Annotate package not working
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@ryan-c-thompson-5618
Last seen 7 months ago
Scripps Research, La Jolla, CA
Hi all, I'm having some trouble using the "lookUp" function in the "annotate" package. Every time I try to call it, I get the following error: Error in as.list.default(envir) : no method for coercing this S4 class to a vector I can generate this error with the following short test case: library(org.Hs.eg.db) library(annotate) entrez.ids <- as.character(1:10) lookUp(entrez.ids, data="org.Hs.eg", what="SYMBOL") Alternatively, simply running the example from the lookUp help page also produces the error. Can anyone help me get this working again? -Ryan Thompson
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 3.1 years ago
United States
----- Original Message ----- > From: "Ryan C. Thompson" <rct at="" thompsonclan.org=""> > To: "bioconductor" <bioconductor at="" r-project.org=""> > Sent: Thursday, January 9, 2014 11:31:28 AM > Subject: [BioC] Annotate package not working > > Hi all, > > I'm having some trouble using the "lookUp" function in the "annotate" > package. Every time I try to call it, I get the following error: > > Error in as.list.default(envir) : > no method for coercing this S4 class to a vector > > I can generate this error with the following short test case: > > library(org.Hs.eg.db) > library(annotate) > entrez.ids <- as.character(1:10) > lookUp(entrez.ids, > data="org.Hs.eg", > what="SYMBOL") > > Alternatively, simply running the example from the lookUp help page > also > produces the error. > > Can anyone help me get this working again? > Can you send your sessionInfo()? It works for me in release and devel. Dan > -Ryan Thompson > > _______________________________________________ > 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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@james-w-macdonald-5106
Last seen 9 hours ago
United States
Hi Ryan, I can't reproduce your error: > library(annotate) > entrez.ids <- as.character(1:10) > lookUp(entrez.ids, + data="org.Hs.eg", + what="SYMBOL") $`1` [1] "A1BG" $`2` [1] "A2M" $`3` [1] "A2MP1" $`4` [1] NA $`5` [1] NA $`6` [1] NA $`7` [1] NA $`8` [1] NA $`9` [1] "NAT1" $`10` [1] "NAT2" > sessionInfo() R version 3.0.2 (2013-09-25) 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 [4] DBI_0.2-7 AnnotationDbi_1.25.2 Biobase_2.22.0 [7] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 You might have some package higher in your search path that re-defines mget() somehow. Anyway, you might consider switching to select(), as it is much more powerful/useful than lookUp(): > select(org.Hs.eg.db, entrez.ids, "SYMBOL") ENTREZID SYMBOL 1 1 A1BG 2 2 A2M 3 3 A2MP1 4 4 <na> 5 5 <na> 6 6 <na> 7 7 <na> 8 8 <na> 9 9 NAT1 10 10 NAT2 Best, Jim On Thursday, January 09, 2014 2:31:28 PM, Ryan C. Thompson wrote: > Hi all, > > I'm having some trouble using the "lookUp" function in the "annotate" > package. Every time I try to call it, I get the following error: > > Error in as.list.default(envir) : > no method for coercing this S4 class to a vector > > I can generate this error with the following short test case: > > library(org.Hs.eg.db) > library(annotate) > entrez.ids <- as.character(1:10) > lookUp(entrez.ids, > data="org.Hs.eg", > what="SYMBOL") > > Alternatively, simply running the example from the lookUp help page > also produces the error. > > Can anyone help me get this working again? > > -Ryan Thompson > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Here is a transcript where I start an R session, source my bug reproducing script, and then run sessionInfo(): $ R --vanilla R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > source("annotation-bug.R") Loading required package: AnnotationDbi Loading required package: BiocGenerics Loading required package: parallel Attaching package: ?BiocGenerics? The following objects are masked from ?package:parallel?: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ?package:stats?: xtabs The following objects are masked from ?package:base?: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist 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: DBI Error in as.list.default(envir) : no method for coercing this S4 class to a vector In addition: Warning message: In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, : No generic function found corresponding to requested imported methods for "as.list" from package "AnnotationDbi" (malformed exports?) > sessionInfo() R version 3.0.2 (2013-09-25) 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 [7] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] colorspace_1.2-4 IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 [5] xtable_1.7-2 On Thu 09 Jan 2014 11:45:22 AM PST, James W. MacDonald wrote: > > Hi Ryan, > > I can't reproduce your error: > >> >> library(annotate) >> entrez.ids <- as.character(1:10) >> lookUp(entrez.ids, > > + data="org.Hs.eg", > + what="SYMBOL") > $`1` > [1] "A1BG" > > $`2` > [1] "A2M" > > $`3` > [1] "A2MP1" > > $`4` > [1] NA > > $`5` > [1] NA > > $`6` > [1] NA > > $`7` > [1] NA > > $`8` > [1] NA > > $`9` > [1] "NAT1" > > $`10` > [1] "NAT2" > >> >> sessionInfo() > > R version 3.0.2 (2013-09-25) > 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 > [4] DBI_0.2-7 AnnotationDbi_1.25.2 Biobase_2.22.0 > [7] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 > > You might have some package higher in your search path that re- defines > mget() somehow. > > Anyway, you might consider switching to select(), as it is much more > powerful/useful than lookUp(): > >> >> select(org.Hs.eg.db, entrez.ids, "SYMBOL") > > ENTREZID SYMBOL > 1 1 A1BG > 2 2 A2M > 3 3 A2MP1 > 4 4 <na> > 5 5 <na> > 6 6 <na> > 7 7 <na> > 8 8 <na> > 9 9 NAT1 > 10 10 NAT2 > > Best, > > Jim > > > > > On Thursday, January 09, 2014 2:31:28 PM, Ryan C. Thompson wrote: >> >> Hi all, >> >> I'm having some trouble using the "lookUp" function in the "annotate" >> package. Every time I try to call it, I get the following error: >> >> Error in as.list.default(envir) : >> no method for coercing this S4 class to a vector >> >> I can generate this error with the following short test case: >> >> library(org.Hs.eg.db) >> library(annotate) >> entrez.ids <- as.character(1:10) >> lookUp(entrez.ids, >> data="org.Hs.eg", >> what="SYMBOL") >> >> Alternatively, simply running the example from the lookUp help page >> also produces the error. >> >> Can anyone help me get this working again? >> >> -Ryan Thompson >> >> _______________________________________________ >> 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 > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099
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----- Original Message ----- > From: "Ryan C. Thompson" <rct at="" thompsonclan.org=""> > To: "James W. MacDonald" <jmacdon at="" uw.edu=""> > Cc: "bioconductor" <bioconductor at="" r-project.org=""> > Sent: Thursday, January 9, 2014 12:28:01 PM > Subject: Re: [BioC] Annotate package not working > > Here is a transcript where I start an R session, source my bug > reproducing script, and then run sessionInfo(): > > $ R --vanilla > > R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" > Copyright (C) 2013 The R Foundation for Statistical Computing > Platform: x86_64-unknown-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > source("annotation-bug.R") > Loading required package: AnnotationDbi > Loading required package: BiocGenerics > Loading required package: parallel > > Attaching package: ?BiocGenerics? > > The following objects are masked from ?package:parallel?: > > clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, > clusterExport, clusterMap, parApply, parCapply, parLapply, > parLapplyLB, parRapply, parSapply, parSapplyLB > > The following object is masked from ?package:stats?: > > xtabs > > The following objects are masked from ?package:base?: > > anyDuplicated, append, as.data.frame, as.vector, cbind, > colnames, > duplicated, eval, evalq, Filter, Find, get, intersect, > is.unsorted, > lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, > pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, > rownames, > sapply, setdiff, sort, table, tapply, union, unique, unlist > > 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: DBI > > Error in as.list.default(envir) : > no method for coercing this S4 class to a vector > In addition: Warning message: > In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], > c(lib.loc, : > No generic function found corresponding to requested imported > methods > for "as.list" from package "AnnotationDbi" (malformed exports?) > > sessionInfo() > R version 3.0.2 (2013-09-25) > 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 > [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 > [7] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] colorspace_1.2-4 IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 > [5] xtable_1.7-2 > Hmm...it works for me with the following sessionInfo, it seems the only differences are R version (I'm running R-patched) and version of xtable, but I tried a newer one and it still worked. Also, I don't have colorspace loaded. Dan R version 3.0.2 Patched (2013-12-18 r64488) 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 [7] BiocGenerics_0.8.0 loaded via a namespace (and not attached): [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 > > On Thu 09 Jan 2014 11:45:22 AM PST, James W. MacDonald wrote: > > > > Hi Ryan, > > > > I can't reproduce your error: > > > >> > >> library(annotate) > >> entrez.ids <- as.character(1:10) > >> lookUp(entrez.ids, > > > > + data="org.Hs.eg", > > + what="SYMBOL") > > $`1` > > [1] "A1BG" > > > > $`2` > > [1] "A2M" > > > > $`3` > > [1] "A2MP1" > > > > $`4` > > [1] NA > > > > $`5` > > [1] NA > > > > $`6` > > [1] NA > > > > $`7` > > [1] NA > > > > $`8` > > [1] NA > > > > $`9` > > [1] "NAT1" > > > > $`10` > > [1] "NAT2" > > > >> > >> sessionInfo() > > > > R version 3.0.2 (2013-09-25) > > 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods > > [8] base > > > > other attached packages: > > [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 > > [4] DBI_0.2-7 AnnotationDbi_1.25.2 Biobase_2.22.0 > > [7] BiocGenerics_0.8.0 > > > > loaded via a namespace (and not attached): > > [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 > > > > You might have some package higher in your search path that > > re-defines > > mget() somehow. > > > > Anyway, you might consider switching to select(), as it is much > > more > > powerful/useful than lookUp(): > > > >> > >> select(org.Hs.eg.db, entrez.ids, "SYMBOL") > > > > ENTREZID SYMBOL > > 1 1 A1BG > > 2 2 A2M > > 3 3 A2MP1 > > 4 4 <na> > > 5 5 <na> > > 6 6 <na> > > 7 7 <na> > > 8 8 <na> > > 9 9 NAT1 > > 10 10 NAT2 > > > > Best, > > > > Jim > > > > > > > > > > On Thursday, January 09, 2014 2:31:28 PM, Ryan C. Thompson wrote: > >> > >> Hi all, > >> > >> I'm having some trouble using the "lookUp" function in the > >> "annotate" > >> package. Every time I try to call it, I get the following error: > >> > >> Error in as.list.default(envir) : > >> no method for coercing this S4 class to a vector > >> > >> I can generate this error with the following short test case: > >> > >> library(org.Hs.eg.db) > >> library(annotate) > >> entrez.ids <- as.character(1:10) > >> lookUp(entrez.ids, > >> data="org.Hs.eg", > >> what="SYMBOL") > >> > >> Alternatively, simply running the example from the lookUp help > >> page > >> also produces the error. > >> > >> Can anyone help me get this working again? > >> > >> -Ryan Thompson > >> > >> _______________________________________________ > >> 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 > > > > > > -- > > James W. MacDonald, M.S. > > Biostatistician > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > _______________________________________________ > 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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I've gotten this error before, and I just now randomly fixed it by reinstalling the AnnotationDbi package over and over until I saw the following line in the output: Creating a generic function for ?as.list? from package ?base? in package ?AnnotationDbi? I previously did not see this message while installing AnnotationDbi. Afterwards, my example worked fine. I have no explanation for why this keeps happening. -Ryan On Thu 09 Jan 2014 02:13:21 PM PST, Dan Tenenbaum wrote: > > > ----- Original Message ----- >> From: "Ryan C. Thompson" <rct at="" thompsonclan.org=""> >> To: "James W. MacDonald" <jmacdon at="" uw.edu=""> >> Cc: "bioconductor" <bioconductor at="" r-project.org=""> >> Sent: Thursday, January 9, 2014 12:28:01 PM >> Subject: Re: [BioC] Annotate package not working >> >> Here is a transcript where I start an R session, source my bug >> reproducing script, and then run sessionInfo(): >> >> $ R --vanilla >> >> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" >> Copyright (C) 2013 The R Foundation for Statistical Computing >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> R is free software and comes with ABSOLUTELY NO WARRANTY. >> You are welcome to redistribute it under certain conditions. >> Type 'license()' or 'licence()' for distribution details. >> >> Natural language support but running