70404) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C 
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 
[5] LC_MONETARY=nb_NO.UTF-8 LC_MESSAGES=en_US.UTF-8 
[7] LC_PAPER=nb_NO.UTF-8 LC_NAME=C 
[9] LC_ADDRESS=C LC_TELEPHONE=C 
[11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] parallel stats graphics grDevices utils datasets [7] methods base

other attached packages: [1] AnnotationHub_2.4.2 BiocGenerics_0.18.0 BiocInstaller_1.24.0

loaded via a namespace (and not attached): [1] Rcpp_0.12.8 IRanges_2.6.1 
[3] digest_0.6.10 mime_0.5 
[5] R6_2.2.0 xtable_1.8-2 
[7] DBI_0.5-1 stats4_3.3.0 
[9] RSQLite_1.1-1 httr_1.2.1 
[11] curl_2.3 S4Vectors_0.10.3 
[13] tools_3.3.0 Biobase_2.32.0 
[15] shiny_0.14.2 httpuv_1.3.3 
[17] AnnotationDbi_1.34.4 memoise_1.0.0 
[19] htmltools_0.3.5 interactiveDisplayBase_1.10.3

hubCache()

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ?hubCache? for signature ?"missing"?

Can anyone please suggest a solution to make it work?

Thanks

annotationhub • 2.2k views
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@valerie-obenchain-4275
Last seen 2.2 years ago
United States

Hi,

It looks like you are a release behind and need to update R/Bioconductor. The current release version of Biocondcutor is 3.4 (AnnotationHub package version 2.6.*). Update instructions are here:

http://www.bioconductor.org/install/

Let us know if you still have the problem after the update.

Valerie

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hello Valerie,

Thank you for your response. My Biocondcutor version when i generated the above output was already 3.4. But the AnnotationHub package version was 2.4.2. I updated it to 2.6.4. But still the problem persists, it is showing the same error.

I also updated R, but still it shows 3.3.0 beta

 

> ah = AnnotationHub()
updating metadata: retrieving 1 resource
Error: database is corrupt; remove it and try again
  database: ?/home/asan//.AnnotationHub/annotationhub.sqlite3?
  reason: missing tables
In addition: Warning message:
download failed
  hub path: ?https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3?
  cache path: ?/home/asan//.AnnotationHub/annotationhub.sqlite3?
  reason: Problem with the SSL CA cert (path? access rights?) 
> sessionInfo()
R version 3.3.0 beta (2016-03-30 r70404)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=nb_NO.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=nb_NO.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets 
[7] methods   base     

other attached packages:
[1] 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_3.3.0                 
 [9] RSQLite_1.1-1                 BiocInstaller_1.24.0         
[11] httr_1.2.1                    curl_2.3                     
[13] S4Vectors_0.12.1              tools_3.3.0                  
[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
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Entering edit mode

OK, those package versions now look like Bioconductor 3.4. I would exit R and then remove the .AnnotationHub directory. The directory will be in your local home so for example to remove mine I would 

rm -r /home/vobencha/.AnnotationHub

Once you've confirmed there is no .AnnotationHub, start R and biocLite("AnnotationHub").

Valerie

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Hello,

I followed you instructions. But it gives the same error. I tried to remove the package and install it again. It still shows the same error after re-installing.

All of the issue might have been because of cache problem. I  tried the solution offered in this link:

 

the first link using curl worked perfectly fine. But when i use "https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3. the system throws a "SSL CA cert" error as you can see below:

> curl::curl_fetch_disk("www.google.com", tempfile())
$url
[1] "http://www.google.no/?gfe_rd=cr&ei=Ig5lWMmtO-vk8Ae2sZb4Bw"

