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Question: org.Hs.eg.db package loading issues
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5.4 years ago by
Guest User12k
Guest User12k wrote:
Hi, When I run the R code on analysis of HuGene2.0ST array, it generated an error as follows: > source("/Users/jial2/Documents/projects/Project422/limmaAnalysis.R") Loading required package: org.Hs.eg.db Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object '.setDummyField' not found Error: package ???org.Hs.eg.db??? could not be loaded Then I run the library individually, it still has the same error message. > library(org.Hs.eg.db) Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object '.setDummyField' not found Error: package or namespace load failed for ???org.Hs.eg.db??? Any suggestions would be highly appreciated. Thanks, -- output of sessionInfo(): > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationDbi_1.22.6 limma_3.16.6 pd.hugene.2.0.st_3.8.0 [4] RSQLite_0.11.4 DBI_0.2-7 oligo_1.24.1 [7] oligoClasses_1.22.0 affyPLM_1.36.0 preprocessCore_1.22.0 [10] arrayQualityMetrics_3.16.0 affyQCReport_1.38.0 lattice_0.20-15 [13] simpleaffy_2.36.1 gcrma_2.32.0 genefilter_1.42.0 [16] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 [19] BiocInstaller_1.10.2 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0 beadarray_2.10.0 [5] BeadDataPackR_1.12.0 Biostrings_2.28.0 bit_1.1-10 Cairo_1.5-2 [9] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 ff_2.2-11 [13] foreach_1.4.1 GenomicRanges_1.12.4 grid_3.0.0 Hmisc_3.12-2 [17] hwriter_1.3 IRanges_1.18.2 iterators_1.0.6 KernSmooth_2.23-10 [21] latticeExtra_0.6-24 plyr_1.8 RColorBrewer_1.0-5 reshape2_1.2.2 [25] rpart_4.1-1 setRNG_2011.11-2 splines_3.0.0 stats4_3.0.0 [29] stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 tools_3.0.0 [33] vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 5.4 years ago by Dan Tenenbaum ♦♦ 8.2k • written 5.4 years ago by Guest User12k
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5.4 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
On Fri, Jul 26, 2013 at 8:41 AM, Guest [guest] <guest at="" bioconductor.org=""> wrote: > > Hi, > > When I run the R code on analysis of HuGene2.0ST array, it generated an error as follows: > >> source("/Users/jial2/Documents/projects/Project422/limmaAnalysis.R") > Loading required package: org.Hs.eg.db > Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: > call: get(name, envir = asNamespace(pkg), inherits = FALSE) > error: object '.setDummyField' not found > Error: package ???org.Hs.eg.db??? could not be loaded > > Then I run the library individually, it still has the same error message. > >> library(org.Hs.eg.db) > Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: > call: get(name, envir = asNamespace(pkg), inherits = FALSE) > error: object '.setDummyField' not found > Error: package or namespace load failed for ???org.Hs.eg.db??? > > Any suggestions would be highly appreciated. > This problem can be solved by updating to R 3.0.1. Dan > Thanks, > > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] AnnotationDbi_1.22.6 limma_3.16.6 pd.hugene.2.0.st_3.8.0 > [4] RSQLite_0.11.4 DBI_0.2-7 oligo_1.24.1 > [7] oligoClasses_1.22.0 affyPLM_1.36.0 preprocessCore_1.22.0 > [10] arrayQualityMetrics_3.16.0 affyQCReport_1.38.0 lattice_0.20-15 > [13] simpleaffy_2.36.1 gcrma_2.32.0 genefilter_1.42.0 > [16] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 > [19] BiocInstaller_1.10.2 > > loaded via a namespace (and not attached): > [1] affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0 beadarray_2.10.0 > [5] BeadDataPackR_1.12.0 Biostrings_2.28.0 bit_1.1-10 Cairo_1.5-2 > [9] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 ff_2.2-11 > [13] foreach_1.4.1 GenomicRanges_1.12.4 grid_3.0.0 Hmisc_3.12-2 > [17] hwriter_1.3 IRanges_1.18.2 iterators_1.0.6 KernSmooth_2.23-10 > [21] latticeExtra_0.6-24 plyr_1.8 RColorBrewer_1.0-5 reshape2_1.2.2 > [25] rpart_4.1-1 setRNG_2011.11-2 splines_3.0.0 stats4_3.0.0 > [29] stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 tools_3.0.0 > [33] vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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
ADD COMMENTlink written 5.4 years ago by Dan Tenenbaum ♦♦ 8.2k
