problem with 'FDb.InfiniumMethylation.hg19'
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Guido Hooiveld ★ 4.1k
@guido-hooiveld-2020
Last seen 3 days ago
Wageningen University, Wageningen, the …
Hi, I would like to report a problem with the annotation package "FDb.InfiniumMethylation.hg19". When I try to explore the content of it for the 450K array as per the example on the help pages, I get an error. Any suggestions on what is going wrong? Thanks and regards, Guido > library(FDb.InfiniumMethylation.hg19) Loading required package: GenomicFeatures Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object(s) are masked from 'package:stats': xtabs The following object(s) are masked from 'package:base': anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, get, intersect, lapply, Map, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: IRanges Loading required package: GenomicRanges Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: Biostrings Loading required package: rtracklayer Warning messages: 1: replacing previous import 'initialize' when loading 'rtracklayer' 2: replacing previous import 'show' when loading 'rtracklayer' > hm450 <- get450k() Error in `seqinfo<-`(`*tmp*`, value = NULL) : the supplied 'seqinfo' must be a Seqinfo object In addition: Warning message: In if is.na(genome(GR))) { : the condition has length > 1 and only the first element will be used > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.18.0 [3] Biostrings_2.26.2 GenomicFeatures_1.10.0 [5] AnnotationDbi_1.20.2 Biobase_2.18.0 [7] GenomicRanges_1.10.2 IRanges_1.16.3 [9] BiocGenerics_0.4.0 BiocInstaller_1.8.2 loaded via a namespace (and not attached): [1] biomaRt_2.14.0 bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 [5] parallel_2.15.1 RCurl_1.95-1.1 Rsamtools_1.10.1 RSQLite_0.11.2 [9] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 zlibbioc_1.4.0 > --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld@wur.nl internet: http://nutrigene.4t.com http://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 [[alternative HTML version deleted]]
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Tim Triche ★ 4.2k
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This is odd. I'll look into it today. Thanks for the bug report. --t On Tue, Oct 23, 2012 at 6:48 AM, Hooiveld, Guido <guido.hooiveld@wur.nl>wrote: > Hi, > I would like to report a problem with the annotation package > "FDb.InfiniumMethylation.hg19". > When I try to explore the content of it for the 450K array as per the > example on the help pages, I get an error. > Any suggestions on what is going wrong? > > Thanks and regards, > Guido > > > > library(FDb.InfiniumMethylation.hg19) > Loading required package: GenomicFeatures > Loading required package: BiocGenerics > > Attaching package: 'BiocGenerics' > > The following object(s) are masked from 'package:stats': > > xtabs > > The following object(s) are masked from 'package:base': > > anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, > get, intersect, lapply, Map, mapply, mget, order, paste, pmax, > pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, > rownames, sapply, setdiff, table, tapply, union, unique > > Loading required package: IRanges > Loading required package: GenomicRanges > Loading required package: AnnotationDbi > Loading required package: Biobase > Welcome to Bioconductor > > Vignettes contain introductory material; view with > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")', and for packages 'citation("pkgname")'. > > Loading required package: Biostrings > Loading required package: rtracklayer > Warning messages: > 1: replacing previous import 'initialize' when loading 'rtracklayer' > 2: replacing previous import 'show' when loading 'rtracklayer' > > hm450 <- get450k() > Error in `seqinfo<-`(`*tmp*`, value = NULL) : > the supplied 'seqinfo' must be a Seqinfo object > In addition: Warning message: > In if is.na(genome(GR))) { : > the condition has length > 1 and only the first element will be used > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-pc-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.18.0 > [3] Biostrings_2.26.2 GenomicFeatures_1.10.0 > [5] AnnotationDbi_1.20.2 Biobase_2.18.0 > [7] GenomicRanges_1.10.2 IRanges_1.16.3 > [9] BiocGenerics_0.4.0 BiocInstaller_1.8.2 > > loaded via a namespace (and not attached): > [1] biomaRt_2.14.0 bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 > [5] parallel_2.15.1 RCurl_1.95-1.1 Rsamtools_1.10.1 RSQLite_0.11.2 > [9] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 zlibbioc_1.4.0 > > > > > --------------------------------------------------------- > Guido Hooiveld, PhD > Nutrition, Metabolism & Genomics Group > Division of Human Nutrition > Wageningen University > Biotechnion, Bomenweg 2 > NL-6703 HD Wageningen > the Netherlands > tel: (+)31 317 485788 > fax: (+)31 317 483342 > email: guido.hooiveld@wur.nl > internet: http://nutrigene.4t.com > http://scholar.google.com/citations?user=qFHaMnoAAAAJ > http://www.researcherid.com/rid/F-4912-2010 > > > [[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 > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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I believe this is a result of not having the BSgenome.Hsapiens.UCSC.hg19 package installed on your system. Try installing the package, loading it into your R session and then running get450k(). It should solve it. Post back if it still does not work. HTH, Moiz On Oct 23, 2012, at 7:19 AM, Tim Triche, Jr. wrote: > This is odd. I'll look into it today. Thanks for the bug report. > > --t > > > On Tue, Oct 23, 2012 at 6:48 AM, Hooiveld, Guido <guido.hooiveld at="" wur.nl="">wrote: > >> Hi, >> I would like to report a problem with the annotation package >> "FDb.InfiniumMethylation.hg19". >> When I try to explore the content of it for the 450K array as per the >> example on the help pages, I get an error. >> Any suggestions on what is going wrong? >> >> Thanks and regards, >> Guido >> >> >>> library(FDb.InfiniumMethylation.hg19) >> Loading required package: GenomicFeatures >> Loading required package: BiocGenerics >> >> Attaching package: 'BiocGenerics' >> >> The following object(s) are masked from 'package:stats': >> >> xtabs >> >> The following object(s) are masked from 'package:base': >> >> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, >> get, intersect, lapply, Map, mapply, mget, order, paste, pmax, >> pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, >> rownames, sapply, setdiff, table, tapply, union, unique >> >> Loading required package: IRanges >> Loading required package: GenomicRanges >> Loading required package: AnnotationDbi >> Loading required package: Biobase >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >> Loading required package: Biostrings >> Loading required package: rtracklayer >> Warning messages: >> 1: replacing previous import 'initialize' when loading 'rtracklayer' >> 2: replacing previous import 'show' when loading 'rtracklayer' >>> hm450 <- get450k() >> Error in `seqinfo<-`(`*tmp*`, value = NULL) : >> the supplied 'seqinfo' must be a Seqinfo object >> In addition: Warning message: >> In if is.na(genome(GR))) { : >> the condition has length > 1 and only the first element will be used >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.18.0 >> [3] Biostrings_2.26.2 GenomicFeatures_1.10.0 >> [5] AnnotationDbi_1.20.2 Biobase_2.18.0 >> [7] GenomicRanges_1.10.2 IRanges_1.16.3 >> [9] BiocGenerics_0.4.0 BiocInstaller_1.8.2 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.14.0 bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 >> [5] parallel_2.15.1 RCurl_1.95-1.1 Rsamtools_1.10.1 RSQLite_0.11.2 >> [9] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 zlibbioc_1.4.0 >>> >> >> >> --------------------------------------------------------- >> Guido