Biomart server almost continuously down?

[Francesco Mazzarotto]

Hello,
I am working with a self-developed R script that annotates sets of variants (through the R package biomaRt) retrieving variant information from the "hsapiens_gene_ensembl" dataset.
In the last few days I noticed that the service is not working properly (I get info back from the server in a non continuous way...maybe it works for 2 minutes, then it does not for 5 minutes, then works again and so on).
The problem is that I keep very often getting the error:

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:


Is this a problem of the Biomart web server, or am I doing something wrong? I really would not know how to resolve this issue, and it is vital for my work!

Thank you very much
Francesco

[Rhoda Kinsella]

Hi Francesco

As a work around, set your host to use the BioMart databases at www.ensembl.org and you can access the same data. 

library(biomaRt)
ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")

etc...

Hope that helps

Cheers

Rhoda

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Rhoda Kinsella Ph.D.

Ensembl Production Project Leader

European Bioinformatics Institute (EMBL-EBI)

European Molecular Biology Laboratory

Wellcome Trust Genome Campus

Hinxton,

Cambridge

CB10 1SD

[Arek Kasprzyk]

Hi Francesco,

thank you for reporting this. There seems to be a problem with the database server.

Please bear with us while we fix the issue

a

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[Alejandra Eugenia Medina Rivera]

Hi

I'm having problems also loading on R

listMarts()

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.

and the web page seams to be down.

I'm using Rhoda's workaround to keep working, thanks!

Cheers

Alejandra

[Arek Kasprzyk]

Hi Alejandra,

thank you for reporting this. The service should be restored now

a

"When the gods wish to punish us, they answer our prayers"

― Oscar Wilde

[JL LT]

Dear Arek,

Is it possible that the system cotinues down?
I've been trying to use biomaRt (the R-package) in diferrent scripts (I had tested before with excellent results) and I keep receiving an error message referred to a problem on biomart servers.

I have several pipelines based in this awesome tool that will not work until that servers respond...

Have you noticed/experienced this problem lately?

Thanks in advance for your kind attention.

With best wises

JL

[Arek Kasprzyk]

Hi JL,

There have been several heavy queries doing distinct count on large snp tables and sitting there for a long time. It is important that we avoid doing that as this compromises the service that we can provide. I have now cleaned up the db server and i am  hoping that this should restore the service to its former glory ;)

a

[Katrin Hörmann]

Dear Arek, 

could it be that there's another issue like the previously reported happening at the moment?

I tried accessing yesterday and today and always receive the error message reported before.

Thanks for taking care of these issues.

Best, Katrin

[Arek Kasprzyk]

Hi Katrin,

could you try again please? I don't seem to be able to reproduce those errors

a

For more options, visit https://groups.google.com/d/optout.

--

Arek Kasprzyk, MD. MSc. Ph.D.

Head of Data Management
Center for Translational Genomics and Bioinformatics
San Raffaele Scientific Institute
Via Olgettina 58
20132 Milano
Italy

[Kevin Ttk]

Hi Arek and Katrin,

during the periode between 17/04/2014 and 22/04/2014, I also had the problem of Katrin several times.
I run several R-scripts in parallel (cmd), that use BiomaRt.

Greets,

Kevin

Op donderdag 17 april 2014 11:17:34 UTC+2 schreef Arek Kasprzyk:

[Katrin Hörmann]

Dear Arek, 

I tried again today several times and always failed.

I'm also working in R with the datasets/hosts/etc: 

library(biomaRt)

unimart <- useMart("unimart",dataset="uniprot",

                   host="www.ebi.ac.uk",path="/uniprot/biomart/martservice")

Whenever I start a query, it takes ages and at some points gets aborted with the error message mentioned before. 

[Arek Kasprzyk]

Hi guys,

there were several rouge queries on the backend that were compromising the service. I have now killed them and this hopefully should fix it

a

[Katrin Hörmann]

Hi Arek, 

thanks for taking care. 