in an English locale >> >> R is a collaborative project with many contributors. >> Type 'contributors()' for more information and >> 'citation()' on how to cite R or R packages in publications. >> >> Type 'demo()' for some demos, 'help()' for on-line help, or >> 'help.start()' for an HTML browser interface to help. >> Type 'q()' to quit R. >> >> > source("annotation-bug.R") >> Loading required package: AnnotationDbi >> Loading required package: BiocGenerics >> Loading required package: parallel >> >> Attaching package: ?BiocGenerics? >> >> The following objects are masked from ?package:parallel?: >> >> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >> clusterExport, clusterMap, parApply, parCapply, parLapply, >> parLapplyLB, parRapply, parSapply, parSapplyLB >> >> The following object is masked from ?package:stats?: >> >> xtabs >> >> The following objects are masked from ?package:base?: >> >> anyDuplicated, append, as.data.frame, as.vector, cbind, >> colnames, >> duplicated, eval, evalq, Filter, Find, get, intersect, >> is.unsorted, >> lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, >> pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, >> rownames, >> sapply, setdiff, sort, table, tapply, union, unique, unlist >> >> 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: DBI >> >> Error in as.list.default(envir) : >> no method for coercing this S4 class to a vector >> In addition: Warning message: >> In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], >> c(lib.loc, : >> No generic function found corresponding to requested imported >> methods >> for "as.list" from package "AnnotationDbi" (malformed exports?) >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets >> methods >> [8] base >> >> other attached packages: >> [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 >> [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 >> [7] BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] colorspace_1.2-4 IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 >> [5] xtable_1.7-2 >> > > Hmm...it works for me with the following sessionInfo, it seems the only differences are R version (I'm running R-patched) and version of xtable, but I tried a newer one and it still worked. Also, I don't have colorspace loaded. > > Dan > > R version 3.0.2 Patched (2013-12-18 r64488) > 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 > [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 > [7] BiocGenerics_0.8.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 > > > >> >> On Thu 09 Jan 2014 11:45:22 AM PST, James W. MacDonald wrote: >>> >>> Hi Ryan, >>> >>> I can't reproduce your error: >>> >>>> >>>> library(annotate) >>>> entrez.ids <- as.character(1:10) >>>> lookUp(entrez.ids, >>> >>> + data="org.Hs.eg", >>> + what="SYMBOL") >>> $`1` >>> [1] "A1BG" >>> >>> $`2` >>> [1] "A2M" >>> >>> $`3` >>> [1] "A2MP1" >>> >>> $`4` >>> [1] NA >>> >>> $`5` >>> [1] NA >>> >>> $`6` >>> [1] NA >>> >>> $`7` >>> [1] NA >>> >>> $`8` >>> [1] NA >>> >>> $`9` >>> [1] "NAT1" >>> >>> $`10` >>> [1] "NAT2" >>> >>>> >>>> sessionInfo() >>> >>> R version 3.0.2 (2013-09-25) >>> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 >>> [4] DBI_0.2-7 AnnotationDbi_1.25.2 Biobase_2.22.0 >>> [7] BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 >>> >>> You might have some package higher in your search path that >>> re-defines >>> mget() somehow. >>> >>> Anyway, you might consider switching to select(), as it is much >>> more >>> powerful/useful than lookUp(): >>> >>>> >>>> select(org.Hs.eg.db, entrez.ids, "SYMBOL") >>> >>> ENTREZID SYMBOL >>> 1 1 A1BG >>> 2 2 A2M >>> 3 3 A2MP1 >>> 4 4 <na> >>> 5 5 <na> >>> 6 6 <na> >>> 7 7 <na> >>> 8 8 <na> >>> 9 9 NAT1 >>> 10 10 NAT2 >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> >>> On Thursday, January 09, 2014 2:31:28 PM, Ryan C. Thompson wrote: >>>> >>>> Hi all, >>>> >>>> I'm having some trouble using the "lookUp" function in the >>>> "annotate" >>>> package. Every time I try to call it, I get the following error: >>>> >>>> Error in as.list.default(envir) : >>>> no method for coercing this S4 class to a vector >>>> >>>> I can generate this error with the following short test case: >>>> >>>> library(org.Hs.eg.db) >>>> library(annotate) >>>> entrez.ids <- as.character(1:10) >>>> lookUp(entrez.ids, >>>> data="org.Hs.eg", >>>> what="SYMBOL") >>>> >>>> Alternatively, simply running the example from the lookUp help >>>> page >>>> also produces the error. >>>> >>>> Can anyone help me get this working again? >>>> >>>> -Ryan Thompson >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >> >> _______________________________________________ >> 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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On 01/09/2014 03:08 PM, Ryan C. Thompson wrote: > I've gotten this error before, and I just now randomly fixed it by reinstalling > the AnnotationDbi package over and over until I saw the following line in the > output: > > Creating a generic function for ?as.list? from package ?base? in package > ?AnnotationDbi? > > I previously did not see this message while installing AnnotationDbi. > Afterwards, my example worked fine. I have no explanation for why this keeps > happening. Hopefully this isn't random, but some other uncontrolled variable. I can reproduce (something like) this by installing AnnotationDbi when there is a generic 'as.list' available in the global environment at install time, e.g., I added this line to my .Rprofile setGeneric("as.list") Then I installed AnnotationDbi R -e "source('http://bioconductor.org/biocLite.R'); biocLite('AnnotationDbi')" (maybe you load a package or something similar during an interactive session where you subsequently installed AnnotationDbi?). Then when I run Ryan's commands in a new R session R -f annotation-bug.R I get > library(annotate) Warning message: In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, : No generic function found corresponding to requested imported methods for "as.list" from package "AnnotationDbi" (malformed exports?) > entrez.ids <- as.character(1:10) > lookUp(entrez.ids, data="org.Hs.eg", what="SYMBOL") Error in as.list.default(envir) : no method for coercing this S4 class to a vector Calls: lookUp -> mget -> mget -> as.list -> as.list.default Execution halted (I only see the warning the first time I load annotate...) Maybe there's a variation of this where there's a generic available at install time but a different generic at run time, e.g., from one package masking another? I think the work-around is to install packages in a new session started with R --vanilla and a solution is to create a generic as.list in BiocGenerics (AnnotationDbi will see and import this). Martin > > -Ryan > > > On Thu 09 Jan 2014 02:13:21 PM PST, Dan Tenenbaum wrote: >> >> >> ----- Original Message ----- >>> From: "Ryan C. Thompson" <rct at="" thompsonclan.org=""> >>> To: "James W. MacDonald" <jmacdon at="" uw.edu=""> >>> Cc: "bioconductor" <bioconductor at="" r-project.org=""> >>> Sent: Thursday, January 9, 2014 12:28:01 PM >>> Subject: Re: [BioC] Annotate package not working >>> >>> Here is a transcript where I start an R session, source my bug >>> reproducing script, and then run sessionInfo(): >>> >>> $ R --vanilla >>> >>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" >>> Copyright (C) 2013 The R Foundation for Statistical Computing >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>> You are welcome to redistribute it under certain conditions. >>> Type 'license()' or 'licence()' for distribution details. >>> >>> Natural language support but running in an English locale >>> >>> R is a collaborative project with many contributors. >>> Type 'contributors()' for more information and >>> 'citation()' on how to cite R or R packages in publications. >>> >>> Type 'demo()' for some demos, 'help()' for on-line help, or >>> 'help.start()' for an HTML browser interface to help. >>> Type 'q()' to quit R. >>> >>> > source("annotation-bug.R") >>> Loading required package: AnnotationDbi >>> Loading required package: BiocGenerics >>> Loading required package: parallel >>> >>> Attaching package: ?BiocGenerics? >>> >>> The following objects are masked from ?package:parallel?: >>> >>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >>> clusterExport, clusterMap, parApply, parCapply, parLapply, >>> parLapplyLB, parRapply, parSapply, parSapplyLB >>> >>> The following object is masked from ?package:stats?: >>> >>> xtabs >>> >>> The following objects are masked from ?package:base?: >>> >>> anyDuplicated, append, as.data.frame, as.vector, cbind, >>> colnames, >>> duplicated, eval, evalq, Filter, Find, get, intersect, >>> is.unsorted, >>> lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, >>> pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, >>> rownames, >>> sapply, setdiff, sort, table, tapply, union, unique, unlist >>> >>> 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: DBI >>> >>> Error in as.list.default(envir) : >>> no method for coercing this S4 class to a vector >>> In addition: Warning message: >>> In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], >>> c(lib.loc, : >>> No generic function found corresponding to requested imported >>> methods >>> for "as.list" from package "AnnotationDbi" (malformed exports?) >>> > sessionInfo() >>> R version 3.0.2 (2013-09-25) >>> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets >>> methods >>> [8] base >>> >>> other attached packages: >>> [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 >>> [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 >>> [7] BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] colorspace_1.2-4 IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 >>> [5] xtable_1.7-2 >>> >> >> Hmm...it works for me with the following sessionInfo, it seems the only >> differences are R version (I'm running R-patched) and version of xtable, but I >> tried a newer one and it still worked. Also, I don't have colorspace loaded. >> >> Dan >> >> R version 3.0.2 Patched (2013-12-18 r64488) >> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 >> [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 >> [7] BiocGenerics_0.8.0 >> >> loaded via a namespace (and not attached): >> [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 >> >> >> >>> >>> On Thu 09 Jan 2014 11:45:22 AM PST, James W. MacDonald wrote: >>>> >>>> Hi Ryan, >>>> >>>> I can't reproduce your error: >>>> >>>>> >>>>> library(annotate) >>>>> entrez.ids <- as.character(1:10) >>>>> lookUp(entrez.ids, >>>> >>>> + data="org.Hs.eg", >>>> + what="SYMBOL") >>>> $`1` >>>> [1] "A1BG" >>>> >>>> $`2` >>>> [1] "A2M" >>>> >>>> $`3` >>>> [1] "A2MP1" >>>> >>>> $`4` >>>> [1] NA >>>> >>>> $`5` >>>> [1] NA >>>> >>>> $`6` >>>> [1] NA >>>> >>>> $`7` >>>> [1] NA >>>> >>>> $`8` >>>> [1] NA >>>> >>>> $`9` >>>> [1] "NAT1" >>>> >>>> $`10` >>>> [1] "NAT2" >>>> >>>>> >>>>> sessionInfo() >>>> >>>> R version 3.0.2 (2013-09-25) >>>> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 >>>> [4] DBI_0.2-7 AnnotationDbi_1.25.2 Biobase_2.22.0 >>>> [7] BiocGenerics_0.8.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 >>>> >>>> You might have some package higher in your search path that >>>> re-defines >>>> mget() somehow. >>>> >>>> Anyway, you might consider switching to select(), as it is much >>>> more >>>> powerful/useful than lookUp(): >>>> >>>>> >>>>> select(org.Hs.eg.db, entrez.ids, "SYMBOL") >>>> >>>> ENTREZID SYMBOL >>>> 1 1 A1BG >>>> 2 2 A2M >>>> 3 3 A2MP1 >>>> 4 4 <na> >>>> 5 5 <na> >>>> 6 6 <na> >>>> 7 7 <na> >>>> 8 8 <na> >>>> 9 9 NAT1 >>>> 10 10 NAT2 >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>> >>>> On Thursday, January 09, 2014 2:31:28 PM, Ryan C. Thompson wrote: >>>>> >>>>> Hi all, >>>>> >>>>> I'm having some trouble using the "lookUp" function in the >>>>> "annotate" >>>>> package. Every time I try to call it, I get the following error: >>>>> >>>>> Error in as.list.default(envir) : >>>>> no method for coercing this S4 class to a vector >>>>> >>>>> I can generate this error with the following short test case: >>>>> >>>>> library(org.Hs.eg.db) >>>>> library(annotate) >>>>> entrez.ids <- as.character(1:10) >>>>> lookUp(entrez.ids, >>>>> data="org.Hs.eg", >>>>> what="SYMBOL") >>>>> >>>>> Alternatively, simply running the example from the lookUp help >>>>> page >>>>> also produces the error. >>>>> >>>>> Can anyone help me get this working again? >>>>> >>>>> -Ryan Thompson >>>>> >>>>> _______________________________________________ >>>>> 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 >>>> >>>> >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> University of Washington >>>> Environmental and Occupational Health Sciences >>>> 4225 Roosevelt Way NE, # 100 >>>> Seattle WA 98105-6099 >>> >>> _______________________________________________ >>> 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 > > _______________________________________________ > 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: Arnold Building M1 B861 Phone: (206) 667-2793
