Error using old ensembldb annotations with R 4.0 +
1
0
Entering edit mode
rbenel ▴ 20
@rbenel-13642
Last seen 12 days ago
Israel

Hi,

I have been using the EnsDb.Hsapiens.v92 for my annotations for the past few years; however, this past week I updated R to 4.1 and the package is no longer compatible..

Any ideas what I can do to fix this? I would like to be consistent in my research and continue using the same version, EnsDb.Hsapiens.v92.

This is the error I receive.

"Error: package or namespace load failed for 'EnsDb.Hsapiens.v92':
 package 'EnsDb.Hsapiens.v92' was installed before R 4.0.0: please re-install it--"
Code should be placed in three backticks as shown below


sessionInfo( )

R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] ensembldb_2.16.4        AnnotationFilter_1.16.0 GenomicFeatures_1.44.0 
 [4] AnnotationDbi_1.54.1    Biobase_2.52.0          GenomicRanges_1.44.0   
 [7] GenomeInfoDb_1.28.1     IRanges_2.26.0          S4Vectors_0.30.0       
[10] BiocGenerics_0.38.0     dplyr_1.0.7             ggplot2_3.3.5          

loaded via a namespace (and not attached):
 [1] MatrixGenerics_1.4.1        viridis_0.6.1              
 [3] httr_1.4.2                  tidyr_1.1.3                
 [5] bit64_4.0.5                 viridisLite_0.4.0          
 [7] assertthat_0.2.1            BiocFileCache_2.0.0        
 [9] blob_1.2.2                  GenomeInfoDbData_1.2.6     
[11] Rsamtools_2.8.0             yaml_2.2.1                 
[13] progress_1.2.2              lattice_0.20-44            
[15] pillar_1.6.2                RSQLite_2.2.7              
[17] glue_1.4.2                  digest_0.6.27              
[19] RColorBrewer_1.1-2          XVector_0.32.0             
[21] colorspace_2.0-2            Matrix_1.3-4               
[23] XML_3.99-0.6                pkgconfig_2.0.3            
[25] pheatmap_1.0.12             biomaRt_2.48.2             
[27] zlibbioc_1.38.0             purrr_0.3.4                
[29] scales_1.1.1                BiocParallel_1.26.1        
[31] tibble_3.1.3                KEGGREST_1.32.0            
[33] generics_0.1.0              ellipsis_0.3.2             
[35] cachem_1.0.5                withr_2.4.2                
[37] SummarizedExperiment_1.22.0 lazyeval_0.2.2             
[39] magrittr_2.0.1              crayon_1.4.1               
[41] memoise_2.0.0               fansi_0.5.0                
[43] xml2_1.3.2                  tools_4.1.0                
[45] prettyunits_1.1.1           hms_1.1.0                  
[47] matrixStats_0.60.0          BiocIO_1.2.0               
[49] lifecycle_1.0.0             stringr_1.4.0              
[51] munsell_0.5.0               DelayedArray_0.18.0        
[53] Biostrings_2.60.2           compiler_4.1.0             
[55] rlang_0.4.11                grid_4.1.0                 
[57] RCurl_1.98-1.3              rstudioapi_0.13            
[59] rjson_0.2.20                rappdirs_0.3.3             
[61] bitops_1.0-7                restfulr_0.0.13            
[63] gtable_0.3.0                DBI_1.1.1                  
[65] curl_4.3.2                  R6_2.5.0                   
[67] GenomicAlignments_1.28.0    gridExtra_2.3              
[69] rtracklayer_1.52.0          fastmap_1.1.0              
[71] bit_4.0.4                   utf8_1.2.2                 
[73] filelock_1.0.2              ProtGenerics_1.24.0        
[75] stringi_1.7.3               Rcpp_1.0.7                 
[77] vctrs_0.3.8                 png_0.1-7                  
[79] dbplyr_2.1.1                tidyselect_1.1.1
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb • 162 views
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0
Entering edit mode
@james-w-macdonald-5106
Last seen 4 minutes ago
United States

It looks like what you are doing is updating R but not updating your packages. You shouldn't do that, as the Bioconductor packages are meant to be used with a particular R version, which is what the error is telling you. If you install a new version of R, and you don't care to have old versions of R/Bioconductor for backward compatibility, you should do

install.packages("BiocManager")
library(BiocManager)
BiocManager::install(ask = FALSE)

Which will update all your installed packages to the correct version.

0
Entering edit mode

Hi,

I have updated all of my packages, but this one won't update as it's based on a specific ensembl version which was also not downloaded from bioconductor and rather shared on this page as a binary...

Any suggestions what I can do to retain this version of ensebml using R 4.0+ now that I have already upgraded R and Bioconductor...

Thanks

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0
Entering edit mode

As the EnsDb.Hsapiens.v92 version I was using didn't update with the move to R 4.1, this is the workaround I found in case anyone has a similar issue.

You can find parts of the code used here: https://www.bioconductor.org/packages/release/bioc/vignettes/ensembldb/inst/doc/ensembldb.html#101_Getting_EnsDb_databases

Section 9 and 10 build your own annotation package

library(AnnotationHub)
library(enembldb)
library(devtools)

ah <- AnnotationHub()

#get specific query 
ahDb <- query(ah, pattern = c("Homo sapiens", "EnsDb", 92))

ahDb

#Fetch the EnsDb and use it.
ahEdb <- ahDb[[1]]

## retrieve all genes
gns <- genes(ahEdb)

## and finally we can generate the package
makeEnsembldbPackage(ensdb = dbfile(dbconn(ahEdb)), version = "0.99.12",
                     maintainer = "Johannes Rainer <johannes.rainer@eurac.edu>",
                     author = "J Rainer")
#Even easier then the above is to use Hadley Wickham’s devtools package. You can then build and install the package from within R.
#Start R within your package directory (so that your package directory is R’s working directory).

  build("EnsDb.Hsapiens.v92")

#To install the R package, you’d type
#gets installed in your working directory 
install("EnsDb.Hsapiens.v92")
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