strange ChIPpeakAnno and rtracklayer interaction.
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@olegstatberkeleyedu-4310
Last seen 7.2 years ago
Hi, all I wanted to annotate my peaks using ChIPpeakAnno with a table from UCSC genome browser that I was going to import using rtracklayer package. The code runs fine if I do this: library(ChIPpeakAnno) library(rtracklayer) session=browserSession() genome(session)='hg19' query=ucscTableQuery(session,'refGene') BUT: if I exchange the order in which I load libraries in a new R session, it crashes: library(rtracklayer) library(ChIPpeakAnno) session=browserSession() genome(session)='hg19' > query=ucscTableQuery(session,'refGene') Error in x[[name, exact = FALSE]] : missing '[[' method for Sequence class GRanges > So there seems to be some sort of weird interaction between ChIPpeakAnno and rtracklayer that causes errors if ChIPpeakAnno is loaded AFTER rtracklayer but not before. It also seems that in general, I need to load ChIPpeakAnno before ANY OTHER packages I use because for example this works: library(ChIPpeakAnno) library(BSgenome.Hsapiens.UCSC.hg19) library(ShortRead) library(rtracklayer) session=browserSession() genome(session)='hg19' query=ucscTableQuery(session,'refGene') but this doesn't: library(BSgenome.Hsapiens.UCSC.hg19) library(ChIPpeakAnno) library(ShortRead) library(rtracklayer) session=browserSession() genome(session)='hg19' query=ucscTableQuery(session,'refGene') Error in x[[name, exact = FALSE]] : missing '[[' method for Sequence class GRanges Session info for this last session is below. Just letting you know that this problem exists. Oleg. > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) 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] rtracklayer_1.9.11 RCurl_1.4-3 [3] bitops_1.0-4.1 ShortRead_1.7.30 [5] Rsamtools_1.1.17 lattice_0.19-13 [7] ChIPpeakAnno_1.5.5 limma_3.5.21 [9] org.Hs.eg.db_2.4.6 GO.db_2.4.5 [11] RSQLite_0.9-2 DBI_0.2-5 [13] AnnotationDbi_1.11.9 BSgenome.Ecoli.NCBI.20080805_1.3.16 [15] multtest_2.5.14 Biobase_2.9.2 [17] biomaRt_2.5.1 BSgenome.Hsapiens.UCSC.hg19_1.3.16 [19] BSgenome_1.17.7 Biostrings_2.17.48 [21] GenomicRanges_1.1.38 IRanges_1.7.39 loaded via a namespace (and not attached): [1] grid_2.12.0 hwriter_1.2 MASS_7.3-8 splines_2.12.0 [5] survival_2.35-8 XML_3.2-0 >
GO annotate rtracklayer ChIPpeakAnno GO annotate rtracklayer ChIPpeakAnno • 750 views
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 3 months ago
United States
Herve, Do you know why the following error occurs depending on the order of package loading? ChIPpeakAnno does not use Granges and this error does not occur in the previous release. Error in x[[name, exact = FALSE]] : missing '[[' method for Sequence class Granges Best regards, Julie ------ Forwarded Message From: "oleg@stat.berkeley.edu" <oleg@stat.berkeley.edu> Date: Thu, 21 Oct 2010 18:58:57 -0400 To: "bioconductor at stat.math.ethz.ch" <bioconductor at="" stat.math.ethz.ch=""> Subject: [BioC] strange ChIPpeakAnno and rtracklayer interaction. Hi, all I wanted to annotate my peaks using ChIPpeakAnno with a table from UCSC genome browser that I was going to import using rtracklayer package. The code runs fine if I do this: library(ChIPpeakAnno) library(rtracklayer) session=browserSession() genome(session)='hg19' query=ucscTableQuery(session,'refGene') BUT: if I exchange the order in which I load libraries in a new R session, it crashes: library(rtracklayer) library(ChIPpeakAnno) session=browserSession() genome(session)='hg19' > query=ucscTableQuery(session,'refGene') Error in x[[name, exact = FALSE]] : missing '[[' method for Sequence class GRanges > So there seems to be some sort of weird interaction between ChIPpeakAnno and rtracklayer that causes errors if ChIPpeakAnno is loaded AFTER rtracklayer but not before. It also seems that in general, I need to load ChIPpeakAnno before ANY OTHER packages I use because for example this works: library(ChIPpeakAnno) library(BSgenome.Hsapiens.UCSC.hg19) library(ShortRead) library(rtracklayer) session=browserSession() genome(session)='hg19' query=ucscTableQuery(session,'refGene') but