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I think this might be the problem. I remember checking "as.list" before and after installing/loading AnnotationDbi, and I think it was sometimes already an S4 generic. I'll experiment a bit more. On Thu 09 Jan 2014 07:15:47 PM PST, Martin Morgan wrote: > On 01/09/2014 03:08 PM, Ryan C. Thompson wrote: >> I've gotten this error before, and I just now randomly fixed it by >> reinstalling >> the AnnotationDbi package over and over until I saw the following >> line in the >> output: >> >> Creating a generic function for ?as.list? from package ?base? in package >> ?AnnotationDbi? >> >> I previously did not see this message while installing AnnotationDbi. >> Afterwards, my example worked fine. I have no explanation for why >> this keeps >> happening. > > Hopefully this isn't random, but some other uncontrolled variable. > > I can reproduce (something like) this by installing AnnotationDbi when > there is a generic 'as.list' available in the global environment at > install time, e.g., I added this line to my .Rprofile > > setGeneric("as.list") > > Then I installed AnnotationDbi > > R -e "source('http://bioconductor.org/biocLite.R'); > biocLite('AnnotationDbi')" > > (maybe you load a package or something similar during an interactive > session where you subsequently installed AnnotationDbi?). Then when I > run Ryan's commands in a new R session > > R -f annotation-bug.R > > I get > > > library(annotate) > Warning message: > In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc, : > No generic function found corresponding to requested imported > methods for "as.list" from package "AnnotationDbi" (malformed exports?) > > entrez.ids <- as.character(1:10) > > lookUp(entrez.ids, data="org.Hs.eg", what="SYMBOL") > Error in as.list.default(envir) : > no method for coercing this S4 class to a vector > Calls: lookUp -> mget -> mget -> as.list -> as.list.default > Execution halted > > (I only see the warning the first time I load annotate...) Maybe > there's a variation of this where there's a generic available at > install time but a different generic at run time, e.g., from one > package masking another? > > I think the work-around is to install packages in a new session > started with > > R --vanilla > > and a solution is to create a generic as.list in BiocGenerics > (AnnotationDbi will see and import this). > > Martin > >> >> -Ryan >> >> >> On Thu 09 Jan 2014 02:13:21 PM PST, Dan Tenenbaum wrote: >>> >>> >>> ----- Original Message ----- >>>> From: "Ryan C. Thompson" <rct at="" thompsonclan.org=""> >>>> To: "James W. MacDonald" <jmacdon at="" uw.edu=""> >>>> Cc: "bioconductor" <bioconductor at="" r-project.org=""> >>>> Sent: Thursday, January 9, 2014 12:28:01 PM >>>> Subject: Re: [BioC] Annotate package not working >>>> >>>> Here is a transcript where I start an R session, source my bug >>>> reproducing script, and then run sessionInfo(): >>>> >>>> $ R --vanilla >>>> >>>> R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" >>>> Copyright (C) 2013 The R Foundation for Statistical Computing >>>> Platform: x86_64-unknown-linux-gnu (64-bit) >>>> >>>> R is free software and comes with ABSOLUTELY NO WARRANTY. >>>> You are welcome to redistribute it under certain conditions. >>>> Type 'license()' or 'licence()' for distribution details. >>>> >>>> Natural language support but running in an English locale >>>> >>>> R is a collaborative project with many contributors. >>>> Type 'contributors()' for more information and >>>> 'citation()' on how to cite R or R packages in publications. >>>> >>>> Type 'demo()' for some demos, 'help()' for on-line help, or >>>> 'help.start()' for an HTML browser interface to help. >>>> Type 'q()' to quit R. >>>> >>>> > source("annotation-bug.R") >>>> Loading required package: AnnotationDbi >>>> Loading required package: BiocGenerics >>>> Loading required package: parallel >>>> >>>> Attaching package: ?BiocGenerics? >>>> >>>> The following objects are masked from ?package:parallel?: >>>> >>>> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, >>>> clusterExport, clusterMap, parApply, parCapply, parLapply, >>>> parLapplyLB, parRapply, parSapply, parSapplyLB >>>> >>>> The following object is masked from ?package:stats?: >>>> >>>> xtabs >>>> >>>> The following objects are masked from ?package:base?: >>>> >>>> anyDuplicated, append, as.data.frame, as.vector, cbind, >>>> colnames, >>>> duplicated, eval, evalq, Filter, Find, get, intersect, >>>> is.unsorted, >>>> lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, >>>> pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, >>>> rownames, >>>> sapply, setdiff, sort, table, tapply, union, unique, unlist >>>> >>>> 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: DBI >>>> >>>> Error in as.list.default(envir) : >>>> no method for coercing this S4 class to a vector >>>> In addition: Warning message: >>>> In namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], >>>> c(lib.loc, : >>>> No generic function found corresponding to requested imported >>>> methods >>>> for "as.list" from package "AnnotationDbi" (malformed exports?) >>>> > sessionInfo() >>>> R version 3.0.2 (2013-09-25) >>>> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets >>>> methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 >>>> [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 >>>> [7] BiocGenerics_0.8.0 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] colorspace_1.2-4 IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 >>>> [5] xtable_1.7-2 >>>> >>> >>> Hmm...it works for me with the following sessionInfo, it seems the only >>> differences are R version (I'm running R-patched) and version of >>> xtable, but I >>> tried a newer one and it still worked. Also, I don't have colorspace >>> loaded. >>> >>> Dan >>> >>> R version 3.0.2 Patched (2013-12-18 r64488) >>> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 >>> [4] DBI_0.2-7 AnnotationDbi_1.24.0 Biobase_2.22.0 >>> [7] BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 >>> >>> >>> >>>> >>>> On Thu 09 Jan 2014 11:45:22 AM PST, James W. MacDonald wrote: >>>>> >>>>> Hi Ryan, >>>>> >>>>> I can't reproduce your error: >>>>> >>>>>> >>>>>> library(annotate) >>>>>> entrez.ids <- as.character(1:10) >>>>>> lookUp(entrez.ids, >>>>> >>>>> + data="org.Hs.eg", >>>>> + what="SYMBOL") >>>>> $`1` >>>>> [1] "A1BG" >>>>> >>>>> $`2` >>>>> [1] "A2M" >>>>> >>>>> $`3` >>>>> [1] "A2MP1" >>>>> >>>>> $`4` >>>>> [1] NA >>>>> >>>>> $`5` >>>>> [1] NA >>>>> >>>>> $`6` >>>>> [1] NA >>>>> >>>>> $`7` >>>>> [1] NA >>>>> >>>>> $`8` >>>>> [1] NA >>>>> >>>>> $`9` >>>>> [1] "NAT1" >>>>> >>>>> $`10` >>>>> [1] "NAT2" >>>>> >>>>>> >>>>>> sessionInfo() >>>>> >>>>> R version 3.0.2 (2013-09-25) >>>>> 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=en_US.UTF-8 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] parallel stats graphics grDevices utils datasets methods >>>>> [8] base >>>>> >>>>> other attached packages: >>>>> [1] annotate_1.40.0 org.Hs.eg.db_2.10.1 RSQLite_0.11.4 >>>>> [4] DBI_0.2-7 AnnotationDbi_1.25.2 Biobase_2.22.0 >>>>> [7] BiocGenerics_0.8.0 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] IRanges_1.20.6 stats4_3.0.2 XML_3.98-1.1 xtable_1.7-1 >>>>> >>>>> You might have some package higher in your search path that >>>>> re-defines >>>>> mget() somehow. >>>>> >>>>> Anyway, you might consider switching to select(), as it is much >>>>> more >>>>> powerful/useful than lookUp(): >>>>> >>>>>> >>>>>> select(org.Hs.eg.db, entrez.ids, "SYMBOL") >>>>> >>>>> ENTREZID SYMBOL >>>>> 1 1 A1BG >>>>> 2 2 A2M >>>>> 3 3 A2MP1 >>>>> 4 4 <na> >>>>> 5 5 <na> >>>>> 6 6 <na> >>>>> 7 7 <na> >>>>> 8 8 <na> >>>>> 9 9 NAT1 >>>>> 10 10 NAT2 >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>> >>>>> >>>>> On Thursday, January 09, 2014 2:31:28 PM, Ryan C. Thompson wrote: >>>>>> >>>>>> Hi all, >>>>>> >>>>>> I'm having some trouble using the "lookUp" function in the >>>>>> "annotate" >>>>>> package. Every time I try to call it, I get the following error: >>>>>> >>>>>> Error in as.list.default(envir) : >>>>>> no method for coercing this S4 class to a vector >>>>>> >>>>>> I can generate this error with the following short test case: >>>>>> >>>>>> library(org.Hs.eg.db) >>>>>> library(annotate) >>>>>> entrez.ids <- as.character(1:10) >>>>>> lookUp(entrez.ids, >>>>>> data="org.Hs.eg", >>>>>> what="SYMBOL") >>>>>> >>>>>> Alternatively, simply running the example from the lookUp help >>>>>> page >>>>>> also produces the error. >>>>>> >>>>>> Can anyone help me get this working again? >>>>>> >>>>>> -Ryan Thompson >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>>> -- >>>>> James W. MacDonald, M.S. >>>>> Biostatistician >>>>> University of Washington >>>>> Environmental and Occupational Health Sciences >>>>> 4225 Roosevelt Way NE, # 100 >>>>> Seattle WA 98105-6099 >>>> >>>> _______________________________________________ >>>> 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 >> >> _______________________________________________ >> 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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