Unfortunately, the service is still not working for me. Just tried it and still stuck with the following error message:

Error in value[[3L]](cond) : 
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

[Arek Kasprzyk]

guys:

the service is working fine here:

just tried:

http://www.biomart.org/biomart/martservice?type=registry

is it possible that you have some connectivity problems on your side?

a

[Katrin Hörmann]

Don't think it's connectivity problems from our side, as I'm able to access anything else and also able to establish a connection to biomart. 

Problems only start with queries, even such that ran successfully last week.

[Arek Kasprzyk]

Hi Katrin,

please send me the exact query that fails and i'll try to reproduce the problem here

[Katrin Hörmann]

ctrl.df <- read.csv2('20140325_Isobar_P5838.P5839.csv', header=TRUE, stringsAsFactors=F)

ctrl.df$protein.acs <- gsub("[,-].*",'',ctrl.df$protein.acs)

library(biomaRt)

unimart <- useMart("unimart",dataset="uniprot",

                   host="www.ebi.ac.uk",path="/uniprot/biomart/martservice")

go.terms=getBM(attributes=c("accession", "db2go_c__dm_description"), filters="accession",

               values=ctrl.df$protein.acs, mart=unimart)

The .csv file is in the attachment. For me, everything works fine until the function getBM is called.

Thanks for putting so much effort.

Best, Katrin

[Arek Kasprzyk]

HI Katrin,

this actually looks like a different problem (a problem with UniProt instance). Please see my reply earlier on today to Dana

https://groups.google.com/forum/?fromgroups#!topic/biomart-users/uXDl_MF__K4

(I am cc'ing Steven who runs this instance. Perhaps he can have some input to this problem)

a

[Steven Rosanoff]

Thank you for your input. We are aware of the issue and trying to correct it. It looks like the source is our tomcat web service consistantly timing out. I will let you know as soon as it is resolved.

Regards,
Steve

-- 
Steven Rosanoff
Software Engineer
EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, UK
Phone: +44 (0)1223 494565
Email: sros...@ebi.ac.uk 

Learn more about EBI at: http://www.ebi.ac.uk

[Bernard Chang]

Hello Steve, could you post an update when things may be working again.  I got the same error message as others have reported.

Cheers,

Bernard

[Steven Rosanoff]

FYI,

We have fixed the performance issues with UniProt Biomart. Please go ahead and re-test your queries.

Regards,
Steve

[Alejandra Eugenia Medina Rivera]

Hi
The service seams to be down again.

Cheers

Alejandra

[Arek Kasprzyk]

Hi Alejandra,

i just checked and it seems to be running normally?

What problems exactly are you experiencing?

a

For more options, visit https://groups.google.com/d/optout.

[Alejandra Eugenia Medina Rivera]

I couldn't start the ensembl biomart session
 >ensembl <- useMart("ensembl")

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML:

Then I checked I had internet and the page seamed to be down, now is up, maybe it was just a momentary thing.

Thanks!

Alejandra

--

Alejandra Eugenia Medina Rivera.

SickKids

[Jose Manuel Garcia Manteiga]

Hi, 

I am having problems to connect to biomart server with biomaRt, too.

We have a cluster that can perfectly connect to biomaRt on host:www.biomart.org:80/biomart/martservice. However, locally in my Mac, when connected with the same institutional network in the lab, we cannot reach the server with the classical error:

Error in value[[3L]](cond) : 

  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.

I reach the www.biomart.org with no problems and the host address in the browser so I do not think there is a problem with proxy settings, and our systems manager says the web page is not filtered. I was wondering whether there is some issue on your side that could affect differently my two biomaRt versions trying to connect, one on the cluster (2.18) and the other locally (2.22). I let you known here my sessionInfo() for both:

The one working from a cluster:

sessionInfo()

R version 3.0.1 (2013-05-16)

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

locale:

 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US       

 [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US   

 [7] LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C        

[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C 

attached base packages:

[1] parallel  stats     graphics  grDevices utils     datasets  methods  

[8] base     

other attached packages:

 [1] R.utils_1.33.0     R.oo_1.18.0        R.methodsS3_1.6.1  Roleswitch_1.4.0  

 [5] DBI_0.3.0          Biobase_2.22.0     Biostrings_2.30.1  XVector_0.2.0     

 [9] IRanges_1.20.7     BiocGenerics_0.8.0 biomaRt_2.18.0     microRNA_1.24.0   

[13] plotrix_3.5-7      reshape_0.8.5      pracma_1.7.0      

loaded via a namespace (and not attached):

