[biomart-users] biomart interface in R not working

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[biomart-users] biomart interface in R not working

Helena Ahlfors
Hi everyone,

I’m wondering if anyone else is having problems with using biomart package in R.

Since mid-November the following line gives an error message:

ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")


Error message:

Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2


Here is the sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.22.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1  bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.4  
 [7] IRanges_2.0.1        parallel_3.1.2       RCurl_1.95-4.5       RSQLite_1.0.0        S4Vectors_0.4.0      stats4_3.1.2        
[13] tools_3.1.2          XML_3.98-1.1        


I hope you can help me with this.

Thank you!

Kind regards,

Helena

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Re: [biomart-users] biomart interface in R not working

Arek Kasprzyk
Hi Helena,

you need to make sure you point your package to the www.ensembl.org host. We are in the process of migrating servers to a new host and www.biomart.org is temporarily out of action.


a.

On 11 December 2015 at 10:08, Helena Ahlfors <[hidden email]> wrote:
Hi everyone,

I’m wondering if anyone else is having problems with using biomart package in R.

Since mid-November the following line gives an error message:

ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")


Error message:

Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2


Here is the sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.22.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1  bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.4  
 [7] IRanges_2.0.1        parallel_3.1.2       RCurl_1.95-4.5       RSQLite_1.0.0        S4Vectors_0.4.0      stats4_3.1.2        
[13] tools_3.1.2          XML_3.98-1.1        


I hope you can help me with this.

Thank you!

Kind regards,

Helena

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Re: [biomart-users] biomart interface in R not working

Helena Ahlfors
Hi Arek,

Thank you for your prompt response and help!

I now manage to get the annotations but is there a way around to use the "getSequence" command as it only seems to work when used with the ensembl BioMart:

Command used:

SEQs <- getSequence(id = ID, type="ensembl_gene_id",seqType="coding_gene_flank",downstream=MAX, mart=mart)

Error message:

Error in martCheck(mart, "ensembl") : 
  This function only works when used with the ensembl BioMart.


Thank you!

Kind regards,

Helena


perjantai 11. joulukuuta 2015 10.19.39 UTC Arek Kasprzyk kirjoitti:
Hi Helena,

you need to make sure you point your package to the <a href="http://www.ensembl.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org\46sa\75D\46sntz\0751\46usg\75AFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.ensembl.org\46sa\75D\46sntz\0751\46usg\75AFQjCNEhRkMjGzJ0Ux5vBUiT-NWHb0ycIg&#39;;return true;">www.ensembl.org host. We are in the process of migrating servers to a new host and <a href="http://www.biomart.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org\46sa\75D\46sntz\0751\46usg\75AFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w&#39;;return true;">www.biomart.org is temporarily out of action.

(<a href="http://www.biomart.org/notice.html" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org%2Fnotice.html\46sa\75D\46sntz\0751\46usg\75AFQjCNH0_r-2IdL4mHjpOljyLQiQHT0xgA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\75http%3A%2F%2Fwww.biomart.org%2Fnotice.html\46sa\75D\46sntz\0751\46usg\75AFQjCNH0_r-2IdL4mHjpOljyLQiQHT0xgA&#39;;return true;">http://www.biomart.org/notice.html)

a.

On 11 December 2015 at 10:08, Helena Ahlfors <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="LxjKaLcWCwAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">helena....@...> wrote:
Hi everyone,

I’m wondering if anyone else is having problems with using biomart package in R.

Since mid-November the following line gives an error message:

ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")


Error message:

Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2


Here is the sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.22.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1  bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.4  
 [7] IRanges_2.0.1        parallel_3.1.2       RCurl_1.95-4.5       RSQLite_1.0.0        S4Vectors_0.4.0      stats4_3.1.2        
[13] tools_3.1.2          XML_3.98-1.1        


I hope you can help me with this.

Thank you!

