biomaRt: error using useDataset or useMart
1
4
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lpsantamaria ▴ 40
@lpsantamaria-13930
Last seen 3.8 years ago

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

 

 

 

 

software error biomart usemart usedataset • 5.9k views
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2
Entering edit mode
Mike Smith ★ 5.2k
@mike-smith
Last seen 49 minutes ago
EMBL Heidelberg / de.NBI

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

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

 

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0
Entering edit mode

It works perfectly now, thank you!

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0
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Please, was the code  updated in both Bioconductor release and devel ?

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0
Entering edit mode

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.

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0
Entering edit mode

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

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