[ChIPpeakAnno] Can not start ChIPpeakAnno after update to version 2.5.9
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sheng zhao ▴ 90
@sheng-zhao-5316
Last seen 9.5 years ago
Germany
Dear all, I updated ChIPpeakAnno to 2.5.9 by: useDevel(TRUE) source("http://www.bioconductor.org/biocLite.R") biocLite("ChIPpeakAnno") After that, I got the following wrong Error information when starting ChIPpeakAnno: Loading required package: DBI Error : .onLoad failed in loadNamespace() for 'GO.db', details: call: ls(envir, all.names = TRUE) error: 7 arguments passed to .Internal(identical) which requires 6 Error: package 'GO.db' could not be loaded Any suggestion? Thanks . ps: Working with ChIPpeakAnno 2.4.0 is fine. Regards, Sheng > sessionInfo() sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] RSQLite_0.11.1 DBI_0.2-5 [3] AnnotationDbi_1.19.9 BSgenome.Ecoli.NCBI.20080805_1.3.17 [5] BSgenome_1.25.1 GenomicRanges_1.9.21 [7] Biostrings_2.25.4 IRanges_1.15.11 [9] multtest_2.13.0 Biobase_2.17.5 [11] biomaRt_2.13.1 BiocGenerics_0.3.0 [13] gplots_2.10.1 KernSmooth_2.23-7 [15] caTools_1.13 bitops_1.0-4.1 [17] gdata_2.8.2 gtools_2.6.2 loaded via a namespace (and not attached): [1] MASS_7.3-18 RCurl_1.91-1 XML_3.9-4 splines_2.15.0 [5] stats4_2.15.0 survival_2.36-14 [[alternative HTML version deleted]]
ChIPpeakAnno ChIPpeakAnno • 1.7k views
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@steve-lianoglou-2771
Last seen 21 months ago
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Hi, On Fri, Jun 1, 2012 at 11:09 AM, sheng zhao <harryzs1981 at="" gmail.com=""> wrote: > Dear all, > > I updated ChIPpeakAnno to 2.5.9 by: > > useDevel(TRUE) > source("http://www.bioconductor.org/biocLite.R") > biocLite("ChIPpeakAnno") > > > > After that, I got the following wrong Error information when starting > ChIPpeakAnno: > > Loading required package: DBI > Error : .onLoad failed in loadNamespace() for 'GO.db', details: > ?call: ls(envir, all.names = TRUE) > ?error: 7 arguments passed to .Internal(identical) which requires 6 > Error: package 'GO.db' could not be loaded > > > Any suggestion? Thanks . > > ps: Working with ChIPpeakAnno 2.4.0 is fine. I suspect you'll need to upgrade the rest of your packages to their devel versions if you want to use the devel version of ChIPpeakAnno (using the devel version works for me). In light of the yearly R release cycle now, the bioc folks have outlined a strategy you might want to follow if you think you want to hop between release and devel versions of packages here: http://bioconductor.org/developers/useDevel/ HTH, -steve > > Regards, > Sheng > >> sessionInfo() > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] grid ? ? ?stats ? ? graphics ?grDevices utils ? ? datasets ?methods > [8] base > > other attached packages: > ?[1] RSQLite_0.11.1 ? ? ? ? ? ? ? ? ? ? ?DBI_0.2-5 > ?[3] AnnotationDbi_1.19.9 ? ? ? ? ? ? ? ?BSgenome.Ecoli.NCBI.20080805_1.3.17 > ?[5] BSgenome_1.25.1 ? ? ? ? ? ? ? ? ? ? GenomicRanges_1.9.21 > ?[7] Biostrings_2.25.4 ? ? ? ? ? ? ? ? ? IRanges_1.15.11 > ?[9] multtest_2.13.0 ? ? ? ? ? ? ? ? ? ? Biobase_2.17.5 > [11] biomaRt_2.13.1 ? ? ? ? ? ? ? ? ? ? ?BiocGenerics_0.3.0 > [13] gplots_2.10.1 ? ? ? ? ? ? ? ? ? ? ? KernSmooth_2.23-7 > [15] caTools_1.13 ? ? ? ? ? ? ? ? ? ? ? ?bitops_1.0-4.1 > [17] gdata_2.8.2 ? ? ? ? ? ? ? ? ? ? ? ? gtools_2.6.2 > > loaded via a namespace (and not attached): > [1] MASS_7.3-18 ? ? ?RCurl_1.91-1 ? ? XML_3.9-4 ? ? ? ?splines_2.15.0 > [5] stats4_2.15.0 ? ?survival_2.36-14 > > ? ? ? ?