On 07/03/2010 10:59 PM, Brad McNeney wrote: > The following call to curl fetches me the information I want (as html) > from a webserver: > > curl -F list_fi...@snptxt -F html_output=on > http://integrin.ucd.ie/cgi-bin/rs2cm.cgi > > The file snptxt is a plain-text file in my working directory with the > following two lines: > > rs6598 > rs123456 > > > In R I try to replicate this with RCurl as follows: > > require(RCurl) > postForm(uri="http://integrin.ucd.ie/cgi-bin/rs2cm.cgi", > "list_file"="@snptxt", "html_output"="on") > > but the table that is supposed to contain my results is empty (table > caption is Genetic Locations). The cgi script has apparently received > the html_output=on information though. >
Hi Brad I think the path to the file to be uploaded needs to be wrapped in a call to fileUpload, along the lines of postForm(uri="http://integrin.ucd.ie/cgi-bin/rs2cm.cgi", list_file=fileUpload("/tmp/snp.txt"), html_output="on") Martin > I get the same results on Linux and Windows -- sessionInfo() for both > follows. Any pointers appreciated. > > Thanks, > > Brad > --- > Brad McNeney > Statistics and Actuarial Science > Simon Fraser University > > Linux: > >> sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-unknown-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] XML_3.1-0 RCurl_1.4-2 bitops_1.0-4.1 > > Windows: > >> sessionInfo() > R version 2.11.1 (2010-05-31) > i386-pc-mingw32 > > locale: > [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 > [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C > [5] LC_TIME=English_Canada.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] XML_3.1-0 RCurl_1.4-2 bitops_1.0-4.1 > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.