Hooiveld, PhD >> Nutrition, Metabolism & Genomics Group >> Division of Human Nutrition >> Wageningen University >> Biotechnion, Bomenweg 2 >> NL-6703 HD Wageningen >> the Netherlands >> tel: (+)31 317 485788 >> fax: (+)31 317 483342 >> email: guido.hooiveld at wur.nl >> internet: http://nutrigene.4t.com >> http://scholar.google.com/citations?user=qFHaMnoAAAAJ >> http://www.researcherid.com/rid/F-4912-2010 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hmmm... well, there's something to add to the Depends: line in the description, then. And the hg18 version for the hg18 FDb. I think it's time to merge the two... Thanks for catching that Moiz. --t On Tue, Oct 23, 2012 at 8:01 AM, Moiz Bootwalla <msbootwalla@gmail.com>wrote: > I believe this is a result of not having the BSgenome.Hsapiens.UCSC.hg19 > package installed on your system. Try installing the package, loading it > into your R session and then running get450k(). It should solve it. Post > back if it still does not work. > > HTH, > > Moiz > > > On Oct 23, 2012, at 7:19 AM, Tim Triche, Jr. wrote: > > > This is odd. I'll look into it today. Thanks for the bug report. > > > > --t > > > > > > On Tue, Oct 23, 2012 at 6:48 AM, Hooiveld, Guido <guido.hooiveld@wur.nl> >wrote: > > > >> Hi, > >> I would like to report a problem with the annotation package > >> "FDb.InfiniumMethylation.hg19". > >> When I try to explore the content of it for the 450K array as per the > >> example on the help pages, I get an error. > >> Any suggestions on what is going wrong? > >> > >> Thanks and regards, > >> Guido > >> > >> > >>> library(FDb.InfiniumMethylation.hg19) > >> Loading required package: GenomicFeatures > >> Loading required package: BiocGenerics > >> > >> Attaching package: 'BiocGenerics' > >> > >> The following object(s) are masked from 'package:stats': > >> > >> xtabs > >> > >> The following object(s) are masked from 'package:base': > >> > >> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, > >> get, intersect, lapply, Map, mapply, mget, order, paste, pmax, > >> pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, > >> rownames, sapply, setdiff, table, tapply, union, unique > >> > >> Loading required package: IRanges > >> Loading required package: GenomicRanges > >> Loading required package: AnnotationDbi > >> Loading required package: Biobase > >> Welcome to Bioconductor > >> > >> Vignettes contain introductory material; view with > >> 'browseVignettes()'. To cite Bioconductor, see > >> 'citation("Biobase")', and for packages 'citation("pkgname")'. > >> > >> Loading required package: Biostrings > >> Loading required package: rtracklayer > >> Warning messages: > >> 1: replacing previous import 'initialize' when loading 'rtracklayer' > >> 2: replacing previous import 'show' when loading 'rtracklayer' > >>> hm450 <- get450k() > >> Error in `seqinfo<-`(`*tmp*`, value = NULL) : > >> the supplied 'seqinfo' must be a Seqinfo object > >> In addition: Warning message: > >> In if is.na(genome(GR))) { : > >> the condition has length > 1 and only the first element will be used > >>> sessionInfo() > >> R version 2.15.1 (2012-06-22) > >> Platform: x86_64-pc-mingw32/x64 (64-bit) > >> > >> locale: > >> [1] LC_COLLATE=English_United States.1252 > >> [2] LC_CTYPE=English_United States.1252 > >> [3] LC_MONETARY=English_United States.1252 > >> [4] LC_NUMERIC=C > >> [5] LC_TIME=English_United States.1252 > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.18.0 > >> [3] Biostrings_2.26.2 GenomicFeatures_1.10.0 > >> [5] AnnotationDbi_1.20.2 Biobase_2.18.0 > >> [7] GenomicRanges_1.10.2 IRanges_1.16.3 > >> [9] BiocGenerics_0.4.0 BiocInstaller_1.8.2 > >> > >> loaded via a namespace (and not attached): > >> [1] biomaRt_2.14.0 bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 > >> [5] parallel_2.15.1 RCurl_1.95-1.1 Rsamtools_1.10.1 RSQLite_0.11.2 > >> [9] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 