[[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 -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Hi Steve, thank you for your help. But I still face this problem even after I reinstalled R (version 2.15.0) and reinstalled all packages I need to devel versions . With other packages I am using, for example: cummerbund 1.99.2, under devel version , everything is working fine. I tested also all thing on windows, everything is working under devel versions. Is it a bug for Mac 10.7.4 ? Regards, Sheng sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] cummeRbund_1.99.2 fastcluster_1.1.6 [3] reshape2_1.2.1 ggplot2_0.9.1 [5] RSQLite_0.11.1 DBI_0.2-5 [7] AnnotationDbi_1.19.9 BSgenome.Ecoli.NCBI.20080805_1.3.17 [9] BSgenome_1.25.1 GenomicRanges_1.9.21 [11] Biostrings_2.25.4 IRanges_1.15.11 [13] multtest_2.13.0 Biobase_2.17.5 [15] biomaRt_2.13.1 BiocGenerics_0.3.0 [17] gplots_2.10.1 KernSmooth_2.23-7 [19] caTools_1.13 bitops_1.0-4.1 [21] gdata_2.8.2 gtools_2.6.2 [23] BiocInstaller_1.5.10 loaded via a namespace (and not attached): [1] MASS_7.3-18 RColorBrewer_1.0-5 RCurl_1.91-1 XML_3.9-4 [5] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 labeling_0.1 [9] memoise_0.1 munsell_0.3 plyr_1.7.1 proto_0.3-9.2 [13] scales_0.2.1 splines_2.15.0 stats4_2.15.0 stringr_0.6 [17] survival_2.36-14 tools_2.15.0 [[alternative HTML version deleted]]
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On 06/02/2012 12:25 AM, sheng zhao wrote: > Hi Steve, > > thank you for your help. > > But I still face this problem even after I reinstalled R (version 2.15.0) > and reinstalled all packages I need to devel versions . > > With other packages I am using, for example: cummerbund 1.99.2, under devel > version > , everything is working fine. > > I tested also all thing on windows, everything is working under devel > versions. > > Is it a bug for Mac 10.7.4 ? Steve is right that the problem is likely to be an outdated package; it is NOT related to operating system. Start a new R session, making sure that no '.Rhistory' or '.RData' are loaded (e.g., from the command line, R --vanilla) then issue the command source('http://bioconductor.org/biocLite.R') biocLite(character()) this should report any out-of-date packages; can you please post the result of this command? Since the original error occurred with GO.db, perhaps you could also report the result of packageDescription("GO.db")$Version. Can you simplify your session, e.g., cummbeRbund, fastcluster, reshape, and ggplot2 are not loaded by ChIPpeakAnno. Martin > > Regards, > Sheng > > sessionInfo() > > R version 2.15.0 (2012-03-30) > > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > > locale: > > [1] C > > > attached base packages: > > [1] grid stats graphics grDevices utils datasets methods > > [8] base > > > other attached packages: > > [1] cummeRbund_1.99.2 fastcluster_1.1.6 > > [3] reshape2_1.2.1 ggplot2_0.9.1 > > [5] RSQLite_0.11.1 DBI_0.2-5 > > [7] AnnotationDbi_1.19.9 BSgenome.Ecoli.NCBI.20080805_1.3.17 > > [9] BSgenome_1.25.1 GenomicRanges_1.9.21 > > [11] Biostrings_2.25.4 IRanges_1.15.11 > > [13] multtest_2.13.0 Biobase_2.17.5 > > [15] biomaRt_2.13.1 BiocGenerics_0.3.0 > > [17] gplots_2.10.1 KernSmooth_2.23-7 > > [19] caTools_1.13 bitops_1.0-4.1 > > [21] gdata_2.8.2 gtools_2.6.2 > > [23] BiocInstaller_1.5.10 > > > loaded via a namespace (and not attached): > > [1] MASS_7.3-18 RColorBrewer_1.0-5 RCurl_1.91-1 XML_3.9-4 > > > [5] colorspace_1.1-1 dichromat_1.2-4 digest_0.5.2 labeling_0.1 > > > [9] memoise_0.1 munsell_0.3 plyr_1.7.1 > proto_0.3-9.2 > > [13] scales_0.2.1 splines_2.15.0 stats4_2.15.0 stringr_0.6 > > > [17] survival_2.36-14 tools_2.15.0 