[biomart-users] Error in curl::curl_fetch_memory(url, handle = handle) : Maximum (10) redirects followed

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[biomart-users] 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

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[biomart-users] Re: Error in curl::curl_fetch_memory(url, handle = handle) : Maximum (10) redirects followed

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

On Wednesday, 11 July 2018 18:21:18 UTC+2, Helen Kershaw wrote:
Hi,

We have a user wanting to use biomart on our HPC cluster
We are hitting the max number of redirects when using host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org" from our HPC cluster. Using host="<a href="http://useast.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHq0BN39xFnGLBUD0wbyHuzAFpp_Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHq0BN39xFnGLBUD0wbyHuzAFpp_Q&#39;;return true;">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="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org":

> mouse = useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org")

> human = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="<a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">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="<a href="http://useast.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHq0BN39xFnGLBUD0wbyHuzAFpp_Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHq0BN39xFnGLBUD0wbyHuzAFpp_Q&#39;;return true;">http://useast.ensembl.org":


> human = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="<a href="http://useast.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHq0BN39xFnGLBUD0wbyHuzAFpp_Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHq0BN39xFnGLBUD0wbyHuzAFpp_Q&#39;;return true;">http://useast.ensembl.org")

> mouse = useMart("ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host="<a href="http://useast.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHq0BN39xFnGLBUD0wbyHuzAFpp_Q&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fuseast.ensembl.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHq0BN39xFnGLBUD0wbyHuzAFpp_Q&#39;;return true;">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 <a href="http://Chromosome.scaffold.name" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2FChromosome.scaffold.name\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE8dgEAUTWwZCJfwIH3GhCBeg3gSQ&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2FChromosome.scaffold.name\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE8dgEAUTWwZCJfwIH3GhCBeg3gSQ&#39;;return true;">Chromosome.scaffold.name Gene.start..bp. <a href="http://RefSeq.mRNA.ID" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2FRefSeq.mRNA.ID\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHWaJeJckDJ0e1uFPBYXB69sjjSlw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2FRefSeq.mRNA.ID\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHWaJeJckDJ0e1uFPBYXB69sjjSlw&#39;;return true;">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

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Re: [biomart-users] Re: Error in curl::curl_fetch_memory(url, handle = handle) : Maximum (10) redirects followed

Helen Kershaw
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

On Fri, Jul 13, 2018 at 8:55 AM, Mike Smith <[hidden email]> wrote:
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


On Wednesday, 11 July 2018 18:21:18 UTC+2, Helen Kershaw wrote:
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

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Helen Kershaw
Application Scientist
Center for Computation and Visualization
Brown University
XSEDE Campus Champion
http://www.ccv.brown.edu

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