Error using parasiteMart
2
I would like to run a WormBaseParasite Biomart in R
https://parasite.wormbase.org/biomart/martview/d0d9a510b4b2a07b52f24615ad26107f
I got an xml and tried to run in R but errors keep coming up
> library(biomaRt)
> listMarts(host = "parasite.wormbase.org")
Error in `[.data.frame`(marts, , c("biomart", "version")) :
undefined columns selected
> wormbase <- useMart(biomart = "parasite_mart",
+ host = "https://parasite.wormbase.org",
+ port = 443)
Error in .useMart(biomart, dataset, host = host, path = path, port = port, :
Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
And I realise such error appear in the Biocoductor manual too "Using a BioMart other than Ensembl"
https://www.bioconductor.org/packages/devel/bioc/vignettes/biomaRt/inst/doc/accessing_other_marts.html
Could someone pls help as the website of wormbaseparasite biomart is never working when I try to export the result.
WormBaseParasite
Ensembl
parasite_mart
Wormbase
BioMart
• 593 views
•
link
updated 6 months ago by
GenoMax
148k
•
written 6 months ago by
Emily
▴
20
This worked for me:
> library(biomaRt)
> listMarts(host = "parasite.wormbase.org")
biomart version
1 parasite_mart WBPS 19 Mart
> useMart(biomart = "parasite_mart", host = "parasite.wormbase.org")
> sessionInfo()
R version 4.3.0 (2023-04-21 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.utf8 LC_CTYPE=English_United Kingdom.utf8 LC_MONETARY=English_United Kingdom.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.utf8
time zone: Europe/London
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.56.1
loaded via a namespace (and not attached):
[1] rappdirs_0.3.3 utf8_1.2.4 generics_0.1.3 bitops_1.0-7 xml2_1.3.5 RSQLite_2.3.7 stringi_1.7.12
[8] hms_1.1.3 digest_0.6.33 magrittr_2.0.3 fastmap_1.1.1 blob_1.2.4 progress_1.2.2 AnnotationDbi_1.62.2
[15] GenomeInfoDb_1.36.2 DBI_1.2.1 BiocManager_1.30.22 httr_1.4.7 purrr_1.0.2 fansi_1.0.6 XML_3.99-0.14
[22] Biostrings_2.68.1 cli_3.6.1 rlang_1.1.1 crayon_1.5.2 dbplyr_2.5.0 XVector_0.40.0 Biobase_2.60.0
[29] bit64_4.0.5 cachem_1.0.8 tools_4.3.0 memoise_2.0.1 dplyr_1.1.2 GenomeInfoDbData_1.2.10 filelock_1.0.3
[36] BiocGenerics_0.46.0 curl_5.2.0 vctrs_0.6.5 R6_2.5.1 png_0.1-8 stats4_4.3.0 lifecycle_1.0.4
[43] BiocFileCache_2.8.0 zlibbioc_1.46.0 KEGGREST_1.40.1 stringr_1.5.0 S4Vectors_0.38.1 IRanges_2.34.1 bit_4.0.5
[50] pkgconfig_2.0.3 pillar_1.9.0 glue_1.7.0 tibble_3.2.1 tidyselect_1.2.1 compiler_4.3.0 prettyunits_1.1.1
[57] RCurl_1.98-1.12
Thanks for reporting this. There was an issue in more recent versions of biomaRt where it failed to parse the list of available datasets advertised by the WormBase ParaSite Mart.
This has now been updated in biomaRt v2.60.1 and should update on Bioconductor in a few days. The vignette will then also update to reflect the fixes.
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my R is most updated version 4.4.0 and I'm using windows PC too, not sure why it doesn't work for me.
even I tried
it shows the same error.
It worked when I used R 4.3.1, thanks!