KEGGgraph: retrieveKGML error (due to wrong ftp path)
1
0
Entering edit mode
@ludwig-geistlinger-3939
Last seen 11 weeks ago
USA/Boston/HMS
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
KEGGgraph KEGGgraph • 1.4k views
ADD COMMENT
0
Entering edit mode
@cristobal-fresno-rodriguez-3838
Last seen 6.4 years ago
Argentina/Cordoba/Universidad Católica …
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]]

Login before adding your answer.

Traffic: 292 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6