zlibbioc_1.4.0 > >>> > >> > >> > >> --------------------------------------------------------- > >> Guido Hooiveld, PhD > >> Nutrition, Metabolism & Genomics Group > >> Division of Human Nutrition > >> Wageningen University > >> Biotechnion, Bomenweg 2 > >> NL-6703 HD Wageningen > >> the Netherlands > >> tel: (+)31 317 485788 > >> fax: (+)31 317 483342 > >> email: guido.hooiveld@wur.nl > >> internet: http://nutrigene.4t.com > >> http://scholar.google.com/citations?user=qFHaMnoAAAAJ > >> http://www.researcherid.com/rid/F-4912-2010 > >> > >> > >> [[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 > >> > > > > > > > > -- > > *A model is a lie that helps you see the truth.* > > * > > * > > Howard Skipper< > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf> > > > > [[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 > > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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Hi, To report back: installing 'the BSgenome.Hsapiens.UCSC.hg19' indeed made the error disappear. There was no need to explicitly load this library, calling just the function get450K() also loaded it. However, FYI, the warning still is present: > hm450 <- get450k() Warning message: In if is.na(genome(GR))) { : the condition has length > 1 and only the first element will be used > Regards, Guido From: Tim Triche, Jr. [mailto:tim.triche@gmail.com] Sent: Tuesday, October 23, 2012 18:37 To: Moiz Bootwalla Cc: Hooiveld, Guido; bioconductor (bioconductor@stat.math.ethz.ch) Subject: Re: [BioC] problem with 'FDb.InfiniumMethylation.hg19' Hmmm... well, there's something to add to the Depends: line in the description, then. And the hg18 version for the hg18 FDb. I think it's time to merge the two... Thanks for catching that Moiz. --t On Tue, Oct 23, 2012 at 8:01 AM, Moiz Bootwalla <msbootwalla@gmail.com<mailto:msbootwalla@gmail.com>> wrote: I believe this is a result of not having the BSgenome.Hsapiens.UCSC.hg19 package installed on your system. Try installing the package, loading it into your R session and then running get450k(). It should solve it. Post back if it still does not work. HTH, Moiz On Oct 23, 2012, at 7:19 AM, Tim Triche, Jr. wrote: > This is odd. I'll look into it today. Thanks for the bug report. > > --t > > > On Tue, Oct 23, 2012 at 6:48 AM, Hooiveld, Guido <guido.hooiveld@wur.nl<mailto:guido.hooiveld@wur.nl>>wrote: > >> Hi, >> I would like to report a problem with the annotation package >> "FDb.InfiniumMethylation.hg19". >> When I try to explore the content of it for the 450K array as per the >> example on the help pages, I get an error. >> Any suggestions on what is going wrong? >> >> Thanks and regards, >> Guido >> >> >>> library(FDb.InfiniumMethylation.hg19) >> Loading required package: GenomicFeatures >> Loading required package: BiocGenerics >> >> Attaching package: 'BiocGenerics' >> >> The following object(s) are masked from 'package:stats': >> >> xtabs >> >> The following object(s) are masked from 'package:base': >> >> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, >> get, intersect, lapply, Map, mapply, mget, order, paste, pmax, >> pmax.int<http: pmax.int="">, pmin, pmin.int<http: pmin.int="">, Position, rbind, Reduce, rep.int<http: rep.int="">, >> rownames, sapply, setdiff, table, tapply, union, unique >> >> Loading required package: IRanges >> Loading required package: GenomicRanges >> Loading required package: AnnotationDbi >> Loading required package: Biobase >> Welcome to Bioconductor >> >> Vignettes contain introductory material; view with >> 'browseVignettes()'. To cite Bioconductor, see >> 'citation("Biobase")', and for packages 'citation("pkgname")'. >> >> Loading required package: Biostrings >> Loading required package: rtracklayer >> Warning messages: >> 1: replacing previous import 'initialize' when loading 'rtracklayer' >> 2: replacing previous import 