Dear BioC developers, as I try to use the retrieveKGML function of the KEGGgraph package, I end up with the following error: ------ retrieveKGML(pathwayid='00010', organism='cel', destfile="/home/cbio/ludwig/test.txt", method="wget") --17:06:46-- ftp://ftp.genome.jp/pub/kegg/xml/organisms/cel/cel00010.xml => `/home/cbio/ludwig/test.txt' Resolving ftp.genome.jp... 133.103.100.184 Connecting to ftp.genome.jp|133.103.100.184|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD /pub/kegg/xml/organisms/cel ... No such directory `pub/kegg/xml/organisms/cel'. Warning message: In download.file(kgml, destfile = destfile, method = method, ...) : download had nonzero exit status ------ This might be due to a wrong hard coded kegg ftp path inside of KEGGgraph, as the recent integration of biopax files has changed the structure of the ftp://ftp.genome.jp/pub/kegg/xml/ directory. This has destroyed the nice functionality of retrieveKGML. Kind Regards Ludwig Geistlinger Institute of Infectious Diseases University of Cape Town

Hi Ludwig, I believe you have an older KEGGgraph version. I have 1.2.2 and no problem to get the xml file. Nevertheless, you can download any xml. download.file(url=" ftp://ftp.genome.jp/pub/kegg/xml/kgml/metabolic/organisms/cel/cel00010 .xml ",destfile="/home/cel00010.xml") graphpath <- parseKGML2Graph(file="/home/cel00010.xml") Hope it works Kachelo 2010/3/29 Ludwig Geistlinger <ludwig.geistlinger@campus.lmu.de> > Dear BioC developers, > > as I try to use the retrieveKGML function of the KEGGgraph package, I end > up with the following error: > > ------ > > retrieveKGML(pathwayid='00010', organism='cel', > destfile="/home/cbio/ludwig/test.txt", method="wget") > --17:06:46-- ftp://ftp.genome.jp/pub/kegg/xml/organisms/cel/cel00010.xml > => `/home/cbio/ludwig/test.txt' > Resolving ftp.genome.jp... 133.103.100.184 > Connecting to ftp.genome.jp|133.103.100.184|:21... connected. > Logging in as anonymous ... Logged in! > ==> SYST ... done. ==> PWD ... done. > ==> TYPE I ... done. ==> CWD /pub/kegg/xml/organisms/cel ... > No such directory `pub/kegg/xml/organisms/cel'. > > Warning message: > In download.file(kgml, destfile = destfile, method = method, ...) : > download had nonzero exit status > > ------ > > This might be due to a wrong hard coded kegg ftp path inside of KEGGgraph, > as the recent integration of biopax files has changed the structure of the > ftp://ftp.genome.jp/pub/kegg/xml/ directory. > This has destroyed the nice functionality of retrieveKGML. > > Kind Regards > > Ludwig Geistlinger > Institute of Infectious Diseases > University of Cape Town > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]