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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Hi Martin, thank you for your help. Follow your guide : ------ source('http://bioconductor.org/biocLite.R') biocLite(character()) ------ I updated all old packages. I also checked the version of GO.db > packageDescription("GO.db")$Version [1] "2.7.1" But I am very sorry to say that I still face this problem.: > library(ChIPpeakAnno) Loading required package: gplots Loading required package: gtools Loading required package: gdata gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. Attaching package: 'gdata' The following object(s) are masked from 'package:stats': nobs The following object(s) are masked from 'package:utils': object.size Loading required package: caTools Loading required package: bitops Loading required package: grid Loading required package: KernSmooth KernSmooth 2.23 loaded Copyright M. P. Wand 1997-2009 Attaching package: 'gplots' The following object(s) are masked from 'package:stats': lowess Loading required package: BiocGenerics Attaching package: 'BiocGenerics' The following object(s) are masked from 'package:gdata': combine The following object(s) are masked from 'package:stats': xtabs The following object(s) are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, colnames, duplicated, eval, get, intersect, lapply, mapply, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, rownames, sapply, setdiff, table, tapply, union, unique Loading required package: biomaRt Loading required package: multtest 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")'. Attaching package: 'multtest' The following object(s) are masked from 'package:gplots': wapply Loading required package: IRanges Attaching package: 'IRanges' The following object(s) are masked from 'package:gplots': space The following object(s) are masked from 'package:caTools': runmean The following object(s) are masked from 'package:gdata': trim Loading required package: Biostrings Loading required package: BSgenome Loading required package: GenomicRanges Loading required package: BSgenome.Ecoli.NCBI.20080805 Loading required package: GO.db Loading required package: AnnotationDbi Attaching package: 'AnnotationDbi' The following object(s) are masked from 'package:BSgenome': species Loading required package: DBI Error : .onLoad failed in loadNamespace() for 'GO.db', details: call: ls(envir, all.names = TRUE) error: 7 arguments passed to .Internal(identical) which requires 6 Error: package 'GO.db' could not be loaded > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] RSQLite_0.11.1 DBI_0.2-5 [3] AnnotationDbi_1.19.9 BSgenome.Ecoli.NCBI.20080805_1.3.17 [5] BSgenome_1.25.1 GenomicRanges_1.9.21 [7] Biostrings_2.25.4 IRanges_1.15.12 [9] multtest_2.13.0 Biobase_2.17.5 [11] biomaRt_2.13.1 BiocGenerics_0.3.0 [13] gplots_2.10.1 KernSmooth_2.23-7 [15] caTools_1.13 bitops_1.0-4.1 [17] gdata_2.8.2 gtools_2.6.2 [19] BiocInstaller_1.5.10 loaded via a namespace (and not attached): [1] MASS_7.3-18 RCurl_1.91-1 XML_3.9-4 splines_2.15.0 [5] stats4_2.15.0 survival_2.36-14 tools_2.15.0 > source('http://bioconductor.org/biocLite.R') > biocLite(character()) BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.5.10. [[alternative HTML version deleted]]
