[BioC] URLs in annotate

Sean Davis sdavis2 at mail.nih.gov
Mon Oct 27 14:43:20 MET 2003

I am using R-1.8.0 and developer level release of bioconductor.  I have been using the HTML access functions (pubmed, etc.), but have found that, at least for the combination of UNIX (MacOS X) and system command (open, which opens any file (or URL) with the "appropriate" application--quite convenient, actually) that I am using, the system call to open the browser is interpreted differently than it should be.  Specifically, the URL that is generated includes the "&" command, which is interpreted by the shell as a delimeter rather than part of a string.  The result is that all of the specificity when the URL is called is lost and a generic pubmed page (or other database) is generated.  The "fix" is simple--just put quotes around the URL generated.  I can do this myself for a local copy of annotate, but I wondered if other users have found the same problem so that the code might be changed generally?


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