Kind regards,

Helena

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Re: [biomart-users] biomart interface in R not working

Steffen Durinck-2
Hi Helena,

Try to update the biomaRt package to the latest release version: 2.26.1
It points by default to ensembl.org  and getSequence should work as well, let me know if it doesn't and send me an example that fails.

Cheers,
Steffen



On Fri, Dec 11, 2015 at 2:25 AM, Helena Ahlfors <[hidden email]> wrote:
Hi Arek,

Thank you for your prompt response and help!

I now manage to get the annotations but is there a way around to use the "getSequence" command as it only seems to work when used with the ensembl BioMart:

Command used:

SEQs <- getSequence(id = ID, type="ensembl_gene_id",seqType="coding_gene_flank",downstream=MAX, mart=mart)

Error message:

Error in martCheck(mart, "ensembl") : 
  This function only works when used with the ensembl BioMart.


Thank you!

Kind regards,

Helena


perjantai 11. joulukuuta 2015 10.19.39 UTC Arek Kasprzyk kirjoitti:
Hi Helena,

you need to make sure you point your package to the www.ensembl.org host. We are in the process of migrating servers to a new host and www.biomart.org is temporarily out of action.


a.

On 11 December 2015 at 10:08, Helena Ahlfors <[hidden email]> wrote:
Hi everyone,

I’m wondering if anyone else is having problems with using biomart package in R.

Since mid-November the following line gives an error message:

ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")


Error message:

Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2


Here is the sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.22.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1  bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.4  
 [7] IRanges_2.0.1        parallel_3.1.2       RCurl_1.95-4.5       RSQLite_1.0.0        S4Vectors_0.4.0      stats4_3.1.2        
[13] tools_3.1.2          XML_3.98-1.1        


I hope you can help me with this.

Thank you!

Kind regards,

Helena

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Re: [biomart-users] biomart interface in R not working

Helena Ahlfors
Hi Steffen,

It works perfectly now! Thank you so much for doing this!

Cheers,

Helena


On 11 Dec 2015, at 16:59, Steffen Durinck <[hidden email]> wrote:

Hi Helena,

Try to update the biomaRt package to the latest release version: 2.26.1
It points by default to ensembl.org  and getSequence should work as well, let me know if it doesn't and send me an example that fails.

Cheers,
Steffen



On Fri, Dec 11, 2015 at 2:25 AM, Helena Ahlfors <[hidden email]> wrote:
Hi Arek,

Thank you for your prompt response and help!

I now manage to get the annotations but is there a way around to use the "getSequence" command as it only seems to work when used with the ensembl BioMart:

Command used:

SEQs <- getSequence(id = ID, type="ensembl_gene_id",seqType="coding_gene_flank",downstream=MAX, mart=mart)

Error message:

Error in martCheck(mart, "ensembl") : 
  This function only works when used with the ensembl BioMart.


Thank you!

Kind regards,

Helena


perjantai 11. joulukuuta 2015 10.19.39 UTC Arek Kasprzyk kirjoitti:
Hi Helena,

you need to make sure you point your package to the www.ensembl.org host. We are in the process of migrating servers to a new host and www.biomart.org is temporarily out of action.


a.

On 11 December 2015 at 10:08, Helena Ahlfors <[hidden email]> wrote:
Hi everyone,

I’m wondering if anyone else is having problems with using biomart package in R.

Since mid-November the following line gives an error message:

ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")


Error message:

Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2


Here is the sessionInfo:

R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.22.0

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1 Biobase_2.26.0       BiocGenerics_0.12.1  bitops_1.0-6         DBI_0.3.1            GenomeInfoDb_1.2.4  
 [7] IRanges_2.0.1        parallel_3.1.2       RCurl_1.95-4.5       RSQLite_1.0.0        S4Vectors_0.4.0      stats4_3.1.2        
[13] tools_3.1.2          XML_3.98-1.1        


I hope you can help me with this.

Thank you!

Kind regards,

Helena

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To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
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