[biomart-users] NA results when running getBM

classic Classic list List threaded Threaded
1 message Options
Reply | Threaded
Open this post in threaded view
|

[biomart-users] NA results when running getBM

Junehawk Lee
Hi, I encountered a weird error when using getBM.

getBM returns NA when run by specific user.

I found getBM works fine with other accounts.

Can anyone help me resolve this issue?

> library(biomaRt)
> ensembl <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
> getBM(attributes = c("hgnc_symbol", "entrezgene"),filters = "hgnc_symbol",values = "MTOR" ,mart = ensembl, verbose=T)
<?xml version='1.0' encoding='UTF-8'?><!DOCTYPE Query><Query  virtualSchemaName = 'default' uniqueRows = '1' count = '0' datasetConfigVersion = '0.6' header='1' requestid= 'biomaRt'> <Dataset name = 'hsapiens_gene_ensembl'><Attribute name = 'hgnc_symbol'/><Attribute name = 'entrezgene'/><Filter name = 'hgnc_symbol' value = 'MTOR' /></Dataset></Query>
#################
Results from server:
[1] NA
Error in if (gsub("\n", "", postRes, fixed = TRUE, useBytes = TRUE) ==  :

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=ko_KR.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=ko_KR.UTF-8        LC_COLLATE=ko_KR.UTF-8
 [5] LC_MONETARY=ko_KR.UTF-8    LC_MESSAGES=ko_KR.UTF-8
 [7] LC_PAPER=ko_KR.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=ko_KR.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] biomaRt_2.37.2

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.17         AnnotationDbi_1.40.0 magrittr_1.5
 [4] BiocGenerics_0.24.0  hms_0.4.2            progress_1.2.0
 [7] IRanges_2.12.0       bit_1.1-14           R6_2.2.2
[10] rlang_0.2.1          httr_1.3.1           stringr_1.3.1
[13] blob_1.1.1           tools_3.5.0          parallel_3.5.0
[16] Biobase_2.38.0       DBI_1.0.0            bit64_0.9-7
[19] digest_0.6.15        assertthat_0.2.0     crayon_1.3.4
[22] S4Vectors_0.16.0     bitops_1.0-6         curl_3.2
[25] RCurl_1.95-4.10      memoise_1.1.0        RSQLite_2.1.1
[28] stringi_1.2.3        compiler_3.5.0       prettyunits_1.0.2
[31] stats4_3.5.0         XML_3.98-1.11        pkgconfig_2.0.1




--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.