'show' when loading 'rtracklayer' >>> hm450 <- get450k() >> Error in `seqinfo<-`(`*tmp*`, value = NULL) : >> the supplied 'seqinfo' must be a Seqinfo object >> In addition: Warning message: >> In if is.na<http: is.na="">(genome(GR))) { : >> the condition has length > 1 and only the first element will be used >>> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-pc-mingw32/x64 (64-bit) >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.18.0 >> [3] Biostrings_2.26.2 GenomicFeatures_1.10.0 >> [5] AnnotationDbi_1.20.2 Biobase_2.18.0 >> [7] GenomicRanges_1.10.2 IRanges_1.16.3 >> [9] BiocGenerics_0.4.0 BiocInstaller_1.8.2 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.14.0 bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 >> [5] parallel_2.15.1 RCurl_1.95-1.1 Rsamtools_1.10.1 RSQLite_0.11.2 >> [9] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 zlibbioc_1.4.0 >>> >> >> >> --------------------------------------------------------- >> Guido Hooiveld, PhD >> Nutrition, Metabolism & Genomics Group >> Division of Human Nutrition >> Wageningen University >> Biotechnion, Bomenweg 2 >> NL-6703 HD Wageningen >> the Netherlands >> tel: (+)31 317 485788 >> fax: (+)31 317 483342 >> email: guido.hooiveld@wur.nl<mailto:guido.hooiveld@wur.nl> >> internet: http://nutrigene.4t.com >> http://scholar.google.com/citations?user=qFHaMnoAAAAJ >> http://www.researcherid.com/rid/F-4912-2010 >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org<mailto:bioconductor@r-project.org> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- > *A model is a lie that helps you see the truth.* > * > * > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org<mailto:bioconductor@r-project.org> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- A model is a lie that helps you see the truth. Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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yes, that should be if(allis.na(genome(GR))) In the code. I'll repackage & reupload it in the next couple of days. Thanks! --t On Tue, Oct 23, 2012 at 12:34 PM, Hooiveld, Guido <guido.hooiveld@wur.nl>wrote: > Hi,**** > > To report back: installing ‘the BSgenome.Hsapiens.UCSC.hg19’ indeed made > the error disappear. There was no need to explicitly load this library, > calling just the function get450K() also loaded it. However, FYI, the > warning still is present:**** > > ** ** > > > hm450 <- get450k()**** > > Warning message:**** > > In if is.na(genome(GR))) { :**** > > the condition has length > 1 and only the first element will be used**** > > >** ** > > ** ** > > Regards,**** > > Guido**** > > ** ** > > *From:* Tim Triche, Jr. [mailto:tim.triche@gmail.com] > *Sent:* Tuesday, October 23, 2012 18:37 > *To:* Moiz Bootwalla > *Cc:* Hooiveld, Guido; bioconductor (bioconductor@stat.math.ethz.ch) > *Subject:* Re: [BioC] problem with 'FDb.InfiniumMethylation.hg19'**** > > ** ** > > Hmmm... well, there's something to add to the Depends: line in the > description, then. **** > > And the hg18 version for the hg18 FDb. **** > > I think it's time to merge the two...**** > > ** ** > > Thanks for catching that Moiz.**** > > ** ** > > --t**** > > ** ** > > ** ** > > On Tue, Oct 23, 2012 at 8:01 AM, Moiz Bootwalla <msbootwalla@gmail.com> > wrote:**** > > I believe this is a result of not having the BSgenome.Hsapiens.UCSC.hg19 > package installed on your system. Try installing the package, loading it > into your R session and then running get450k(). It should solve it. Post > back if it still does not work. > > HTH, > > Moiz**** > > > > On Oct 23, 2012, at 7:19 AM, Tim Triche, Jr. wrote: > > > This is odd. I'll look into it today. Thanks for the bug report. > > > > --t > > > > > > On Tue, Oct 23, 2012 at 6:48 AM, Hooiveld, Guido <guido.hooiveld@wur.nl> >wrote: > > > >> Hi, > >> I would like to report a problem with the annotation package > >> "FDb.InfiniumMethylation.hg19". > >> When I try