1. Is R free even to government entities?
R is free for everyone, even for Government entities. Every worker in your organization could install R on his/her computer.
R is freely available under the GNU General Public License.
The cost of using R are related only with training of users.
2. What is the risk of contamination (viruses) in R software?
As we know and from our experience, R has no risk for getting viruses. But, anyway, is good to have installed normal antivirus software on your computer.
3. What can be done if there is a problem with the R software? Are there resources for diagnosing and fixing R-software “malfunctions”?
Debugging is a functionality of R, and we recommend to read the following statement: http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/debug.shtml
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