[ensembl-dev] Problems with biomaRt

[Türküler Özgümüş]

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
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
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 to
http://www.ensembl.org:80/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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