Dear BioC mailing-list,
I came across this error using the latest R version and BioMart:
> library("biomaRt")
> mart = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl", mart=mart)
Checking attributes ... ok
Checking filters ... ok
> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
> utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl,
type="entrezgene")
V1
1
2 <html><head><meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
3
<title>ERROR: The requested URL could not be retrieved</title>
4 <style type="text/css"></style>
5
</head><body>
6
ERROR
Error in getBM(c(seqType, type), filters = type, values = id, mart =
mart,
:
The query to the BioMart webservice returned an invalid result: the
number
of columns in the result table does not equal the number of attributes
in
the query. Please report this to the mailing list.
I looked through the BioC mailing-list for similar errors but found
only one
quite similar last year. It was related to a bug in BioMart. Is this
the
same?
Here is my session-info:
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-apple-darwin9.8.0
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] RCurl_1.4-2
[2] bitops_1.0-4.1
[3] ChIPpeakAnno_1.4.1
[4] limma_3.4.4
[5] org.Hs.eg.db_2.4.1
[6] GO.db_2.4.1
[7] RSQLite_0.9-2
[8] DBI_0.2-5
[9] AnnotationDbi_1.10.2
[10] BSgenome.Ecoli.NCBI.20080805_1.3.16
[11] multtest_2.5.14
[12] Biobase_2.8.0
[13] biomaRt_2.4.0
[14] chipseq_0.4.1
[15] ShortRead_1.6.2
[16] Rsamtools_1.0.8
[17] lattice_0.18-8
[18] BSgenome.Athaliana.TAIR.04232008_1.3.16
[19] BSgenome_1.16.5
[20] Biostrings_2.16.9
[21] GenomicRanges_1.0.8
[22] IRanges_1.6.15
loaded via a namespace (and not attached):
[1] MASS_7.3-6 XML_3.1-1 grid_2.11.1 hwriter_1.2
[5] splines_2.11.1 survival_2.35-8 tcltk_2.11.1 tools_2.11.1
Thank you very much for any feed-back,
best
r
[[alternative HTML version deleted]]
Ren?
Have you tried again in the meantime, as this looks more like a
temporary glitch on the biomart backend?
ie it works form me:
> library("biomaRt")
> mart = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl", mart=mart)
Checking attributes ... ok
Checking filters ... ok
> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
> utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl,
type="entrezgene")
>
> utr['entrezgene']
entrezgene
1 25
2 102
3 25
4 87
>
(although, I am not quite sure, what you are trying to fetch from
biomart)
regards, Hans
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu
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=C 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_2.4.0
loaded via a namespace (and not attached):
[1] RCurl_1.4-3 XML_3.1-1
>
On 09/06/2010 10:58 AM, Ren? Dreos wrote:
> Dear BioC mailing-list,
>
> I came across this error using the latest R version and BioMart:
>
>> library("biomaRt")
>> mart = useMart("ensembl")
>> ensembl = useDataset("hsapiens_gene_ensembl", mart=mart)
> Checking attributes ... ok
> Checking filters ... ok
>> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
>> utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl,
> type="entrezgene")
>
> V1
> 1 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
> 2<html><head><meta> HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
> 3
> ERROR: The requested URL could not be retrieved
> 4<style> type="text/css"></style>
> 5
> </head><body>
> 6
>
ERROR
> Error in getBM(c(seqType, type), filters = type, values = id, mart =
mart,
> :
> The query to the BioMart webservice returned an invalid result:
the number
> of columns in the result table does not equal the number of
attributes in
> the query. Please report this to the mailing list.
>
> I looked through the BioC mailing-list for similar errors but found
only one
> quite similar last year. It was related to a bug in BioMart. Is this
the
> same?
>
> Here is my session-info:
>> sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] RCurl_1.4-2
> [2] bitops_1.0-4.1
> [3] ChIPpeakAnno_1.4.1
> [4] limma_3.4.4
> [5] org.Hs.eg.db_2.4.1
> [6] GO.db_2.4.1
> [7] RSQLite_0.9-2
> [8] DBI_0.2-5
> [9] AnnotationDbi_1.10.2
> [10] BSgenome.Ecoli.NCBI.20080805_1.3.16
> [11] multtest_2.5.14
> [12] Biobase_2.8.0
> [13] biomaRt_2.4.0
> [14] chipseq_0.4.1
> [15] ShortRead_1.6.2
> [16] Rsamtools_1.0.8
> [17] lattice_0.18-8
> [18] BSgenome.Athaliana.TAIR.04232008_1.3.16
> [19] BSgenome_1.16.5
> [20] Biostrings_2.16.9
> [21] GenomicRanges_1.0.8
> [22] IRanges_1.6.15
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-6 XML_3.1-1 grid_2.11.1 hwriter_1.2
> [5] splines_2.11.1 survival_2.35-8 tcltk_2.11.1 tools_2.11.1
>
>
> Thank you very much for any feed-back,
>
> best
> r
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
Dear Hans,
thank you very much for your feedback. Now everything is working!
best
r
On 6 September 2010 12:20, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:
> René
>
> Have you tried again in the meantime, as this looks more like a
temporary
> glitch on the biomart backend?
