Error in curl::curl_fetch_memory(url, handle = handle) : Maximum (10) redirects followed

[Helen Kershaw]

Hi,

We have a user wanting to use biomart on our HPC cluster
We are hitting the max number of redirects when using host="www.ensembl.org" from our HPC cluster. Using host="http://useast.ensembl.org" seems fine.  The output from both is given at the bottom of this email. 

Is there an option we can give to getLDS (or other biomart settings) to follow the redirects?

Cheers,
Helen

Using host="www.ensembl.org":

> mouse = useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host="www.ensembl.org")

> human = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org")

> getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", 

+ values = "TP53",mart = human, attributesL = c("refseq_mrna","chromosome_name","start_position"), 

+ martL = mouse)

Error in curl::curl_fetch_memory(url, handle = handle) : 

  Maximum (10) redirects followed

Using host="http://useast.ensembl.org":

> human = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="http://useast.ensembl.org")

> mouse = useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host="http://useast.ensembl.org")

> getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", 

+ values = "TP53",mart = human, attributesL = c("refseq_mrna","chromosome_name","start_position"), 

+ martL = mouse)

  HGNC.symbol Chromosome.scaffold.name Gene.start..bp. RefSeq.mRNA.ID

1        TP53                       17         7661779               

2        TP53                       17         7661779   NM_001127233

3        TP53                       17         7661779      NM_011640

  Chromosome.scaffold.name.1 Gene.start..bp..1

1                         11          69580359

2                         11          69580359

3                         11          69580359

[Mike Smith]

Hi Helen,

Can you include the output of sessionInfo() so I can see what version of biomaRt you have?  Recent versions of biomaRt should no be redirected when connecting to Ensembl (I explicitly turn of the geolocation redirection) but it may be that I've missed something in the package code.

Thanks,

Mike

[Kershaw, Helen]

Hi Mike,

Here is the output from sessionInfo():

> sessionInfo()

R version 3.4.2 (2017-09-28)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: CentOS release 6.7 (Final)

Matrix products: default

BLAS: /gpfs/runtime/opt/R/3.4.2/lib64/R/lib/libRblas.so

LAPACK: /gpfs/runtime/opt/R/3.4.2/lib64/R/lib/libRlapack.so

locale:

 [1] LC_CTYPE=en_US.UTF-8       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_2.34.2

loaded via a namespace (and not attached):

 [1] Rcpp_0.12.15         AnnotationDbi_1.40.0 magrittr_1.5        

 [4] BiocGenerics_0.24.0  progress_1.1.2       IRanges_2.12.0      

 [7] bit_1.1-12           R6_2.2.2             rlang_0.2.0         

[10] httr_1.3.1           stringr_1.3.0        blob_1.1.0          

[13] tools_3.4.2          parallel_3.4.2       Biobase_2.38.0      

[16] DBI_0.8              bit64_0.9-7          digest_0.6.15       

[19] assertthat_0.2.0     tibble_1.4.2         S4Vectors_0.16.0    

[22] bitops_1.0-6         curl_3.1             RCurl_1.95-4.10     

[25] memoise_1.1.0        RSQLite_2.0          stringi_1.1.6       

[28] compiler_3.4.2       pillar_1.2.1         prettyunits_1.0.2   

[31] stats4_3.4.2         XML_3.98-1.10    

Cheers,

Helen

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Helen Kershaw

Application Scientist

Center for Computation and Visualization
Brown University

XSEDE Campus Champion
http://www.ccv.brown.edu