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Question: biomaRt: error using useDataset or useMart
4
gravatar for lpsantamaria
10 months ago by
lpsantamaria40
lpsantamaria40 wrote:

I'm trying to get the "hsapiens_gene_ensembl" dataset from the "ENSEMBL_MART_ENSEMBL" mart.

Using both of these functions:

human <- useMart( "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "www.ensembl.org" )

human <- useDataset( "hsapiens_gene_ensembl", mart = useMart( "ensembl" ) )

I sometimes get the following error message:

Error in checkDataset(dataset = dataset, mart = mart) :
  The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.

If I run the same line calling useMart or useDataset, several times it eventually works. Apparently, inside the checkDataset() function, listDatasets()$dataset returns a set of 50 datasets: sometimes hsapiens_gene_ensembl is one of them (and the call to useMart works), and sometimes not (and I get the error message).

Sesion Info:

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

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

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

other attached packages:
 [1] GSEABase_1.40.1                         graph_1.56.0                            annotate_1.56.1                        
 [4] XML_3.98-1.9                            TFEA.ChIP_0.99.7                        org.Hs.eg.db_3.5.0                     
 [7] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.30.0                  AnnotationDbi_1.40.0                   
[10] Biobase_2.38.0                          GenomicRanges_1.30.0                    GenomeInfoDb_1.14.0                    
[13] IRanges_2.12.0                          S4Vectors_0.16.0                        BiocGenerics_0.24.0                    
[16] dplyr_0.7.4                             biomaRt_2.34.0                         

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.8.0 progress_1.1.2             lattice_0.20-35            yaml_2.1.15                rtracklayer_1.38.2        
 [6] blob_1.1.0                 rlang_0.1.4                glue_1.2.0                 DBI_0.7                    BiocParallel_1.12.0       
[11] bit64_0.9-7                bindrcpp_0.2               matrixStats_0.52.2         GenomeInfoDbData_0.99.1    bindr_0.1                 
[16] stringr_1.2.0              zlibbioc_1.24.0            Biostrings_2.46.0          memoise_1.1.0              knitr_1.17                
[21] RUnit_0.4.31               Rcpp_0.12.14               xtable_1.8-2               DelayedArray_0.4.1         XVector_0.18.0            
[26] bit_1.1-12                 Rsamtools_1.30.0           RMySQL_0.10.13             digest_0.6.12              stringi_1.1.6             
[31] grid_3.4.3                 tools_3.4.3                bitops_1.0-6               magrittr_1.5               RCurl_1.95-4.8            
[36] tibble_1.3.4               RSQLite_2.0                pkgconfig_2.0.1            Matrix_1.2-11              prettyunits_1.0.2         
[41] assertthat_0.2.0           R6_2.2.2                   GenomicAlignments_1.14.1   compiler_3.4.3

 

 

 

 

ADD COMMENTlink modified 10 months ago by Mike Smith3.0k • written 10 months ago by lpsantamaria40
2
gravatar for Mike Smith
10 months ago by
Mike Smith3.0k
EMBL Heidelberg / de.NBI
Mike Smith3.0k wrote:

Several people have reported this issue already.  Please try installing the latest developmental version of the package using:

BiocInstaller::biocLite('grimbough/biomaRt')
library(biomaRt)

 

ADD COMMENTlink written 10 months ago by Mike Smith3.0k

It works perfectly now, thank you!

ADD REPLYlink written 10 months ago by lpsantamaria40

Please, was the code  updated in both Bioconductor release and devel ?

ADD REPLYlink written 10 months ago by tiagochst150

Yes, the necessary changes have been made to both the release and devel version.  It take a little while for changes to propagate into the download, but it looks like they're there now.  If you're using the release branch then you need biomaRt version 2.34.1 or greater.

ADD REPLYlink written 10 months ago by Mike Smith3.0k

FYI

> library(biomaRt)
Error: package or namespace load failed for ‘biomaRt’ in get0(".packageName", env, inherits = FALSE):
 lazy-load database '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/biomaRt/R/biomaRt.rdb' is corrupt

ADD REPLYlink written 5 months ago by JoeMG0
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