How to manage AnnotationHub snapshots / most OrgDB are missing?
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0
Entering edit mode
Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 9 weeks ago
United States

I have projects split between R 3.6.3 and 4.0.0 and I am having trouble properly managing cached versions / snapshotDates of AnnotationHub resources. I first noticed this because apparently the newest snapshotDate "2020-04-27" is missing most of the OrgDb from NCBI. The AnnotationHub How To vignette has:

library(AnnotationHub)
ah <- AnnotationHub()
## snapshotDate(): 2020-03-31
query(ah, "OrgDb")
## AnnotationHub with 1708 records
## # snapshotDate(): 2020-03-31

However, there is a new snapshotDate available but it is missing most of these OrgDb:

> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2020-04-27
> query(ah, "OrgDb")
AnnotationHub with 19 records
# snapshotDate(): 2020-04-27

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] AnnotationHub_2.20.0 BiocFileCache_1.12.0 dbplyr_1.4.3         BiocGenerics_0.34.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6                  pillar_1.4.4                  compiler_4.0.0                BiocManager_1.30.10          
 [5] later_1.0.0                   tools_4.0.0                   digest_0.6.25                 bit_1.1-15.2                 
 [9] RSQLite_2.2.0                 memoise_1.1.0                 lifecycle_0.2.0               tibble_3.0.1                 
[13] pkgconfig_2.0.3               rlang_0.4.6                   shiny_1.4.0.2                 DBI_1.1.0                    
[17] rstudioapi_0.11               curl_4.3                      yaml_2.2.1                    fastmap_1.0.1                
[21] dplyr_0.8.5                   httr_1.4.1                    IRanges_2.22.1                vctrs_0.3.0                  
[25] S4Vectors_0.26.1              rappdirs_0.3.1                stats4_4.0.0                  bit64_0.9-7                  
[29] tidyselect_1.1.0              Biobase_2.48.0                glue_1.4.1                    R6_2.4.1                     
[33] AnnotationDbi_1.50.0          purrr_0.3.4                   blob_1.2.1                    magrittr_1.5                 
[37] promises_1.1.0                ellipsis_0.3.1                htmltools_0.4.0               assertthat_0.2.1             
[41] xtable_1.8-4                  mime_0.9                      interactiveDisplayBase_1.26.0 httpuv_1.5.2                 
[45] crayon_1.3.4                  BiocVersion_3.11.1 

The main AnnotationHub vignette seems to say that I could switch to a different snapshotDate by simply doing the below, but it doesn't work, I still get the same truncated list of OrgDbs:

> possibleDates(ah)
  [1] "2013-03-19" "2013-03-21" "2013-03-26" "2013-04-04" "2013-04-29" "2013-06-24" "2013-06-25" "2013-06-26" "2013-06-27"
# ...
[127] "2019-10-29" "2020-01-28" "2020-02-28" "2020-03-31" "2020-04-27"
> snapshotDate(ah) <- "2020-03-31"
> query(ah, "OrgDb")
AnnotationHub with 19 records
# snapshotDate(): 2020-03-31

I am also having weird issues when running two instances of RStudio at the same time, one with R 4.0.0 and one with R 3.6.3. I am having trouble replicating everything weird that I saw but this seems to be replicable:

# 1. Open RStudio running R 4.0.0. Force refresh of of cache with:
> library(AnnotationHub)
> ah <- refreshHub(hubClass="AnnotationHub")
  |================================================================| 100%

snapshotDate(): 2020-04-27
> query(ah, "OrgDb")
AnnotationHub with 19 records
# snapshotDate(): 2020-04-27

