curl: (3) url malformed

[Joseph Flanagan]

When I was packratting a project, I got an error, which I can¨t remember now. Now when I occasionally do things with packrat (say, check the status), I get a ` curl: (3) <url> malformed`. As far as I can tell, everything works, but I'm not sure why I'm getting this error. This is repeated: I did delete packrat from the project and tried to start over. Any ideas?

[Kevin Ushey]

What is the output of `getOption("repos")` in your project?

On Tue, Oct 20, 2015 at 12:05 PM, Joseph Flanagan <jflan...@gmail.com> wrote:

When I was packratting a project, I got an error, which I can¨t remember now. Now when I occasionally do things with packrat (say, check the status), I get a ` curl: (3) <url> malformed`. As far as I can tell, everything works, but I'm not sure why I'm getting this error. This is repeated: I did delete packrat from the project and tried to start over. Any ideas?

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[Joseph Flanagan]

CRAN 

                           "https://cran.rstudio.com/" 

                                              BioCsoft 

           "http://bioconductor.org/packages/3.2/bioc" 

                                               BioCann 

"http://bioconductor.org/packages/3.2/data/annotation" 

                                               BioCexp 

"http://bioconductor.org/packages/3.2/data/experiment" 

                                             BioCextra 

          "http://bioconductor.org/packages/3.2/extra" 

curl: (3) <url> malformed

curl: (3) <url> malformed

curl: (3) <url> malformed

curl: (3) <url> malformed

curl: (3) <url> malformed

curl: (3) <url> malformed

[Kevin Ushey]

What version of packrat are you using? You might need to update to the latest development version (there was a bug in the handling of BioC repositories). Try:

    if (!require("devtools")) install.packages("devtools")

    devtools::install_github("rstudio/packrat")

If that doesn't help, try updating BiocInstaller and confirming that the URLs generated by

    contrib.url(getOption("repos"))

are valid.

Thanks,

Kevin