>
> ie it works form me:
>
>
> > library("biomaRt")
> > mart = useMart("ensembl")
> > ensembl = useDataset("hsapiens_gene_ensembl", mart=mart)
> Checking attributes ... ok
> Checking filters ... ok
> > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
> > utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl,
> type="entrezgene")
> >
> > utr['entrezgene']
> entrezgene
> 1 25
> 2 102
> 3 25
> 4 87
> >
>
> (although, I am not quite sure, what you are trying to fetch from
biomart)
>
>
> regards, Hans
>
>
>
>
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> 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=C 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_2.4.0
>
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.4-3 XML_3.1-1
>
> >
>
>
>
>
> On 09/06/2010 10:58 AM, René Dreos wrote:
>
>> Dear BioC mailing-list,
>>
>> I came across this error using the latest R version and BioMart:
>>
>> library("biomaRt")
>>> mart = useMart("ensembl")
>>> ensembl = useDataset("hsapiens_gene_ensembl", mart=mart)
>>>
>> Checking attributes ... ok
>> Checking filters ... ok
>>
>>> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
>>> utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl,
>>>
>> type="entrezgene")
>>
>> V1
>> 1> Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
>> 2<html><head><meta>> HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
>> 3
>> ERROR: The requested URL could not be retrieved
>> 4<style>>
>> type="text/css"></style>
>> 5
>> </head><body>
>> 6
>>
ERROR
>> Error in getBM(c(seqType, type), filters = type, values = id, mart
= mart,
>> :
>> The query to the BioMart webservice returned an invalid result:
the
>> number
>> of columns in the result table does not equal the number of
attributes in
>> the query. Please report this to the mailing list.
>>
>> I looked through the BioC mailing-list for similar errors but found
only
>> one
>> quite similar last year. It was related to a bug in BioMart. Is
this the
>> same?
>>
>> Here is my session-info:
>>
>>> sessionInfo()
>>>
>> R version 2.11.1 (2010-05-31)
>> x86_64-apple-darwin9.8.0
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods
base
>>
>> other attached packages:
>> [1] RCurl_1.4-2
>> [2] bitops_1.0-4.1
>> [3] ChIPpeakAnno_1.4.1
>> [4] limma_3.4.4
>> [5] org.Hs.eg.db_2.4.1
>> [6] GO.db_2.4.1
>> [7] RSQLite_0.9-2
>> [8] DBI_0.2-5
>> [9] AnnotationDbi_1.10.2
>> [10] BSgenome.Ecoli.NCBI.20080805_1.3.16
>> [11] multtest_2.5.14
>> [12] Biobase_2.8.0
>> [13] biomaRt_2.4.0
>> [14] chipseq_0.4.1
>> [15] ShortRead_1.6.2
>> [16] Rsamtools_1.0.8
>> [17] lattice_0.18-8
>> [18] BSgenome.Athaliana.TAIR.04232008_1.3.16
>> [19] BSgenome_1.16.5
>> [20] Biostrings_2.16.9
>> [21] GenomicRanges_1.0.8
>> [22] IRanges_1.6.15
>>
>> loaded via a namespace (and not attached):
>> [1] MASS_7.3-6 XML_3.1-1 grid_2.11.1 hwriter_1.2
>> [5] splines_2.11.1 survival_2.35-8 tcltk_2.11.1 tools_2.11.1
>>
>>
>> Thank you very much for any feed-back,
>>
>> best
>> r
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor@stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>
[[alternative HTML version deleted]]
ERROR
>> Error in getBM(c(seqType, type), filters = type, values = id, mart = mart, >> : >> The query to the BioMart webservice returned an invalid result: the >> number >> of columns in the result table does not equal the number of attributes in >> the query. Please report this to the mailing list. >> >> I looked through the BioC mailing-list for similar errors but found only >> one >> quite similar last year. It was related to a bug in BioMart. Is this the >> same? >> >> Here is my session-info: >> >>> sessionInfo() >>> >> R version 2.11.1 (2010-05-31) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] RCurl_1.4-2 >> [2] bitops_1.0-4.1 >> [3] ChIPpeakAnno_1.4.1 >> [4] limma_3.4.4 >> [5] org.Hs.eg.db_2.4.1 >> [6] GO.db_2.4.1 >> [7] RSQLite_0.9-2 >> [8] DBI_0.2-5 >> [9] AnnotationDbi_1.10.2 >> [10] BSgenome.Ecoli.NCBI.20080805_1.3.16 >> [11] multtest_2.5.14 >> [12] Biobase_2.8.0 >> [13] biomaRt_2.4.0 >> [14] chipseq_0.4.1 >> [15] ShortRead_1.6.2 >> [16] Rsamtools_1.0.8 >> [17] lattice_0.18-8 >> [18] BSgenome.Athaliana.TAIR.04232008_1.3.16 >> [19] BSgenome_1.16.5 >> [20] Biostrings_2.16.9 >> [21] GenomicRanges_1.0.8 >> [22] IRanges_1.6.15 >> >> loaded via a namespace (and not attached): >> [1] MASS_7.3-6 XML_3.1-1 grid_2.11.1 hwriter_1.2 >> [5] splines_2.11.1 survival_2.35-8 tcltk_2.11.1 tools_2.11.1 >> >> >> Thank you very much for any feed-back, >> >> best >> r >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > [[alternative HTML version deleted]]