this doesn't: library(BSgenome.Hsapiens.UCSC.hg19) library(ChIPpeakAnno) library(ShortRead) library(rtracklayer) session=browserSession() genome(session)='hg19' query=ucscTableQuery(session,'refGene') Error in x[[name, exact = FALSE]] : missing '[[' method for Sequence class GRanges Session info for this last session is below. Just letting you know that this problem exists. Oleg. > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) 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] rtracklayer_1.9.11 RCurl_1.4-3 [3] bitops_1.0-4.1 ShortRead_1.7.30 [5] Rsamtools_1.1.17 lattice_0.19-13 [7] ChIPpeakAnno_1.5.5 limma_3.5.21 [9] org.Hs.eg.db_2.4.6 GO.db_2.4.5 [11] RSQLite_0.9-2 DBI_0.2-5 [13] AnnotationDbi_1.11.9 BSgenome.Ecoli.NCBI.20080805_1.3.16 [15] multtest_2.5.14 Biobase_2.9.2 [17] biomaRt_2.5.1 BSgenome.Hsapiens.UCSC.hg19_1.3.16 [19] BSgenome_1.17.7 Biostrings_2.17.48 [21] GenomicRanges_1.1.38 IRanges_1.7.39 loaded via a namespace (and not attached): [1] grid_2.12.0 hwriter_1.2 MASS_7.3-8 splines_2.12.0 [5] survival_2.35-8 XML_3.2-0 > _______________________________________________ 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 ------ End of Forwarded Message
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@michael-lawrence-3846
Last seen 21 days ago
United States
`Hi, Somehow the 'update,ANY' method defined by GenomicRanges is being superseded by stats::update() (which is the ANY method in all other packages). If I change update,ANY to update,GenomicRanges, everything works. I'll go ahead and commit this change, but this still seems like an issue with the methods package. Not sure why it only happens with ChIPpeakAnno. Michael On Thu, Oct 21, 2010 at 3:58 PM, <oleg@stat.berkeley.edu> wrote: > Hi, all > > I wanted to annotate my peaks using ChIPpeakAnno with a table from UCSC > genome browser that I was going to import using rtracklayer package. The > code runs fine if I do this: > > library(ChIPpeakAnno) > library(rtracklayer) > session=browserSession() > genome(session)='hg19' > query=ucscTableQuery(session,'refGene') > > > BUT: if I exchange the order in which I load libraries in a new R session, > it crashes: > > library(rtracklayer) > library(ChIPpeakAnno) > session=browserSession() > genome(session)='hg19' > > query=ucscTableQuery(session,'refGene') > Error in x[[name, exact = FALSE]] : > missing '[[' method for Sequence class GRanges > > > > > So there seems to be some sort of weird interaction between ChIPpeakAnno > and rtracklayer that causes errors if ChIPpeakAnno is loaded AFTER > rtracklayer but not before. > > It also seems that in general, I need to load ChIPpeakAnno before ANY > OTHER packages I use because for example this works: > > library(ChIPpeakAnno) > library(BSgenome.Hsapiens.UCSC.hg19) > library(ShortRead) > library(rtracklayer) > session=browserSession() > genome(session)='hg19' > query=ucscTableQuery(session,'refGene') > > but this doesn't: > > library(BSgenome.Hsapiens.UCSC.hg19) > library(ChIPpeakAnno) > library(ShortRead) > library(rtracklayer) > session=browserSession() > genome(session)='hg19' > query=ucscTableQuery(session,'refGene') > Error in x[[name, exact = FALSE]] : > missing '[[' method for Sequence class GRanges > > > Session info for this last session is below. Just letting you know that > this problem exists. > > Oleg. > > > > sessionInfo() > R version 2.12.0 (2010-10-15) > Platform: x86_64-unknown-linux-gnu (64-bit) > > 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] rtracklayer_1.9.11 RCurl_1.4-3 > [3] bitops_1.0-4.1 ShortRead_1.7.30 > [5] Rsamtools_1.1.17 lattice_0.19-13 > [7] ChIPpeakAnno_1.5.5 limma_3.5.21 > [9] org.Hs.eg.db_2.4.6 GO.db_2.4.5 > [11] RSQLite_0.9-2 DBI_0.2-5 > [13] AnnotationDbi_1.11.9 > BSgenome.Ecoli.NCBI.20080805_1.3.16 > [15] multtest_2.5.14 Biobase_2.9.2 > [17] biomaRt_2.5.1 BSgenome.Hsapiens.UCSC.hg19_1.3.16 > [19] BSgenome_1.17.7 Biostrings_2.17.48 > [21] GenomicRanges_1.1.38 IRanges_1.7.39 > > loaded via a namespace (and not attached): > [1] grid_2.12.0 hwriter_1.2 MASS_7.3-8 splines_2.12.0 > [5] survival_2.35-8 XML_3.2-0 > > > > _______________________________________________ > 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]]