# 2. Open another RStudio running 3.6.3. I had previously downloaded a snapshotDate of "2019-10-29" and it seems to find this one at first:
> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2019-10-29
> query(ah, "OrgDb")
AnnotationHub with 1708 records
# snapshotDate(): 2019-10-29 
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_1.4.2         BiocGenerics_0.32.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.4.6                  later_1.0.0                   pillar_1.4.3                 
 [4] compiler_3.6.3                BiocManager_1.30.10           tools_3.6.3                  
 [7] digest_0.6.25                 bit_1.1-15.2                  RSQLite_2.2.0                
[10] memoise_1.1.0                 lifecycle_0.2.0               tibble_3.0.0                 
[13] pkgconfig_2.0.3               rlang_0.4.5                   shiny_1.4.0.2                
[16] DBI_1.1.0                     cli_2.0.2                     rstudioapi_0.11              
[19] curl_4.3                      yaml_2.2.1                    fastmap_1.0.1                
[22] dplyr_0.8.5                   httr_1.4.1                    IRanges_2.20.2               
[25] vctrs_0.2.4                   S4Vectors_0.24.3              rappdirs_0.3.1               
[28] stats4_3.6.3                  bit64_0.9-7                   tidyselect_1.0.0             
[31] Biobase_2.46.0                glue_1.4.0                    R6_2.4.1                     
[34] AnnotationDbi_1.48.0          fansi_0.4.1                   purrr_0.3.3                  
[37] blob_1.2.1                    magrittr_1.5                  promises_1.1.0               
[40] ellipsis_0.3.0                htmltools_0.4.0               assertthat_0.2.1             
[43] xtable_1.8-4                  mime_0.9                      interactiveDisplayBase_1.24.0
[46] httpuv_1.5.2                  crayon_1.3.4                  BiocVersion_3.10.1 

# 3. Switch back to 4.0.0 and then refresh hub again

> ah <- refreshHub(hubClass="AnnotationHub")
>   |================================================================| 100%

snapshotDate(): 2020-04-27
> query(ah, "OrgDb")
AnnotationHub with 19 records
# snapshotDate(): 2020-04-27


# 4. Switch back to 3.6.3; query OrgDb and see that is it wrong. Refresh hub and query again

> query(ah, "OrgDb")
AnnotationHub with 0 records
# snapshotDate(): 2019-10-29
> ah <- refreshHub(hubClass="AnnotationHub")
  |=======================================================================================| 100%

snapshotDate(): 2019-10-29
> query(ah, "OrgDb")
AnnotationHub with 1708 records
# snapshotDate(): 2019-10-29

# 5. Switch back to 4.0.0 and query for OrgDb again and see that is wrong:
> query(ah, "OrgDb")
AnnotationHub with 0 records
# snapshotDate(): 2020-04-27

I've been wading through the help page for ?AnnotationHub and I probably have to do some combination of the cache and localHub options but I cannot find any good examples of how to do this. So my specific questions are:

  1. How do I set and switch between local caches of specific snapshotDates for different versions of R?
  2. How do I switch to the 2020-03-31 snapshotDate in 4.0.0?
  3. What happened to all the OrgDB packages in snapshotDate 2020-04-27?!?

Thanks

AnnotationHub OrgDb snapshotDate • 190 views
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shepherl 2.8k
@lshep
Last seen 12 hours ago
United States

OrgDbs are a special case because they are only valid for a particular Bioconductor version. So you would have to Switch the Bioconductor version in order to use a older snapshot date for the OrgDbs (otherwise what you are doing is correct). I am in the process of adding the OrgDbs from NCBI. There is an error in the code to generate them that I am currently in the process of debugging but hope to have them uploaded in the next few days to be available for R 4.0.0 Bioc 3.11/Bioc3.12

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Entering edit mode

I apologize for the inconvenience this has causes and will let you know when they are available.

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No worries! Thank you for all your work on AnnotationHub. We work with many non-model organisms and AnnotationHub is extremely useful.

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shepherl 2.8k
@lshep
Last seen 12 hours ago
United States

The orgDbs have been added. Please let me know if you have any further issues.

> BiocManager::version()
[1] '3.11'
> ah = AnnotationHub()
snapshotDate(): 2020-04-27
> query(ah, "OrgDb")
AnnotationHub with 1480 records
# snapshotDate(): 2020-04-27
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Escherichia coli, [Nectria] haematococca_mpVI_77-13-4, Zymosepto...
# $rdataclass: OrgDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH79568"]]' 

            title                                        
  AH79568 | org.Ag.eg.db.sqlite                          
  AH79569 | org.At.tair.db.sqlite                        
  AH79570 | org.Bt.eg.db.sqlite                          
  AH79571 | org.Cf.eg.db.sqlite                          
  AH79572 | org.Gg.eg.db.sqlite                          
  ...       ...                                          
  AH81959 | org.Bathycoccus_prasinos.eg.sqlite           
  AH81960 | org.Kwoniella_pini_CBS_10737.eg.sqlite       
  AH81961 | org.Burkholderia_cepacia_ATCC_25416.eg.sqlite
  AH81962 | org.Burkholderia_cepacia_DSM_7288.eg.sqlite  
  AH81963 | org.Burkholderia_cepacia_LMG_1222.eg.sqlite  
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