Question: annotate htmlpage error
0
gravatar for Georg Otto
7.7 years ago by
Georg Otto120
Georg Otto120 wrote:
Hi, after updating the annotate package from 1.32.1 to 1.32.2 I get an error using the htmlpage function. Here with the old version: > htmlpage(list(deg$id), file = "test-1.html", othernames = list(othernames), table.head = table.head, repository = list("ens"), species ="Rattus_norvegicus") > sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annotate_1.32.1 AnnotationDbi_1.16.19 Biobase_2.14.0 loaded via a namespace (and not attached): [1] DBI_0.2-5 IRanges_1.12.6 RSQLite_0.11.1 xtable_1.7-0 now with the new version: > htmlpage(list(deg$id), file = "test-1.html", othernames = list(othernames), table.head = table.head, repository = list("ens"), species ="Rattus_norvegicus") Error: To make links for Ensembl, you need to pass a 'species' argument. > sessionInfo() R version 2.14.2 (2012-02-29) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] annotate_1.32.2 AnnotationDbi_1.16.19 Biobase_2.14.0 loaded via a namespace (and not attached): [1] DBI_0.2-5 IRanges_1.12.6 RSQLite_0.11.1 xtable_1.7-0 It seems that the "species" argument is not passed correctly. Can this be fixed? Best, Georg
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ADD COMMENTlink modified 7.7 years ago • written 7.7 years ago by Georg Otto120
Answer: annotate htmlpage error
0
gravatar for Martin Morgan
7.7 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
On 03/14/2012 01:13 PM, Georg Otto wrote: > Hi, > > after updating the annotate package from 1.32.1 to 1.32.2 I get an error > using the htmlpage function. Here with the old version: Sorry, probably my fault; I've tried to update this in v. 1.32.3. If you provide a fully reproducible example (deg$id, othernames, table.head as necessary to reproduce just the bug) I could be more sure of the fix. Martin > >> htmlpage(list(deg$id), file = "test-1.html", othernames = list(othernames), table.head = table.head, repository = list("ens"), species ="Rattus_norvegicus") > >> sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] annotate_1.32.1 AnnotationDbi_1.16.19 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] DBI_0.2-5 IRanges_1.12.6 RSQLite_0.11.1 xtable_1.7-0 > > > now with the new version: > > >> htmlpage(list(deg$id), file = "test-1.html", othernames = list(othernames), table.head = table.head, repository = list("ens"), species ="Rattus_norvegicus") > Error: To make links for Ensembl, you need to pass a 'species' argument. > > >> sessionInfo() > R version 2.14.2 (2012-02-29) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] annotate_1.32.2 AnnotationDbi_1.16.19 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] DBI_0.2-5 IRanges_1.12.6 RSQLite_0.11.1 xtable_1.7-0 > > > It seems that the "species" argument is not passed correctly. > > Can this be fixed? > > Best, > > Georg > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
ADD COMMENTlink written 7.7 years ago by Martin Morgan ♦♦ 24k
Hi Martin, On 3/14/2012 4:36 PM, Martin Morgan wrote: > On 03/14/2012 01:13 PM, Georg Otto wrote: >> Hi, >> >> after updating the annotate package from 1.32.1 to 1.32.2 I get an error >> using the htmlpage function. Here with the old version: > > Sorry, probably my fault; I've tried to update this in v. 1.32.3. If > you provide a fully reproducible example (deg$id, othernames, > table.head as necessary to reproduce just the bug) I could be more > sure of the fix. Martin library(annotate) library(org.Hs.eg.db) gnlst2 <- list(egs = head(Rkeys(org.Hs.egENSEMBL),3)) example(htmlpage) htmlpage(gnlst2, "test.html","Some gene expression data", otherdata, c("Ens", table.head[-c(1:3)]), repository=list("ens"), species = "Homo_sapiens") Best, Jim > >> >>> htmlpage(list(deg$id), file = "test-1.html", othernames = >>> list(othernames), table.head = table.head, repository = list("ens"), >>> species ="Rattus_norvegicus") >> >>> sessionInfo() >> R version 2.14.2 (2012-02-29) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] annotate_1.32.1 AnnotationDbi_1.16.19 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.12.6 RSQLite_0.11.1 