Hello all, I was tring to annotate zelbrafish microarray data using genbank function, but I got the following errors. Could you tell me what the problem is? library(XML) library(annotate) genbank("AW116961") Entity: line 47: parser error : Opening and ending tag mismatch: link line 29 and head </head> ^ Entity: line 67: parser error : EntityRef: expecting ';' ryBox" action="http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi?CMD=search &DB ........ ........ *** caught segfault *** address 0xc0000000, cause 'memory not mapped' Segmentation fault but if i show the result using browser like genbank("AW116961",disp=c("browser")), it works fine. what is the problem??? Thanks in advance Regards, Yanju

Hi Yanju, yanju wrote: > Hello all, > > I was tring to annotate zelbrafish microarray data using genbank > function, but I got the following errors. Could you tell me what the > problem is? > > library(XML) > library(annotate) > genbank("AW116961") You will have to give more information (as the posting guide suggests), namely the ouput from sessionInfo(). Anyway, this works OK for me. > library(XML) > library(annotate) > a <- genbank("AW116961") Read 402 items Read 569 items > sessionInfo() R version 2.4.1 (2006-12-18) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" "methods" [8] "base" other attached packages: annotate Biobase XML "1.12.1" "1.12.2" "1.4-0" Best, Jim > > > Entity: line 47: parser error : Opening and ending tag mismatch: link > line 29 and head > </head> > ^ > Entity: line 67: parser error : EntityRef: expecting ';' > ryBox" > action="http://www.ncbi.nlm.nih.gov/entrez/utils/pmqty.fcgi?CMD=sear ch&DB > ........ > ........ > > *** caught segfault *** > address 0xc0000000, cause 'memory not mapped' > Segmentation fault > > but if i show the result using browser like > genbank("AW116961",disp=c("browser")), it works fine. > what is the problem??? > > Thanks in advance > > Regards, > Yanju > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.