Thanks Dan! It works. Li On 7/26/13 1:43 PM, "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> wrote: >On Fri, Jul 26, 2013 at 8:41 AM, Guest [guest] <guest at="" bioconductor.org=""> >wrote: >> >> Hi, >> >> When I run the R code on analysis of HuGene2.0ST array, it generated an >>error as follows: >> >>> source("/Users/jial2/Documents/projects/Project422/limmaAnalysis.R") >> Loading required package: org.Hs.eg.db >> Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: >> call: get(name, envir = asNamespace(pkg), inherits = FALSE) >> error: object '.setDummyField' not found >> Error: package ???org.Hs.eg.db??? could not be loaded >> >> Then I run the library individually, it still has the same error >>message. >> >>> library(org.Hs.eg.db) >> Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: >> call: get(name, envir = asNamespace(pkg), inherits = FALSE) >> error: object '.setDummyField' not found >> Error: package or namespace load failed for ???org.Hs.eg.db??? >> >> Any suggestions would be highly appreciated. >> > > >This problem can be solved by updating to R 3.0.1. >Dan > > >> Thanks, >> >> >> -- output of sessionInfo(): >> >>> sessionInfo() >> R version 3.0.0 (2013-04-03) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] AnnotationDbi_1.22.6 limma_3.16.6 >>pd.hugene.2.0.st_3.8.0 >> [4] RSQLite_0.11.4 DBI_0.2-7 oligo_1.24.1 >> [7] oligoClasses_1.22.0 affyPLM_1.36.0 >>preprocessCore_1.22.0 >> [10] arrayQualityMetrics_3.16.0 affyQCReport_1.38.0 >>lattice_0.20-15 >> [13] simpleaffy_2.36.1 gcrma_2.32.0 >>genefilter_1.42.0 >> [16] affy_1.38.1 Biobase_2.20.1 >>BiocGenerics_0.6.0 >> [19] BiocInstaller_1.10.2 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0 >>beadarray_2.10.0 >> [5] BeadDataPackR_1.12.0 Biostrings_2.28.0 bit_1.1-10 >>Cairo_1.5-2 >> [9] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 >>ff_2.2-11 >> [13] foreach_1.4.1 GenomicRanges_1.12.4 grid_3.0.0 >>Hmisc_3.12-2 >> [17] hwriter_1.3 IRanges_1.18.2 iterators_1.0.6 >>KernSmooth_2.23-10 >> [21] latticeExtra_0.6-24 plyr_1.8 RColorBrewer_1.0-5 >>reshape2_1.2.2 >> [25] rpart_4.1-1 setRNG_2011.11-2 splines_3.0.0 >>stats4_3.0.0 >> [29] stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 >>tools_3.0.0 >> [33] vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 >>zlibbioc_1.6.0 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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
ADD REPLYlink written 5.4 years ago by Jia, Li NIH/NCI [C]70
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gravatar for Ekta Jain
5.4 years ago by
Ekta Jain50
Ekta Jain50 wrote:
Hi, I got some error too when I was trying to load the org.Hs.eg.db in R. I downloaded the .zip file of the package and then installed it manually as a local package, it worked for me. Hope it works for you as well. Regards Ekta Jain Research Analyst Biotechnology and Bio-resources Division The Energy and Resources Institute, India Habitat Centre Lodhi Road, New Delhi - 110033 #09958818853 ekta.jain at teri.res.in -----bioconductor-bounces at r-project.org wrote: ----- To: bioconductor at r-project.org, jial2 at mail.nih.gov From: "Guest [guest]" Sent by: bioconductor-bounces at r-project.org Date: 07/26/2013 09:13PM Subject: [BioC] org.Hs.eg.db package loading issues Hi, When I run the R code on analysis of HuGene2.0ST array, it generated an error as follows: > source("/Users/jial2/Documents/projects/Project422/limmaAnalysis.R") Loading required package: org.Hs.eg.db Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object '.setDummyField' not found Error: package ???????org.Hs.eg.db???????? could not be loaded Then I run the library individually, it still has the same error message. > library(org.Hs.eg.db) Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object '.setDummyField' not found Error: package or namespace load failed for ???????org.Hs.eg.db???????? Any suggestions would be highly appreciated. Thanks, -- output of sessionInfo(): > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationDbi_1.22.6 limma_3.16.6 pd.hugene.2.0.st_3.8.0 [4] RSQLite_0.11.4 DBI_0.2-7 oligo_1.24.1 [7] oligoClasses_1.22.0 affyPLM_1.36.0 preprocessCore_1.22.0 [10] arrayQualityMetrics_3.16.0 affyQCReport_1.38.0 lattice_0.20-15 [13] simpleaffy_2.36.1 gcrma_2.32.0 genefilter_1.42.0 [16] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 [19] BiocInstaller_1.10.2 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0 beadarray_2.10.0 [5] BeadDataPackR_1.12.0 Biostrings_2.28.0 bit_1.1-10 Cairo_1.5-2 [9] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 ff_2.2-11 [13] foreach_1.4.1 GenomicRanges_1.12.4 grid_3.0.0 Hmisc_3.12-2 [17] hwriter_1.3 IRanges_1.18.2 iterators_1.0.6 KernSmooth_2.23-10 [21] latticeExtra_0.6-24 plyr_1.8 RColorBrewer_1.0-5 reshape2_1.2.2 [25] rpart_4.1-1 setRNG_2011.11-2 splines_3.0.0 stats4_3.0.0 [29] stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 tools_3.0.0 [33] vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org [1]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [2]http://news.gmane.org/gmane.science.biology.informatics.conductor ---------------------------------------------------------------------- --------- ----------------------------- Disclaimer: The information contained in this e-mail is intended for...{{dropped:12}} References 1. https://stat.ethz.ch/mailman/listinfo/bioconductor 2. http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 5.4 years ago by Ekta Jain50
