biomaRt: error using useDataset or useMart
1
4
Entering edit mode
lpsantamaria ▴ 40
@lpsantamaria-13930
Last seen 7.0 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 • 8.7k views
ADD COMMENT
2
Entering edit mode
Mike Smith ★ 6.6k
@mike-smith
Last seen 16 hours ago
EMBL Heidelberg

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 COMMENT
0
Entering edit mode

It works perfectly now, thank you!

ADD REPLY
0
Entering edit mode

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

ADD REPLY
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.

ADD REPLY
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

ADD REPLY

Login before adding your answer.

Traffic: 489 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6