Search
Question: Problem with AnnotationHub()
1
gravatar for rex.burger
10 months ago by
rex.burger10
rex.burger10 wrote:

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 It showed 86 packages are out of date.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

ADD COMMENTlink modified 10 months ago by Valerie Obenchain ♦♦ 6.4k • written 10 months ago by rex.burger10
0
gravatar for Valerie Obenchain
10 months ago by
Valerie Obenchain ♦♦ 6.4k
United States
Valerie Obenchain ♦♦ 6.4k wrote:

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

ADD COMMENTlink written 10 months ago by Valerie Obenchain ♦♦ 6.4k

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
ADD REPLYlink modified 10 months ago • written 10 months ago by rex.burger10

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

ADD REPLYlink written 10 months ago by Valerie Obenchain ♦♦ 6.4k

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by rex.burger10

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

ADD REPLYlink written 10 months ago by Valerie Obenchain ♦♦ 6.4k

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

 

 

ADD REPLYlink written 10 months ago by Valerie Obenchain ♦♦ 6.4k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 177 users visited in the last hour