Question: BiomaRt useMart() issues
0
gravatar for burak kutlu
5.6 years ago by
burak kutlu200
burak kutlu200 wrote:
Hello There seems to be an issue with the useMart() which spits out the following error that has been observed before with an old version of Biomart and was fixed by updating. https://lists.biomart.org/pipermail/users/2012-June/002673.html Many thanks in advance -burak ensembl <- useMart("ensembl") Opening and ending tag mismatch: meta line 5 and head EntityRef: expecting ';' Opening and ending tag mismatch: br line 67 and body Opening and ending tag mismatch: br line 64 and html Premature end of data in tag br line 62 Premature end of data in tag br line 59 Premature end of data in tag br line 57 Premature end of data in tag hr line 47 Premature end of data in tag img line 45 Premature end of data in tag body line 44 Premature end of data in tag head line 4 Premature end of data in tag html line 3 Error: 1: Opening and ending tag mismatch: meta line 5 and head 2: EntityRef: expecting ';' 3: Opening and ending tag mismatch: br line 67 and body 4: Opening and ending tag mismatch: br line 64 and html 5: Premature end of data in tag br line 62 6: Premature end of data in tag br line 59 7: Premature end of data in tag br line 57 8: Premature end of data in tag hr line 47 9: Premature end of data in tag img line 45 10: Premature end of data in tag body line 44 11: Premature end of data in tag head line 4 12: Premature end of data in tag html line 3 I think I am using the latest version. R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C [6] LC_MESSAGES=C LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: [1] splines parallel stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.16.0 PFAM.db_2.9.0 GO.db_2.9.0 GOstats_2.26.0 Category_2.26.0 [6] BiocInstaller_1.10.3 dataframes2xls_0.4.5 multtest_2.16.0 GSEABase_1.22.0 annotate_1.38.0 [11] zoo_1.7-10 edgeR_3.2.4 limma_3.16.7 iRefR_1.1 RBGL_1.36.2 [16] graph_1.38.3 igraph_0.6.5-2 org.Hs.eg.db_2.9.0 RSQLite_0.11.4 DBI_0.2-7 [21] AnnotationDbi_1.22.6 Biobase_2.20.1 BiocGenerics_0.6.0 R.utils_1.26.2 R.oo_1.13.9 [26] R.methodsS3_1.4.4 loaded via a namespace (and not attached): [1] AnnotationForge_1.2.2 IRanges_1.18.3 MASS_7.3-28 RCurl_1.95-4.1 [5] XML_3.98-1.1 biclust_1.0.2 colorspace_1.2-2 genefilter_1.42.0 [9] grid_3.0.1 lattice_0.20-21 stats4_3.0.1 survival_2.37-4 [13] tools_3.0.1 xtable_1.7-1 [[alternative HTML version deleted]]
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ADD COMMENTlink modified 5.6 years ago by Steffen Durinck540 • written 5.6 years ago by burak kutlu200
Answer: BiomaRt useMart() issues
0
gravatar for Steffen Durinck
5.6 years ago by
Steffen Durinck540 wrote:
Hi Burak, This was probably a temporary connection issue as I can not replicate the error. Can you try this again and see if it is resolved? Best regards, Steffen On Sat, Aug 24, 2013 at 3:43 PM, burak kutlu <burak_kutlu@yahoo.com> wrote: > Hello > There seems to be an issue with the useMart() which spits out the > following error that has been observed before with an old version of > Biomart and was fixed by updating. > https://lists.biomart.org/pipermail/users/2012-June/002673.html > > Many thanks in advance > -burak > > ensembl <- useMart("ensembl") > > Opening and ending tag mismatch: meta line 5 and head > EntityRef: expecting ';' > Opening and ending tag mismatch: br line 67 and body > Opening and ending tag mismatch: br line 64 and html > Premature end of data in tag br line 62 > Premature end of data in tag br line 59 > Premature end of data in tag br line 57 > Premature end of data in tag hr line 47 > Premature end of data in tag img line 45 > Premature end of data in tag body line 44 > Premature end of data in tag head line 4 > Premature end of data in tag html line 3 Error: 1: Opening and ending tag > mismatch: meta line 5 and head > 2: EntityRef: expecting ';' > 3: Opening and ending tag mismatch: br line 67 and body > 4: Opening and ending tag mismatch: br line 64 and html > 5: Premature end of data in tag br line 62 > 6: Premature end of data in tag br line 59 > 7: Premature end of data in tag br line 57 > 8: Premature end of data in tag hr line 47 > 9: Premature end of data in tag img line 45 > 10: Premature end of data in tag body line 44 > 11: Premature end of data in tag head line 4 > 12: Premature end of data in tag html line 3 > > I think I am using the latest version. > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 > LC_NUMERIC=C LC_TIME=C LC_COLLATE=C > LC_MONETARY=C [6] LC_MESSAGES=C LC_PAPER=C > LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=C LC_IDENTIFICATION=C attached base packages: > [1] splines parallel stats graphics grDevices utils datasets > methods base other attached packages: [1] biomaRt_2.16.0 > PFAM.db_2.9.0 GO.db_2.9.0 GOstats_2.26.0 > Category_2.26.0 [6] BiocInstaller_1.10.3 dataframes2xls_0.4.5 > multtest_2.16.0 GSEABase_1.22.0 annotate_1.38.0 > [11] zoo_1.7-10 edgeR_3.2.4 limma_3.16.7 > iRefR_1.1 RBGL_1.36.2 > [16] graph_1.38.3 igraph_0.6.5-2 org.Hs.eg.db_2.9.0 > RSQLite_0.11.4 DBI_0.2-7 > [21] AnnotationDbi_1.22.6 Biobase_2.20.1 BiocGenerics_0.6.0 > R.utils_1.26.2 R.oo_1.13.9 > [26] R.methodsS3_1.4.4 loaded via a namespace (and not attached): [1] > AnnotationForge_1.2.2 IRanges_1.18.3 MASS_7.3-28 > RCurl_1.95-4.1 [5] XML_3.98-1.1 biclust_1.0.2 > colorspace_1.2-2 genefilter_1.42.0 [9] grid_3.0.1 > lattice_0.20-21 stats4_3.0.1 survival_2.37-4 > [13] tools_3.0.1 xtable_1.7-1 > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.6 years ago by Steffen Durinck540
Hello Steffen I did suspect that it was the case, as it worked only a couple of days ago... Unfortunately, I still get the same error as of Aug 26 2.57 pm UTC-08:00 Thank you -burak ________________________________ From: Steffen Durinck <durinck.steffen@gene.com> Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> Sent: Monday, August 26, 2013 11:12 AM Subject: Re: [BioC] BiomaRt useMart() issues Hi Burak, This was probably a temporary connection issue as I can not replicate the error. Can you try this again and see if it is resolved? Best regards, Steffen Hello >There seems to be an issue with the useMart() which spits out the following error that has been observed before with an old version of Biomart and was fixed by updating. >https://lists.biomart.org/pipermail/users/2012-June/002673.html > >Many thanks in advance >-burak > >ensembl <- useMart("ensembl") > >Opening and ending tag mismatch: meta line 5 and head >EntityRef: expecting ';' >Opening and ending tag mismatch: br line 67 and body >Opening and ending tag mismatch: br line 64 and html >Premature end of data in tag br line 62 >Premature end of data in tag br line 59 >Premature end of data in tag br line 57 >Premature end of data in tag hr line 47 >Premature end of data in tag img line 45 >Premature end of data in tag body line 44 >Premature end of data in tag head line 4 >Premature end of data in tag html line 3 Error: 1: Opening and ending tag mismatch: meta line 5 and head >2: EntityRef: expecting ';' >3: Opening and ending tag mismatch: br line 67 and body >4: Opening and ending tag mismatch: br line 64 and html >5: Premature end of data in tag br line 62 >6: Premature end of data in tag br line 59 >7: Premature end of data in tag br line 57 >8: Premature end of data in tag hr line 47 >9: Premature end of data in tag img line 45 >10: Premature end of data in tag body line 44 >11: Premature end of data in tag head line 4 >12: Premature end of data in tag html line 3 > >I think I am using the latest version. >R version 3.0.1 (2013-05-16) >Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C         LC_TIME=C LC_COLLATE=C         LC_MONETARY=C        [6] LC_MESSAGES=C LC_PAPER=C           LC_NAME=C            LC_ADDRESS=C LC_TELEPHONE=C >[11] LC_MEASUREMENT=C     LC_IDENTIFICATION=C  attached base packages: >[1] splines   parallel  stats     graphics  grDevices utils datasets  methods   base      other attached packages: [1] biomaRt_2.16.0       PFAM.db_2.9.0        GO.db_2.9.0 GOstats_2.26.0       Category_2.26.0      [6] BiocInstaller_1.10.3 dataframes2xls_0.4.5 multtest_2.16.0      GSEABase_1.22.0 annotate_1.38.0 >[11] zoo_1.7-10           edgeR_3.2.4          limma_3.16.7 iRefR_1.1            RBGL_1.36.2 >[16] graph_1.38.3         igraph_0.6.5-2       org.Hs.eg.db_2.9.0 RSQLite_0.11.4       DBI_0.2-7 >[21] AnnotationDbi_1.22.6 Biobase_2.20.1       BiocGenerics_0.6.0 R.utils_1.26.2       R.oo_1.13.9 >[26] R.methodsS3_1.4.4    loaded via a namespace (and not attached): [1] AnnotationForge_1.2.2 IRanges_1.18.3        MASS_7.3-28 RCurl_1.95-4.1        [5] XML_3.98-1.1          biclust_1.0.2 colorspace_1.2-2      genefilter_1.42.0     [9] grid_3.0.1 lattice_0.20-21       stats4_3.0.1          survival_2.37-4 >[13] tools_3.0.1           xtable_1.7-1 >        [[alternative HTML version deleted]] > > >_______________________________________________ >Bioconductor mailing list >Bioconductor@r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 5.6 years ago by burak kutlu200
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