$status_code
[1] 200

$headers
  [1] 48 54 54 50 2f 31 2e 31 20 33 30 32 20 46 6f 75 6e 64 0d 0a 43 61 63 68 65
 [26] 2d 43 6f 6e 74 72 6f 6c 3a 20 70 72 69 76 61 74 65 0d 0a 43 6f 6e 74 65 6e
 [51] 74 2d 54 79 70 65 3a 20 74 65 78 74 2f 68 74 6d 6c 3b 20 63 68 61 72 73 65
 [76] 74 3d 55 54 46 2d 38 0d 0a 4c 6f 63 61 74 69 6f 6e 3a 20 68 74 74 70 3a 2f
[101] 2f 77 77 77 2e 67 6f 6f 67 6c 65 2e 6e 6f 2f 3f 67 66 65 5f 72 64 3d 63 72
[126] 26 65 69 3d 49 67 35 6c 57 4d 6d 74 4f 2d 76 6b 38 41 65 32 73 5a 62 34 42
[151] 77 0d 0a 43 6f 6e 74 65 6e 74 2d 4c 65 6e 67 74 68 3a 20 32 35 38 0d 0a 44
[176] 61 74 65 3a 20 54 68 75 2c 20 32 39 20 44 65 63 20 32 30 31 36 20 31 33 3a
[201] 32 32 3a 34 32 20 47 4d 54 0d 0a 0d 0a 48 54 54 50 2f 31 2e 31 20 32 30 30
[226] 20 4f 4b 0d 0a 44 61 74 65 3a 20 54 68 75 2c 20 32 39 20 44 65 63 20 32 30
[251] 31 36 20 31 33 3a 32 32 3a 34 33 20 47 4d 54 0d 0a 45 78 70 69 72 65 73 3a
[276] 20 2d 31 0d 0a 43 61 63 68 65 2d 43 6f 6e 74 72 6f 6c 3a 20 70 72 69 76 61
[301] 74 65 2c 20 6d 61 78 2d 61 67 65 3d 30 0d 0a 43 6f 6e 74 65 6e 74 2d 54 79
[326] 70 65 3a 20 74 65 78 74 2f 68 74 6d 6c 3b 20 63 68 61 72 73 65 74 3d 49 53
[351] 4f 2d 38 38 35 39 2d 31 0d 0a 50 33 50 3a 20 43 50 3d 22 54 68 69 73 20 69
[376] 73 20 6e 6f 74 20 61 20 50 33 50 20 70 6f 6c 69 63 79 21 20 53 65 65 20 68
[401] 74 74 70 73 3a 2f 2f 77 77 77 2e 67 6f 6f 67 6c 65 2e 63 6f 6d 2f 73 75 70
[426] 70 6f 72 74 2f 61 63 63 6f 75 6e 74 73 2f 61 6e 73 77 65 72 2f 31 35 31 36
[451] 35 37 3f 68 6c 3d 65 6e 20 66 6f 72 20 6d 6f 72 65 20 69 6e 66 6f 2e 22 0d
[476] 0a 43 6f 6e 74 65 6e 74 2d 45 6e 63 6f 64 69 6e 67 3a 20 67 7a 69 70 0d 0a
[501] 53 65 72 76 65 72 3a 20 67 77 73 0d 0a 43 6f 6e 74 65 6e 74 2d 4c 65 6e 67
[526] 74 68 3a 20 34 35 31 31 0d 0a 58 2d 58 53 53 2d 50 72 6f 74 65 63 74 69 6f
[551] 6e 3a 20 31 3b 20 6d 6f 64 65 3d 62 6c 6f 63 6b 0d 0a 58 2d 46 72 61 6d 65
[576] 2d 4f 70 74 69 6f 6e 73 3a 20 53 41 4d 45 4f 52 49 47 49 4e 0d 0a 53 65 74
[601] 2d 43 6f 6f 6b 69 65 3a 20 4e 49 44 3d 39 33 3d 4a 76 53 68 6c 4a 63 72 44
[626] 55 52 36 66 5a 4a 5f 45 48 2d 7a 6a 6d 31 4e 71 47 41 6e 53 49 38 53 34 69
[651] 6e 46 59 42 39 38 6a 35 56 55 6d 72 30 58 4b 64 34 6c 71 6f 64 64 73 41 41
[676] 4c 63 61 6e 32 34 48 61 75 69 6f 6d 66 5f 66 36 6c 4d 4d 68 6b 69 61 41 2d
[701] 71 50 35 43 77 37 74 4e 53 6a 45 72 79 52 47 6e 6a 33 49 43 52 62 38 78 7a
[726] 73 39 64 65 62 33 63 38 73 6a 43 34 36 5f 30 76 6c 53 65 3b 20 65 78 70 69
[751] 72 65 73 3d 46 72 69 2c 20 33 30 2d 4a 75 6e 2d 32 30 31 37 20 31 33 3a 32
[776] 32 3a 34 33 20 47 4d 54 3b 20 70 61 74 68 3d 2f 3b 20 64 6f 6d 61 69 6e 3d
[801] 2e 67 6f 6f 67 6c 65 2e 6e 6f 3b 20 48 74 74 70 4f 6e 6c 79 0d 0a 0d 0a

$modified
[1] NA

$times
     redirect    namelookup       connect   pretransfer starttransfer 
     0.074197      0.001130      0.037088      0.037116      0.105725 
        total 
     0.180334 

$content
[1] "/tmp/Rtmp955Zf1/file11de66f69701"


> curl::curl_fetch_disk("https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3", tempfile())
Error in curl::curl_fetch_disk("https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3",  : 
  Problem with the SSL CA cert (path? access rights?)

 

Is there a problem with cache as discussed here -> https://stat.ethz.ch/pipermail/bioc-devel/2015-September/007970.html

How do i delete everything in the cache?

Thanks.

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Entering edit mode

No, that post is very old and the issues have been addressed. The 'cache' is the .AnnotationHub/ directory with the sqlite file, index file and individual downloaded resources. If you removed the .AnnotationHub directory you removed the cache.

I don't know why you're having problems with the SSL CA cert. I'll check with Greg who may have more insight to the problem.

Valerie

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Entering edit mode

Several of us have tested and can't reproduce the problem. From the command line (not in R):

~/sandbox >curl -I https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3
HTTP/1.1 200 OK
Date: Thu, 29 Dec 2016 16:00:09 GMT
Server: Apache/2.4.9 (Ubuntu)
X-Content-Type-Options: nosniff
X-Powered-By: Phusion Passenger 4.0.46
Last-Modified: Thu, 29 Dec 2016 02:50:57 GMT
Content-Length: 63170560
Status: 200 OK
Content-Type: application/octet-stream

From within R:

> curlGetHeaders("https://annotationhub.bioconductor.org/metadata/annotationhub.sqlite3")
 [1] "HTTP/1.1 200 OK\r\n"                             
 [2] "Date: Thu, 29 Dec 2016 16:04:07 GMT\r\n"         
 [3] "Server: Apache/2.4.9 (Ubuntu)\r\n"               
 [4] "X-Content-Type-Options: nosniff\r\n"             
 [5] "X-Powered-By: Phusion Passenger 4.0.46\r\n"      
 [6] "Last-Modified: Thu, 29 Dec 2016 02:50:57 GMT\r\n"
 [7] "Content-Length: 63170560\r\n"                    
 [8] "Status: 200 OK\r\n"                              
 [9] "Content-Type: application/octet-stream\r\n"      
[10] "\r\n"                                            
attr(,"status")
[1] 200

I'm not sure what your system set up is - maybe you could follow up with your local sys admin.

Valerie

 

 

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