Question: R failing to load genome files from EnsDb.Hsapiens.v86
1
gravatar for michaelschoeber
5 months ago by
Austria/Vienna/CCRI
michaelschoeber10 wrote:

Hi, 

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!

Best,

Michael

ADD COMMENTlink modified 3 months ago by Bioconductor Community ♦♦ 0 • written 5 months ago by michaelschoeber10
1

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
|DBSCHEMAVERSION: 2.0
| 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/libRblas.so
LAPACK: /home/lori/bin/R-devel/lib/libRlapack.so

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=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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 5 months ago • written 5 months ago by shepherl ♦♦ 1.3k

I tried 

library(EnsDb.Hsapiens.v86)

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

sessionInfo()
 

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

locale:
[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 5 months ago • written 5 months ago by michaelschoeber10
1

What is the output when you do

library(EnsDb.Hsapiens.v86)
ls('package:EnsDb.Hsapiens.v86')
ADD REPLYlink written 5 months ago by shepherl ♦♦ 1.3k

In that case the output is 

> library(EnsDb.Hsapiens.v86)
> ls('package:EnsDb.Hsapiens.v86')
character(0)
> 
ADD REPLYlink written 5 months ago by michaelschoeber10
1

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

BiocManager::install("EnsDb.Hsapiens.v86")
ADD REPLYlink written 5 months ago by shepherl ♦♦ 1.3k
1

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 5 months ago • written 5 months ago by Johannes Rainer1.4k
> dir(system.file("extdata", package = "EnsDb.Hsapiens.v86"))
character(0)

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 5 months ago by michaelschoeber10
1

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 5 months ago by Johannes Rainer1.4k
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