Question: R failing to load genome files from EnsDb.Hsapiens.v86
gravatar for michaelschoeber
12 months ago by
michaelschoeber10 wrote:


I would like to construct a tx2gene data frame for summarizing transcript expression to gene level expression via tximport. 

I did not get any errors when installing the "ensembldb" or the "EnsDb.Hsapiens.v86" packages as far as I noticed, I can also load them normally via the library function, however when i try to assign EnsDb.Hsapiens.v86 to some variable R tells me "Error: object 'EnsDb.Hsapiens.v86' not found".

I tried to install the packages in different ways, also tried "EnsDb.Hsapiens.v75", as well as "TxDb.Hsapiens.UCSC.hg19.knownGene", with the same outcome. Might there be something going on with the library?

Either way I am pretty much stuck on this and would really appreciate some help. Thanks in advance!



ADD COMMENTlink modified 10 months ago by Bioconductor Community ♦♦ 0 • written 12 months ago by michaelschoeber10

Could you please provide the code you are using and any output. Also please provide sessionInfo() so we know which version of R/Bioc and OS you are using.

I currently can do the following with no error:

> library(EnsDb.Hsapiens.v86) 
> db = EnsDb.Hsapiens.v86 
> db
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.0
|Creation time: Thu May 18 16:32:27 2017
|ensembl_version: 86
|ensembl_host: localhost
|Organism: homo_sapiens
|taxonomy_id: 9606
|genome_build: GRCh38
| No. of genes: 63970.
| No. of transcripts: 216741.
|Protein data available.

> sessionInfo()
R Under development (unstable) (2018-11-18 r75627)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /home/lori/bin/R-devel/lib/
LAPACK: /home/lori/bin/R-devel/lib/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.7.2          
 [3] AnnotationFilter_1.7.0    GenomicFeatures_1.35.3   
 [5] AnnotationDbi_1.45.0      Biobase_2.43.0           
 [7] GenomicRanges_1.35.1      GenomeInfoDb_1.19.1      
 [9] IRanges_2.17.1            S4Vectors_0.21.5         
[11] BiocGenerics_0.29.1       BiocManager_1.30.4
ADD REPLYlink modified 12 months ago • written 12 months ago by shepherl ♦♦ 1.7k

I tried 


edb <- EnsDb.Hsapiens.v86
Tx <- transcripts(edb)


The console output is as following:

> library(EnsDb.Hsapiens.v86)
> edb <- EnsDb.Hsapiens.v86
Error: object 'EnsDb.Hsapiens.v86' not found
> Tx <- transcripts(edb)
Error in transcripts(edb) : object 'edb' not found
> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=German_Austria.1252  LC_CTYPE=German_Austria.1252    LC_MONETARY=German_Austria.1252
[4] LC_NUMERIC=C                    LC_TIME=German_Austria.1252    

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

other attached packages:
 [1] EnsDb.Hsapiens.v75_2.99.0               TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [3] BiocManager_1.30.4                      rhdf5_2.26.0                           
 [5] DESeq2_1.22.1                           SummarizedExperiment_1.12.0            
 [7] DelayedArray_0.8.0                      BiocParallel_1.16.0                    
 [9] matrixStats_0.54.0                      forcats_0.3.0                          
[11] stringr_1.3.1                           dplyr_0.7.8                            
[13] purrr_0.2.5                             tidyr_0.8.2                            
[15] tibble_1.4.2                            ggplot2_3.1.0                          
[17] tidyverse_1.2.1                         readr_1.1.1                            
[19] tximport_1.10.0                         EnsDb.Hsapiens.v86_2.99.0              
[21] ensembldb_2.6.2                         AnnotationFilter_1.6.0                 
[23] GenomicFeatures_1.34.1                  AnnotationDbi_1.44.0                   
[25] Biobase_2.42.0                          GenomicRanges_1.34.0                   
[27] GenomeInfoDb_1.18.1                     IRanges_2.16.0                         
[29] S4Vectors_0.20.1                        BiocGenerics_0.28.0                    