xtable_1.7-0 >> >> >> now with the new version: >> >> >>> htmlpage(list(deg$id), file = "test-1.html", othernames = >>> list(othernames), table.head = table.head, repository = list("ens"), >>> species ="Rattus_norvegicus") >> Error: To make links for Ensembl, you need to pass a 'species' argument. >> >> >>> sessionInfo() >> R version 2.14.2 (2012-02-29) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] annotate_1.32.2 AnnotationDbi_1.16.19 Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] DBI_0.2-5 IRanges_1.12.6 RSQLite_0.11.1 xtable_1.7-0 >> >> >> It seems that the "species" argument is not passed correctly. >> >> Can this be fixed? >> >> Best, >> >> Georg >> >> _______________________________________________ >> 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
ADD REPLYlink written 7.7 years ago by James W. MacDonald52k
Answer: annotate htmlpage error
0
gravatar for Georg Otto
7.7 years ago by
Georg Otto120
Georg Otto120 wrote:
"James W. MacDonald" <jmacdon at="" uw.edu=""> writes: > Hi Martin, > > On 3/14/2012 4:36 PM, Martin Morgan wrote: >> On 03/14/2012 01:13 PM, Georg Otto wrote: >>> Hi, >>> >>> after updating the annotate package from 1.32.1 to 1.32.2 I get an error >>> using the htmlpage function. Here with the old version: >> >> Sorry, probably my fault; I've tried to update this in v. 1.32.3. If >> you provide a fully reproducible example (deg$id, othernames, >> table.head as necessary to reproduce just the bug) I could be more >> sure of the fix. Martin > > library(annotate) > library(org.Hs.eg.db) > gnlst2 <- list(egs = head(Rkeys(org.Hs.egENSEMBL),3)) > example(htmlpage) > htmlpage(gnlst2, "test.html","Some gene expression data", otherdata, > c("Ens", table.head[-c(1:3)]), repository=list("ens"), species = > "Homo_sapiens") > > Thanks Jim. I can confirm tah Martin's fix works. However it generates a dead link. In getQuery4ENSEMBL() the link is created like this: out <- paste("http://www.ensembl.org/", species, "/Search/Summary?species=", species, ";idx=;q=", ids, sep = "") However (dependant on where you exactly want to point the link to) it should read like this: out <- paste("http://www.ensembl.org/", species, "/Gene/Summary?g=", ids, sep = "") Best, Georg
ADD COMMENTlink written 7.7 years ago by Georg Otto120
Hi Georg, On 3/19/2012 11:24 AM, Georg Otto wrote: > "James W. MacDonald"<jmacdon at="" uw.edu=""> writes: > >> Hi Martin, >> >> On 3/14/2012 4:36 PM, Martin Morgan wrote: >>> On 03/14/2012 01:13 PM, Georg Otto wrote: >>>> Hi, >>>> >>>> after updating the annotate package from 1.32.1 to 1.32.2 I get an error >>>> using the htmlpage function. Here with the old version: >>> Sorry, probably my fault; I've tried to update this in v. 1.32.3. If >>> you provide a fully reproducible example (deg$id, othernames, >>> table.head as necessary to reproduce just the bug) I could be more >>> sure of the fix. Martin >> library(annotate) >> library(org.Hs.eg.db) >> gnlst2<- list(egs = head(Rkeys(org.Hs.egENSEMBL),3)) >> example(htmlpage) >> htmlpage(gnlst2, "test.html","Some gene expression data", otherdata, >> c("Ens", table.head[-c(1:3)]), repository=list("ens"), species = >> "Homo_sapiens") >> >> > Thanks Jim. I can confirm tah Martin's fix works. However it generates a > dead link. In getQuery4ENSEMBL() the link is created like this: > > out<- paste("http://www.ensembl.org/", species, "/Search/Summary?species=", > species, ";idx=;q=", ids, sep = "") > > However (dependant on where you exactly want to point the link to) it > should read like this: > > out<- paste("http://www.ensembl.org/", species, "/Gene/Summary?g=", > ids, sep = "") It was already updated in version 1.33.6, but was pointing to the transcript variation page. I have now updated it to point to the summary page as you request. This is in version 1.33.8, which will propagate to the download server in a day or so. Best, Jim > > > Best, > > Georg > > _______________________________________________ > 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
ADD REPLYlink written 7.7 years ago by James W. MacDonald52k
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