[1] GenomicRanges_1.14.4 plyr_1.8.1           Rcpp_0.11.2         

[4] RCurl_1.95-4.3       stats4_3.0.1         tools_3.0.1         

[7] XML_3.98-1.1 

The one not working in local:

R version 3.1.1 (2014-07-10)

Platform: x86_64-apple-darwin13.1.0 (64-bit)

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:

[1] biomaRt_2.22.0     limma_3.22.1       R.utils_1.34.0     R.oo_1.18.0        R.methodsS3_1.6.1  vimcom.plus_0.9-93 setwidth_1.0-3    

[8] colorout_1.0-2    

loaded via a namespace (and not attached):

 [1] acepack_1.3-3.3           annotate_1.44.0           AnnotationDbi_1.28.0      base64enc_0.1-2           BatchJobs_1.4            

 [6] BBmisc_1.7                Biobase_2.26.0            BiocGenerics_0.12.0       BiocParallel_1.0.0        bitops_1.0-6             

[11] brew_1.0-6                caTools_1.17.1            checkmate_1.5.0           cluster_1.15.3            codetools_0.2-9          

[16] colorspace_1.2-4          DBI_0.3.1                 DESeq2_1.6.1              digest_0.6.4              fail_1.2                 

[21] foreach_1.4.2             foreign_0.8-61            Formula_1.1-2             gdata_2.13.3              genefilter_1.48.1        

[26] geneplotter_1.44.0        GenomeInfoDb_1.2.0        GenomicRanges_1.18.1      ggplot2_1.0.0             gplots_2.14.2            

[31] grid_3.1.1                gtable_0.1.2              gtools_3.4.1              Hmisc_3.14-5              IRanges_2.0.0            

[36] iterators_1.0.7           KernSmooth_2.23-13        lattice_0.20-29           latticeExtra_0.6-26       locfit_1.5-9.1           

[41] MASS_7.3-35               munsell_0.4.2             nnet_7.3-8                parallel_3.1.1            plyr_1.8.1               

[46] proto_0.3-10              RColorBrewer_1.0-5        Rcpp_0.11.3               RcppArmadillo_0.4.450.1.0 RCurl_1.95-4.3           

[51] reshape2_1.4              rpart_4.1-8               RSQLite_0.11.4            S4Vectors_0.4.0           scales_0.2.4             

[56] sendmailR_1.2-1           splines_3.1.1             stats4_3.1.1              stringr_0.6.2             survival_2.37-7          

[61] tools_3.1.1               XML_3.98-1.1              xtable_1.7-4              XVector_0.6.0            

Thanks in advance for your help.

Jose

[Arek Kasprzyk]

Ciao Jose,

long time, no see ;)

Let's try to simplify the problem a bit by bypassing biomaRt layer altogether. Please run this simple test from your cluster and your mac:

wget -O registry_test.xml http://www.biomart.org/biomart/martservice?type=registry

and let me know if you are getting the correct output in the registry_test.xml

cheers,

a

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[Jose Manuel Garcia Manteiga]

Hi Arek!

I asked also our systems manager and finally we worked it out. It seemed that at some level the firewall filters were not defined properly. They have now opened the right ports, we have access and it is working fine from local and from the cluster without any modification of the R script.

Thanks!

--

--------------------------------------

Jose M. Garcia Manteiga PhD

Data Analysis in Functional Genomics

Center for Translational Genomics and BioInformatics

Dibit2-Basilica, 4A3

San Raffaele Scientific Institute

Via Olgettina 58, 20132 Milano (MI), Italy

Tel: +39-02-2643-9144

e-mail: garciamantei...@hsr.it 

[Darya Vanichkina]

at some level the firewall filters were not defined properly. They have now opened the right ports, we have access and it is working fine from local and from the cluster without any modification of the R script.