Thanks Ekta! I just got message from Dan who suggested to update to 3.0.1, which works. Have a nice weekend! Li From: Ekta Jain <ekta.jain@teri.res.in<mailto:ekta.jain@teri.res.in>> Date: Fri, 26 Jul 2013 21:16:48 +0530 To: "Guest [guest]" <guest at="" bioconductor.org<mailto:guest="" at="" bioconductor.org="">> Cc: <bioconductor at="" r-project.org<mailto:bioconductor="" at="" r-project.org="">>, Mac User <jial2 at="" mail.nih.gov<mailto:jial2="" at="" mail.nih.gov="">> Subject: Re: [BioC] org.Hs.eg.db package loading issues Hi, I got some error too when I was trying to load the org.Hs.eg.db in R. I downloaded the .zip file of the package and then installed it manually as a local package, it worked for me. Hope it works for you as well. Regards Ekta Jain Research Analyst Biotechnology and Bio-resources Division The Energy and Resources Institute, India Habitat Centre Lodhi Road, New Delhi - 110033 #09958818853 ekta.jain at teri.res.in<mailto:ekta.jain at="" teri.res.in=""> -----bioconductor-bounces at r-project.org<mailto:-----bioconductor- bounces="" at="" r-project.org=""> wrote: ----- To: bioconductor at r-project.org<mailto:bioconductor at="" r-project.org="">, jial2 at mail.nih.gov<mailto:jial2 at="" mail.nih.gov=""> From: "Guest [guest]" Sent by: bioconductor-bounces at r-project.org<mailto:bioconductor- bounces="" at="" r-project.org=""> Date: 07/26/2013 09:13PM Subject: [BioC] org.Hs.eg.db package loading issues Hi, When I run the R code on analysis of HuGene2.0ST array, it generated an error as follows: > source("/Users/jial2/Documents/projects/Project422/limmaAnalysis.R") Loading required package: org.Hs.eg.db Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object '.setDummyField' not found Error: package ???org.Hs.eg.db??? could not be loaded Then I run the library individually, it still has the same error message. > library(org.Hs.eg.db) Error : .onLoad failed in loadNamespace() for 'org.Hs.eg.db', details: call: get(name, envir = asNamespace(pkg), inherits = FALSE) error: object '.setDummyField' not found Error: package or namespace load failed for ???org.Hs.eg.db??? Any suggestions would be highly appreciated. Thanks, -- output of sessionInfo(): > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationDbi_1.22.6 limma_3.16.6 pd.hugene.2.0.st_3.8.0 [4] RSQLite_0.11.4 DBI_0.2-7 oligo_1.24.1 [7] oligoClasses_1.22.0 affyPLM_1.36.0 preprocessCore_1.22.0 [10] arrayQualityMetrics_3.16.0 affyQCReport_1.38.0 lattice_0.20-15 [13] simpleaffy_2.36.1 gcrma_2.32.0 genefilter_1.42.0 [16] affy_1.38.1 Biobase_2.20.1 BiocGenerics_0.6.0 [19] BiocInstaller_1.10.2 loaded via a namespace (and not attached): [1] affxparser_1.32.3 affyio_1.28.0 annotate_1.38.0 beadarray_2.10.0 [5] BeadDataPackR_1.12.0 Biostrings_2.28.0 bit_1.1-10 Cairo_1.5-2 [9] cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 ff_2.2-11 [13] foreach_1.4.1 GenomicRanges_1.12.4 grid_3.0.0 Hmisc_3.12-2 [17] hwriter_1.3 IRanges_1.18.2 iterators_1.0.6 KernSmooth_2.23-10 [21] latticeExtra_0.6-24 plyr_1.8 RColorBrewer_1.0-5 reshape2_1.2.2 [25] rpart_4.1-1 setRNG_2011.11-2 splines_3.0.0 stats4_3.0.0 [29] stringr_0.6.2 survival_2.37-4 SVGAnnotation_0.93-1 tools_3.0.0 [33] vsn_3.28.0 XML_3.95-0.2 xtable_1.7-1 zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ---------------------------------------------------------------------- -------------------------------------- Disclaimer: The information contained in this e-mail is intended for the person or entity to which it is addressed, and it may contain confidential and/or privilegedmaterial. Any review or other use of this mail or taking any action based on it by persons or entities other than the intended recipient is strictly prohibited. If you receive this e-mail by mistake, please contact the sender, and delete all copies of this mail.This e-mail has been scanned and verified by McAfee SaaS Email Security, formerly MX Logic.
ADD REPLYlink written 5.4 years ago by Jia, Li NIH/NCI [C]70
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