Question: AnnBuilder: problem with kegg url?
0
gravatar for Matthias E. Futschik
12.0 years ago by
Matthias E. Futschik20 wrote:
hi all, I try to use ABPkgBuilder (session info below) with following code (partly from the vignette) ##### library(AnnBuilder) read.table(file.path(.path.package("AnnBuilder"), "data", "thgu95a"), sep = "\t", header = FALSE, as.is = TRUE) myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") myBaseType <- "gb" myDir <- tempdir() ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, pkgName = "myPkg", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "myname", maintainer = "myname at myemail.com"), fromWeb = TRUE) ##### The last command however failed: Error in parseKEGGGenome(url = kegggenomeUrl) : Faild to obtain KEGG organism code Checking for the url gives getOption("AnnBuilderSourceUrls")$KEGGGENOME [1] "ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/genome" However, this directory does not exist anymore! Which should be the correct one? And how do I fix this within the ABPkgBuilder command? thanks, Matthias. ps: I could save my troubles if there is an annotation package for the complete set of human entrezids (which includes go + kegg + pfam) - is there? > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONETAR Y=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" "base" other attached packages: GO AnnBuilder RSQLite DBI annotate XML Biobase "1.14.1" "1.12.0" "0.5-4" "0.2-3" "1.12.1" "1.6-0" "1.12.2" > *************************************************** Matthias E. Futschik Institute for Theoretical Biology Charite - Medical School Humboldt-University Invalidenstrasse 43 10115 Berlin Germany email: m.futschik at biologie.hu-berlin.de phone: + 49-30-2093 9106 fax: + 49-30-2093 8801 URL: http://itb.biologie.hu-berlin.de/~futschik ***************************************************
ADD COMMENTlink modified 12.0 years ago by Marc Carlson7.2k • written 12.0 years ago by Matthias E. Futschik20
Answer: AnnBuilder: problem with kegg url?
0
gravatar for Marc Carlson
12.0 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Matthias E. Futschik wrote: > hi all, > I try to use ABPkgBuilder (session info below) > with following code (partly from the vignette) > > ##### > library(AnnBuilder) > read.table(file.path(.path.package("AnnBuilder"), "data", "thgu95a"), > sep = "\t", header = FALSE, as.is = TRUE) > myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") > myBaseType <- "gb" > myDir <- tempdir() > ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, > pkgName = "myPkg", pkgPath = myDir, > organism = "Homo sapiens", version = "1.1.0", author = list(authors = > "myname", > maintainer = "myname at myemail.com"), fromWeb = TRUE) > ##### > > The last command however failed: > > Error in parseKEGGGenome(url = kegggenomeUrl) : > Faild to obtain KEGG organism code > > Checking for the url gives > > getOption("AnnBuilderSourceUrls")$KEGGGENOME > [1] "ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/genome" > > However, this directory does not exist anymore! > Which should be the correct one? And how do I fix this > within the ABPkgBuilder command? > > thanks, > Matthias. > > ps: I could save my troubles if there is an annotation package for > the complete set of human entrezids (which includes go + kegg + pfam) - > is there? > > >> sessionInfo() >> > R version 2.4.1 (2006-12-18) > i386-pc-mingw32 > > locale: > LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONET ARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > "methods" "base" > > other attached packages: > GO AnnBuilder RSQLite DBI annotate XML Biobase > "1.14.1" "1.12.0" "0.5-4" "0.2-3" "1.12.1" "1.6-0" "1.12.2" > > > > > *************************************************** > Matthias E. Futschik > Institute for Theoretical Biology > Charite - Medical School > Humboldt-University > Invalidenstrasse 43 > 10115 Berlin > Germany > > email: m.futschik at biologie.hu-berlin.de > phone: + 49-30-2093 9106 > fax: + 49-30-2093 8801 > URL: > http://itb.biologie.hu-berlin.de/~futschik *************************************************** > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > I believe that the package that you desire is called: org.Hs.eg.db And it can be found here: http://www.bioconductor.org/packages/2.1/data/annotation/ Please let us know how this works for you. And if you need any help using it, please let me know that too. Marc
ADD COMMENTlink written 12.0 years ago by Marc Carlson7.2k
Hi Matthias, Just an additional comment to Marc's answer: you must use R-2.6.0 (just released yesterday) if you want to be able to install and use org.Hs.eg.db (and this is currently true for any other .db package). Also, as with any Bioconductor package, the recommended way to install a package is to use biocLite (from R-2.6.0 ): > source("http://bioconductor.org/biocLite.R") > biocLite("org.Hs.eg.db") Those org.*.*.db packages are new in Bioconductor 2.1 (BioC 2.1 will be released tomorrow but you can start using it right now). Please let us now if you find any problem or need help with this package. Thanks! H. Marc Carlson wrote: > Matthias E. Futschik wrote: >> hi all, >> I try to use ABPkgBuilder (session info below) >> with following code (partly from the vignette) >> >> ##### >> library(AnnBuilder) >> read.table(file.path(.path.package("AnnBuilder"), "data", "thgu95a"), >> sep = "\t", header = FALSE, as.is = TRUE) >> myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") >> myBaseType <- "gb" >> myDir <- tempdir() >> ABPkgBuilder(baseName = myBase, baseMapType = myBaseType, >> pkgName = "myPkg", pkgPath = myDir, >> organism = "Homo sapiens", version = "1.1.0", author = list(authors = >> "myname", >> maintainer = "myname at myemail.com"), fromWeb = TRUE) >> ##### >> >> The last command however failed: >> >> Error in parseKEGGGenome(url = kegggenomeUrl) : >> Faild to obtain KEGG organism code >> >> Checking for the url gives >> >> getOption("AnnBuilderSourceUrls")$KEGGGENOME >> [1] "ftp://ftp.genome.ad.jp/pub/kegg/tarfiles/genome" >> >> However, this directory does not exist anymore! >> Which should be the correct one? And how do I fix this >> within the ABPkgBuilder command? >> >> thanks, >> Matthias. >> >> ps: I could save my troubles if there is an annotation package for >> the complete set of human entrezids (which includes go + kegg + pfam) - >> is there? >> >> >>> sessionInfo() >>> >> R version 2.4.1 (2006-12-18) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=German_Germany.1252;LC_CTYPE=German_Germany.1252;LC_MONE TARY=German_Germany.1252;LC_NUMERIC=C;LC_TIME=German_Germany.1252 >> >> attached base packages: >> [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" >> "methods" "base" >> >> other attached packages: >> GO AnnBuilder RSQLite DBI annotate XML Biobase >> "1.14.1" "1.12.0" "0.5-4" "0.2-3" "1.12.1" "1.6-0" "1.12.2" >> >> >> >> >> *************************************************** >> Matthias E. Futschik >> Institute for Theoretical Biology >> Charite - Medical School >> Humboldt-University >> Invalidenstrasse 43 >> 10115 Berlin >> Germany >> >> email: m.futschik at biologie.hu-berlin.de >> phone: + 49-30-2093 9106 >> fax: + 49-30-2093 8801 >> URL: >> http://itb.biologie.hu-berlin.de/~futschik *************************************************** >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > I believe that the package that you desire is called: org.Hs.eg.db > > And it can be found here: > > http://www.bioconductor.org/packages/2.1/data/annotation/ > > > Please let us know how this works for you. And if you need any help > using it, please let me know that too. > > Marc > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 12.0 years ago by Hervé Pagès ♦♦ 14k
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