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This is a nice example, concisely generating a problem that I encountered a couple of weeks ago. My impression was that the update method defined in multtest was the culprit. I can't say why. But when I remove the references to multtest in ChIPpeakAnno's DESCRIPTION and NAMESPACE files, so that multtest is neither loaded nor attached, and reinstall ChIPpeakAnno, the error does not occur in the second command sequence given by Oleg. This does not include Michael's new fix -- I haven't updated GenomicRanges. On Fri, Oct 22, 2010 at 6:03 PM, Michael Lawrence <lawrence.michael at="" gene.com=""> wrote: > `Hi, > > Somehow the 'update,ANY' method defined by GenomicRanges is being superseded > by stats::update() (which is the ANY method in all other packages). If I > change update,ANY to update,GenomicRanges, everything works. I'll go ahead > and commit this change, but this still seems like an issue with the methods > package. Not sure why it only happens with ChIPpeakAnno. > > Michael > > On Thu, Oct 21, 2010 at 3:58 PM, <oleg at="" stat.berkeley.edu=""> wrote: > >> Hi, all >> >> I wanted to annotate my peaks using ChIPpeakAnno with a table from UCSC >> genome browser that I was going to import using rtracklayer package. ?The >> code runs fine if I do this: >> >> library(ChIPpeakAnno) >> library(rtracklayer) >> session=browserSession() >> genome(session)='hg19' >> query=ucscTableQuery(session,'refGene') >> >> >> BUT: if I exchange the order in which I load libraries in a new R session, >> it crashes: >> >> library(rtracklayer) >> library(ChIPpeakAnno) >> session=browserSession() >> genome(session)='hg19' >> > query=ucscTableQuery(session,'refGene') >> Error in x[[name, exact = FALSE]] : >> ?missing '[[' method for Sequence class GRanges >> > >> >> >> So there seems to be some sort of weird interaction between ChIPpeakAnno >> and rtracklayer that causes errors if ChIPpeakAnno is loaded AFTER >> rtracklayer but not before. >> >> It also seems that in general, I need to load ChIPpeakAnno before ANY >> OTHER packages I use because for example this works: >> >> library(ChIPpeakAnno) >> library(BSgenome.Hsapiens.UCSC.hg19) >> library(ShortRead) >> library(rtracklayer) >> session=browserSession() >> genome(session)='hg19' >> query=ucscTableQuery(session,'refGene') >> >> but this doesn't: >> >> library(BSgenome.Hsapiens.UCSC.hg19) >> library(ChIPpeakAnno) >> library(ShortRead) >> library(rtracklayer) >> session=browserSession() >> genome(session)='hg19' >> query=ucscTableQuery(session,'refGene') >> Error in x[[name, exact = FALSE]] : >> ?missing '[[' method for Sequence class GRanges >> >> >> Session info for this last session is below. Just letting you know that >> this problem exists. >> >> Oleg. >> >> >> > sessionInfo() >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> 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] rtracklayer_1.9.11 ? ? ? ? ? ? ? ? ?RCurl_1.4-3 >> ?[3] bitops_1.0-4.1 ? ? ? ? ? ? ? ? ? ? ?ShortRead_1.7.30 >> ?[5] Rsamtools_1.1.17 ? ? ? ? ? ? ? ? ? ?lattice_0.19-13 >> ?[7] ChIPpeakAnno_1.5.5 ? ? ? ? ? ? ? ? ?limma_3.5.21 >> ?[9] org.Hs.eg.db_2.4.6 ? ? ? ? ? ? ? ? ?GO.db_2.4.5 >> [11] RSQLite_0.9-2 ? ? ? ? ? ? ? ? ? ? ? DBI_0.2-5 >> [13] AnnotationDbi_1.11.9 >> ?BSgenome.Ecoli.NCBI.20080805_1.3.16 >> [15] multtest_2.5.14 ? ? ? ? ? ? ? ? ? ? Biobase_2.9.2 >> [17] biomaRt_2.5.1 ? ? ? ? ? ? ? ? ? ? ? BSgenome.Hsapiens.UCSC.hg19_1.3.16 >> [19] BSgenome_1.17.7 ? ? ? ? ? ? ? ? ? ? Biostrings_2.17.48 >> [21] GenomicRanges_1.1.38 ? ? ? ? ? ? ? ?IRanges_1.7.39 >> >> loaded via a namespace (and not attached): >> [1] grid_2.12.0 ? ? hwriter_1.2 ? ? MASS_7.3-8 ? ? ?splines_2.12.0 >> [5] survival_2.35-8 XML_3.2-0 >> > >> >> _______________________________________________ >> 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 >> > > ? ? ? ?[[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 >
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