to explore the content of it for the 450K array as per the > >> example on the help pages, I get an error. > >> Any suggestions on what is going wrong? > >> > >> Thanks and regards, > >> Guido > >> > >> > >>> library(FDb.InfiniumMethylation.hg19) > >> Loading required package: GenomicFeatures > >> Loading required package: BiocGenerics > >> > >> Attaching package: 'BiocGenerics' > >> > >> The following object(s) are masked from 'package:stats': > >> > >> xtabs > >> > >> The following object(s) are masked from 'package:base': > >> > >> anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find, > >> get, intersect, lapply, Map, mapply, mget, order, paste, pmax, > >> pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int, > >> rownames, sapply, setdiff, table, tapply, union, unique > >> > >> Loading required package: IRanges > >> Loading required package: GenomicRanges > >> Loading required package: AnnotationDbi > >> Loading required package: Biobase > >> Welcome to Bioconductor > >> > >> Vignettes contain introductory material; view with > >> 'browseVignettes()'. To cite Bioconductor, see > >> 'citation("Biobase")', and for packages 'citation("pkgname")'. > >> > >> Loading required package: Biostrings > >> Loading required package: rtracklayer > >> Warning messages: > >> 1: replacing previous import 'initialize' when loading 'rtracklayer' > >> 2: replacing previous import 'show' when loading 'rtracklayer' > >>> hm450 <- get450k() > >> Error in `seqinfo<-`(`*tmp*`, value = NULL) : > >> the supplied 'seqinfo' must be a Seqinfo object > >> In addition: Warning message: > >> In if is.na(genome(GR))) { : > >> the condition has length > 1 and only the first element will be used > >>> sessionInfo() > >> R version 2.15.1 (2012-06-22) > >> Platform: x86_64-pc-mingw32/x64 (64-bit) > >> > >> locale: > >> [1] LC_COLLATE=English_United States.1252 > >> [2] LC_CTYPE=English_United States.1252 > >> [3] LC_MONETARY=English_United States.1252 > >> [4] LC_NUMERIC=C > >> [5] LC_TIME=English_United States.1252 > >> > >> attached base packages: > >> [1] stats graphics grDevices utils datasets methods base > >> > >> other attached packages: > >> [1] FDb.InfiniumMethylation.hg19_1.0.1 rtracklayer_1.18.0 > >> [3] Biostrings_2.26.2 GenomicFeatures_1.10.0 > >> [5] AnnotationDbi_1.20.2 Biobase_2.18.0 > >> [7] GenomicRanges_1.10.2 IRanges_1.16.3 > >> [9] BiocGenerics_0.4.0 BiocInstaller_1.8.2 > >> > >> loaded via a namespace (and not attached): > >> [1] biomaRt_2.14.0 bitops_1.0-4.1 BSgenome_1.26.1 DBI_0.2-5 > >> [5] parallel_2.15.1 RCurl_1.95-1.1 Rsamtools_1.10.1 RSQLite_0.11.2 > >> [9] stats4_2.15.1 tools_2.15.1 XML_3.95-0.1 zlibbioc_1.4.0 > >>> > >> > >> > >> --------------------------------------------------------- > >> Guido Hooiveld, PhD > >> Nutrition, Metabolism & Genomics Group > >> Division of Human Nutrition > >> Wageningen University > >> Biotechnion, Bomenweg 2 > >> NL-6703 HD Wageningen > >> the Netherlands > >> tel: (+)31 317 485788 > >> fax: (+)31 317 483342 > >> email: guido.hooiveld@wur.nl > >> internet: http://nutrigene.4t.com > >> http://scholar.google.com/citations?user=qFHaMnoAAAAJ > >> http://www.researcherid.com/rid/F-4912-2010 > >> > >> > >> [[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 > >> > > > > > > > > --**** > > > *A model is a lie that helps you see the truth.* > > * > > * > > Howard Skipper< > http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>**** > > > > > [[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**** > > > > **** > > ** ** > > -- > *A model is a lie that helps you see the truth.***** > > ** ** > > Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> > **** > > ** ** > -- *A model is a lie that helps you see the truth.* * * Howard Skipper<http: cancerres.aacrjournals.org="" content="" 31="" 9="" 1173.full.pdf=""> [[alternative HTML version deleted]]
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