loaded via a namespace (and not attached):
 [1] colorspace_1.3-2         htmlTable_1.12           XVector_0.22.0           base64enc_0.1-3         
 [5] rstudioapi_0.8           bit64_0.9-7              lubridate_1.7.4          xml2_1.2.0              
 [9] splines_3.5.1            geneplotter_1.60.0       knitr_1.20               Formula_1.2-3           
[13] jsonlite_1.5             Rsamtools_1.34.0         broom_0.5.0              annotate_1.60.0         
[17] cluster_2.0.7-1          compiler_3.5.1           httr_1.3.1               backports_1.1.2         
[21] assertthat_0.2.0         Matrix_1.2-15            lazyeval_0.2.1           cli_1.0.1               
[25] acepack_1.4.1            htmltools_0.3.6          prettyunits_1.0.2        tools_3.5.1             
[29] bindrcpp_0.2.2           gtable_0.2.0             glue_1.3.0               GenomeInfoDbData_1.2.0  
[33] Rcpp_1.0.0               cellranger_1.1.0         Biostrings_2.50.1        nlme_3.1-137            
[37] rtracklayer_1.42.0       rvest_0.3.2              XML_3.98-1.16            zlibbioc_1.28.0         
[41] scales_1.0.0             hms_0.4.2                ProtGenerics_1.14.0      RColorBrewer_1.1-2      
[45] yaml_2.2.0               curl_3.2                 memoise_1.1.0            gridExtra_2.3           
[49] biomaRt_2.38.0           rpart_4.1-13             latticeExtra_0.6-28      stringi_1.2.4           
[53] RSQLite_2.1.1            genefilter_1.64.0        checkmate_1.8.5          rlang_0.3.0.1           
[57] pkgconfig_2.0.2          bitops_1.0-6             lattice_0.20-38          Rhdf5lib_1.4.0          
[61] bindr_0.1.1              GenomicAlignments_1.18.0 htmlwidgets_1.3          bit_1.1-14              
[65] tidyselect_0.2.5         plyr_1.8.4               magrittr_1.5             R6_2.3.0                
[69] Hmisc_4.1-1              DBI_1.0.0                pillar_1.3.0             haven_1.1.2             
[73] foreign_0.8-71           withr_2.1.2              survival_2.43-1          RCurl_1.95-4.11         
[77] nnet_7.3-12              modelr_0.1.2             crayon_1.3.4             progress_1.2.0          
[81] locfit_1.5-9.1           grid_3.5.1               readxl_1.1.0             data.table_1.11.8       
[85] blob_1.1.1               digest_0.6.18            xtable_1.8-3             munsell_0.5.0           

Thank you for your quick reply!

ADD REPLYlink modified 12 months ago • written 12 months ago by michaelschoeber10

What is the output when you do

ADD REPLYlink written 12 months ago by shepherl ♦♦ 1.7k

In that case the output is 

> library(EnsDb.Hsapiens.v86)
> ls('package:EnsDb.Hsapiens.v86')
ADD REPLYlink written 12 months ago by michaelschoeber10

I'm still unable to reproduce this - Could you try reinstalling with

ADD REPLYlink written 12 months ago by shepherl ♦♦ 1.7k

This is indeed strange. By default, when loading the EnsDb.Hsapiens.v86 all sqlite files in the package's extdata folder get bound and exported as a variable. Can you verify that your package contains such an sqlite file?

> dir(system.file("extdata", package = "EnsDb.Hsapiens.v86"))
[1] "EnsDb.Hsapiens.v86.sqlite"
ADD REPLYlink modified 12 months ago • written 12 months ago by Johannes Rainer1.5k
> dir(system.file("extdata", package = "EnsDb.Hsapiens.v86"))

I think this is more of an installation problem than anything. I will try to reinstall R.

Thank you for your help so far!

ADD REPLYlink written 12 months ago by michaelschoeber10

Yes, looks like that. You could also specifically look in the package libary directory  (EnsDb.Hsapiens.v86/extdata) in the path where your library is (which you get with .libPaths() in R).

Please let me know if re-installation solved the problem.

ADD REPLYlink written 12 months ago by Johannes Rainer1.5k
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