Hi! I'm having the exact same problem, and was wondering whether you could please elaborate as to which ports/settings you actually had to have modified to get it to work? Thanks in advance!!! 

e-mail: garciamanteiga.josem...@hsr.it 

[Arek Kasprzyk]

Hi Darya,

sorry for not replying sooner but i misplaced your email somehow.

I am probably not the best person to answer your question but this depends what port the service that you are trying to access is running on. For most this would be port 80 (e.g Ensembl)

a.

--

e-mail: garciamantei...@hsr.it 

[Maryiam Shöâeè]

Unfortunately for me, even 

(host="grch37.ensembl.org", path="/biomart/martservice") doesn't work! 

On Thursday, April 28, 2016 at 1:05:32 PM UTC+1, vasundha...@stonybrook.edu wrote:

Hello!

I seem to be having the same problem here since about 18 hours. I tried the "wget -O registry_test.xml http://www.biomart.org/biomart/martservice?type=registry" command and got "404 Not Found
2016-04-28 18:06:58 ERROR 404: Not Found."

Within R environment, listMarts gives me no result,
> library('biomaRt')
> listMarts()
[1] biomart version
<0 rows> (or 0-length row.names)

whereas specifying host as

listMarts(host="grch37.ensembl.org", path="/biomart/martservice") works. Yet for host = ensembl.org and biomart.org, it fails. I want to use chr38.

Please help!

> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.2 LTS)

locale:
 [1] LC_CTYPE=en_US.UTF-8    LC_NUMERIC=C            LC_TIME=C             
 [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=C           LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C          
[10] LC_TELEPHONE=C          LC_MEASUREMENT=C        LC_IDENTIFICATION=C   

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:

[1] biomaRt_2.26.1

loaded via a namespace (and not attached):

 [1] IRanges_2.4.8        parallel_3.2.5       DBI_0.3.1          
 [4] RCurl_1.95-4.8       Biobase_2.30.0       AnnotationDbi_1.32.3
 [7] RSQLite_1.0.0        S4Vectors_0.8.11     BiocGenerics_0.16.1
[10] stats4_3.2.5         bitops_1.0-6         XML_3.98-1.4  

[Menglan Xiang]

The server still seems to be down?

> mouse=useMart("ensembl", dataset="mmusculus_gene_ensembl")

Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) :

  The given dataset:  mmusculus_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.

[Arek Kasprzyk]

Hi,

try www.ensembl.org as a host. it has the latest data.

a.

On 28 April 2016 at 10:15, <vasundha...@stonybrook.edu> wrote:

Hello!

I seem to be having the same problem here since about 18 hours. I tried the "wget -O registry_test.xml http://www.biomart.org/biomart/martservice?type=registry" command and got "404 Not Found
2016-04-28 18:06:58 ERROR 404: Not Found."

Within R environment, listMarts gives me no result,
> library('biomaRt')
> listMarts()
[1] biomart version
<0 rows> (or 0-length row.names)

whereas specifying host as

listMarts(host="grch37.ensembl.org", path="/biomart/martservice") works. Yet for host = ensembl.org and biomart.org, it fails. I want to use chr38.

Please help!

> sessionInfo()
R version 3.2.5 (2016-04-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.2 LTS)

locale:
 [1] LC_CTYPE=en_US.UTF-8    LC_NUMERIC=C            LC_TIME=C             
 [4] LC_COLLATE=en_US.UTF-8  LC_MONETARY=C           LC_MESSAGES=en_US.UTF-8

 [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C          
[10] LC_TELEPHONE=C          LC_MEASUREMENT=C        LC_IDENTIFICATION=C   

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:

[1] biomaRt_2.26.1

loaded via a namespace (and not attached):

 [1] IRanges_2.4.8        parallel_3.2.5       DBI_0.3.1          
 [4] RCurl_1.95-4.8       Biobase_2.30.0       AnnotationDbi_1.32.3
 [7] RSQLite_1.0.0        S4Vectors_0.8.11     BiocGenerics_0.16.1
[10] stats4_3.2.5         bitops_1.0-6         XML_3.98-1.4  

On Wednesday, October 29, 2014 at 6:06:54 PM UTC+9, Arek Kasprzyk wrote:

Visit this group at https://groups.google.com/group/biomart-users.