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On 06/02/2012 01:00 PM, sheng zhao wrote: > Hi Martin, > > thank you for your help. > > Follow your guide : > ------ > source('http://bioconductor.org/biocLite.R') > biocLite(character()) > ------ > > I updated all old packages. > I also checked the version of GO.db > > > packageDescription("GO.db")$Version > [1] "2.7.1" > > > But I am very sorry to say that I still face this problem.: Does, in a new R --vanilla session, simply trying to load GO.db cause the problem, library(GO.db) ? > > > > library(ChIPpeakAnno) > Loading required package: gplots > Loading required package: gtools > Loading required package: gdata > gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED. > > gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED. > > Attaching package: 'gdata' > > The following object(s) are masked from 'package:stats': > > nobs > > The following object(s) are masked from 'package:utils': > > object.size > > Loading required package: caTools > Loading required package: bitops > Loading required package: grid > Loading required package: KernSmooth > KernSmooth 2.23 loaded > Copyright M. P. Wand 1997-2009 > > Attaching package: 'gplots' > > The following object(s) are masked from 'package:stats': > > lowess > > Loading required package: BiocGenerics > > Attaching package: 'BiocGenerics' > > The following object(s) are masked from 'package:gdata': > > combine > > The following object(s) are masked from 'package:stats': > > xtabs > > The following object(s) are masked from 'package:base': > > Filter, Find, Map, Position, Reduce, anyDuplicated, cbind, > colnames, duplicated, eval, get, intersect, lapply, mapply, mget, > order, paste, pmax, pmax.int <http: pmax.int="">, pmin, pmin.int > <http: pmin.int="">, rbind, rep.int <http: rep.int="">, > rownames, sapply, setdiff, table, tapply, union, unique > > Loading required package: biomaRt > Loading required package: multtest > 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")'. > > > Attaching package: 'multtest' > > The following object(s) are masked from 'package:gplots': > > wapply > > Loading required package: IRanges > > Attaching package: 'IRanges' > > The following object(s) are masked from 'package:gplots': > > space > > The following object(s) are masked from 'package:caTools': > > runmean > > The following object(s) are masked from 'package:gdata': > > trim > > Loading required package: Biostrings > Loading required package: BSgenome > Loading required package: GenomicRanges > Loading required package: BSgenome.Ecoli.NCBI.20080805 > Loading required package: GO.db > Loading required package: AnnotationDbi > > Attaching package: 'AnnotationDbi' > > The following object(s) are masked from 'package:BSgenome': > > species > > Loading required package: DBI > Error : .onLoad failed in loadNamespace() for 'GO.db', details: > call: ls(envir, all.names = TRUE) > error: 7 arguments passed to .Internal(identical) which requires 6 > Error: package 'GO.db' could not be loaded > > > > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] RSQLite_0.11.1 DBI_0.2-5 > [3] AnnotationDbi_1.19.9 > BSgenome.Ecoli.NCBI.20080805_1.3.17 > [5] BSgenome_1.25.1 GenomicRanges_1.9.21 > [7] Biostrings_2.25.4 IRanges_1.15.12 > [9] multtest_2.13.0 Biobase_2.17.5 > [11] biomaRt_2.13.1 BiocGenerics_0.3.0 > [13] gplots_2.10.1 KernSmooth_2.23-7 > [15] caTools_1.13 bitops_1.0-4.1 > [17] gdata_2.8.2 gtools_2.6.2 > [19] BiocInstaller_1.5.10 > > loaded via a namespace (and not attached): > [1] MASS_7.3-18 RCurl_1.91-1 XML_3.9-4 splines_2.15.0 > [5] stats4_2.15.0 survival_2.36-14 tools_2.15.0 > > source('http://bioconductor.org/biocLite.R') > > biocLite(character()) > BioC_mirror: http://bioconductor.org > Using R version 2.15, BiocInstaller version 1.5.10. > > -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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