[ensembl-dev] Problems with biomaRt

[Anne Lyle]

Hi Türküler

Sorry about this. We’ve been having some DNS issues owing to our data centre migration, which may be why the archive URLs are not being recognised. I’ll pass this on to our IT department to check that the redirects are in place.

Cheers

Anne



> On 19 Mar 2020, at 22:42, Türküler Özgümüş <turkulerc at gmail.com> wrote:
> 
> Hi,
> 
> I had a problem with the below code. It is not about the code itself since the first time I ran it I got the results. But then because of a downstream error, unrelated to this one, I had to run it again. I ran it several times and every time there were different error messages until at the end it ran as expected. I got my results but I don't understand the problem here. So, I am reporting :) 
> 
> Best regards,
> Turkuler
> 
> Code:
> library(biomaRt)
> mart <- useEnsembl(biomart = "ENSEMBL_MART_ENSEMBL", version=99, dataset = "hsapiens_gene_ensembl")
> tx2gene <- getBM(attributes = c("ensembl_transcript_id", "transcript_version", "ensembl_gene_id", "external_gene_name","entrezgene_id"), mart = mart)
> 
> Message #1
> Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
>   Unexpected format to the list of available marts.
> Please check the following URL manually, and try ?listMarts for advice.
> http://dec2019.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt <http://dec2019.archive.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt>
> Calls: useEnsembl -> useMart -> listMarts
> Execution halted
> 
> Message #2 (Archive version changes but error message stays the same here)
> Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE,  : 
>   Unexpected format to the list of available marts.
> Please check the following URL manually, and try ?listMarts for advice.
> http://jan2020.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt <http://jan2020.archive.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt>
> Calls: useEnsembl -> useMart -> listMarts
> Execution halted
> 
> Message #3
> Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
>   line 1 did not have 3 elements
> Calls: getBM -> read.table -> scan
> Execution halted
> 
> Message #4
> Error in useMart(biomart = biomart, dataset = dataset, host = host, verbose = verbose) : 
>   Incorrect BioMart name, use the listMarts function to see which BioMart databases are available
> Calls: useEnsembl -> useMart
> Execution halted
> 
> Message #5 (In this case it continues to the following lines without any problem)
> Note: requested host was redirected from
> http://jan2020.archive.ensembl.org <http://jan2020.archive.ensembl.org/> to http://www.ensembl.org:80/biomart/martservice <http://www.ensembl.org/biomart/martservice>
> This often occurs when connecting to the archive URL for the current Ensembl release
> You can check the current version number using listEnsemblArchives()
> 
> sessionInfo()
> R version 3.5.2 (2018-12-20)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Red Hat Enterprise Linux
> 
> Matrix products: default
> BLAS: /gpfs/gpfs0/RHEL7-Tools/Software/R/3.5.2/lib64/R/lib/libRblas.so
> LAPACK: /gpfs/gpfs0/RHEL7-Tools/Software/R/3.5.2/lib64/R/lib/libRlapack.so
> 
> locale:
>  [1] LC_CTYPE=C                 LC_NUMERIC=C              
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
>  [1] biomaRt_2.38.0  forcats_0.4.0   stringr_1.4.0   dplyr_0.8.3    
>  [5] purrr_0.3.2     readr_1.3.1     tidyr_0.8.3     tibble_2.1.3   
>  [9] ggplot2_3.2.0   tidyverse_1.2.1
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