[Arek Kasprzyk]

please set the host to http://www.ensembl.org/

a.

Visit this group at https://groups.google.com/group/biomart-users.

[Arek Kasprzyk]

Hi Maryiam,

please set the host to www.ensembl.org

it has the latest data.

a.

Visit this group at https://groups.google.com/group/biomart-users.

[Maryiam Shöâeè]

I have, but unfortunately nothing works. I have tried both the archived version and the up to date version. 

I am using 

ensembl = useMart(biomart = "ENSEMBL_MART_SNP", dataset = "hsapiens_snp",  host = "www.ensembl.org")

and then 

snpbiomart <- getBM(c("refsnp_id","allele"), filters = c("chr_name","start"), values = list(col1=snptrial2[,1],col2=snptrial2[,2]), mart = ensembl)

but I have been having the same problem for over a week regardless of what I try to rectify it. 

My data is in build 37 so at some point I would have to be able to use the archived versions. Any suggestions would be most welcomed. 

[Arek Kasprzyk]

Hi Miriam,

In this case we need to ask someone from Ensembl to help us (I cc'ed Thomas here).

a.

[Thomas Maurel]

Dear Miriam,

I’ve just tried the first command and I can connect to the ensembl variation mart. 

Could you please let me know if you get any error when you try to connect to www.ensembl.org?

Also, could you please share with me “snptrial2” or just a sample so I can have a look and test your query?

Thanks a lot,

Regards,

Thomas

--

Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

[Maryiam Shöâeè]

Hi Thomas

The problem isn't with the initial connecting. I can connect to ensembl even with the archived versions. The issue arises when I run the command getBM

snpbiomart <- getBM(c("refsnp_id","allele"), filters = c("chr_name","start"), values = list(col1=snptrial2[,1],col2=snptrial2[,2]), mart = ensembl)

 

I always get an error saying that I am either not connected to the internet or the server at Ensembl is down. 

I don't know if it is something I am doing wrong, or it's an error on Ensembl's side. Having used similar commands previously I know it should work, but everytime I have run this command, after hours and hours of waiting I get the error message I specified above. The SNPtrail2 file is minimal in size (attached). There is not a large amount of queries I am asking from biomart, so I don't understand why it's taking so long, and only to return an error. 

[Thomas Maurel]

Dear Maryiam,

Thanks for the detailed explanation but I am afraid that we are aware of this issue and are looking into it. Even if you are querying 3 small regions, there is quite a lot of data requested in the background which seems to timeout and return this error to you. Our Variation data has greatly increased for human and mouse recently and this is causing issue for this particular filter.

I will investigate and see if we can improve anything from our side. In the meantimes please feel free to use a different filter (e.g: variant name if you have them) or only query one region at a time.

Apologies for any inconvenience caused.

Best regards,

Thomas

<snptrial2.txt>

[Anthony Colombo]

I am having issues calling getBM,   with the host as www.ensembl.org,   what is the status ?  thank you very much

[Amonida Zadissa]

Dear Anthony and Afiqah,

There were some large queries that were causing the Ensembl BioMart
server to slow down. The server has now been restarted and works well.

Sorry for the inconvenience this has caused.

Best regards,
Amonida

--
Amonida Zadissa
Ensembl Production - QC
EMBL-EBI
Hinxton
England

We had to restart the Ensembl BioMart server due to some queries that
had locked the server. The server is now up and

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[Amonida Zadissa]

Dear Afiqah,

I'm afraid I can not help with the Biomart installation but Arek (CC'ed)
should be able to give some tips about installing BioMart locally.

Also, please send your emails to the biomart-users list instead of
private message as the list is the best place for asking questions and
getting useful pointers with regards to BioMart.

Best regards,
Amonida

--
Amonida Zadissa
Ensembl Production - QC
EMBL-EBI
Hinxton
England

On 29/05/2016 09:50, Afiqah Aleng wrote:> Hi,
> Thanks for your reply. I really appreciate it.
>
> Actually, I tried to create database using Biomart on Windows 8. I followed all
> the instructions using given manual. But, I failed to go to the next step after
> I clicked 'start server'. I still got a message as attached. Is it because of
> the server down? Or is it because of something else?
>
> I hope to hear from you soon.
>
> Thanks a lot.
>
> Afiqah

[Afiqah Aleng]

Hi,

Thanks for reply. Currently, I tried to create database using biomart on ubuntu. And it works. So, I guess, it might because of this tool is not working properly on Windows platform. 

Thanks 

Afiqah

[Arek Kasprzyk]

Hi Afiqah,

BioMart has only been really tested on *nix systems. Try Mac OS or Linux.

a.

[Afiqah Aleng]

Hi Arek,

Thanks for reply. 

Currently, I'm having problem on the home page after clicking on start server. The was 'an error has occurred on the server' stated on the home page. Is it because of the biomart server or something else?

Thanks 

Afiqah

<mailto:biomart-users+unsub...@googlegroups.com>.

[Mai Kawaguchi]

Hello

I'm having an issue connecting to biomart ensemble to convert affy u133 plus IDs to u133a IDs.

Is the server down for this moment?

When will it start functioning again?

thank you for your help.

Sincerely,

Mai Kawaguchi

[Dan Staines]

On 2016-06-08 03:41, Mai Kawaguchi wrote:
> Hello
> I'm having an issue connecting to biomart ensemble to convert affy
> u133 plus IDs to u133a IDs.

Could you please supply a few more details to help us find out whats
happening? In particular, are you using ensembl.org or a mirror site?
Are you using the web interface, biomaRt, martservice or the API? How
many IDs are you trying to convert? What error are you seeing? When was
this happening?

> Is the server down for this moment?
> When will it start functioning again?

I've just checked, and filtering by affy_hg_u133_plus_2 and displaying
affy_hg_u133 appears to be working fine via the web interface:
http://www.ensembl.org/biomart/martview/0c75c283c5beeef1591ea0891b31036d?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_gene_ensembl.default.feature_page.ensembl_gene_id|hsapiens_gene_ensembl.default.feature_page.ensembl_transcript_id|hsapiens_gene_ensembl.default.feature_page.affy_hg_u133a&FILTERS=hsapiens_gene_ensembl.default.filters.affy_hg_u133_plus_2."241843_at,241844_at"&VISIBLEPANEL=resultspanel

If you're trying to do something different, please let me know.

Regards,

Dan.

--
Dan Staines, PhD
Genomics Technology Infrastructure Coordinator
EMBL-EBI, Wellcome Trust Genome Campus
Cambridge CB10 1SD, UK
Tel: +44-(0)1223-492507

[Arek Kasprzyk]

Hi Afiqah,

what system are you installing BioMart on?

a.

<mailto:biomart-user...@googlegroups.com>.

Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.

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[Afiqah Aleng]

Hi Arek,

Ubuntu 14.04.4 Virtualbox. Or do I have to use another operating system?

Afiqah

[Dan Staines]

There was a hardware problem on our Asia mirror - this is now resolved
and the server is working again. Please let us know if you have any
further problems.

Best,

[Arek Kasprzyk]

Hi Afiqah,

no, the system is fine. We just need a bit more information. 

Please look at the 

stdouterr.*.log in the BioMart-0.9.1/dist/logs and see if there are any helpful error messages there

a.

[Afiqah Aleng]

Arek,

Thanks for reply. I already managed to connect to the localhost:9000. I just need to set path JAVA_HOME and ANT_HOME in /etc/environment. Before this, I set path for ANT_HOME in /etc/profile and JAVA_HOME in ~.bashrc. 

Thanks

Afiqah

[peer.w...@gmail.com]

Hey there,

I am trying to use the GenomeGraphs package in R which requires the biomaRt package. When I try to access the biomart server I am getting the following error:

> mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")

Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.  Check http://www.biomart.org and verify if this website is available.
Error: XML content does not seem to be XML: 

I've tryied almost every suggestion that I was able to find in the internet - without any success (changing hosts, biomarts, path and dataset). Is the server really down? -from my browser it seems pretty alright! No problems here.

Any help is highly apprechiated!

Best
Peer