Warning message:
In fun(libname, pkgname) :
  mzR has been built against a different Rcpp version (0.11.2)
than is installed on your system (0.11.3). This might lead to errors
when loading mzR. If you encounter such issues, please send a report,
including the output of sessionInfo() to the Bioc mailing list at 
http://www.bioconductor.org/help/mailing-list. For details see also
https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.

> biocLite("mzR")
Error in `row.names<-.data.frame`(`*tmp*`, value = aa) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique value when setting 'row.names': 'http://rkward.sf.net/R/' 
Error in `row.names<-.data.frame`(`*tmp*`, value = aa) : 
  duplicate 'row.names' are not allowed

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252 
[2] LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] igraph_0.7.1         BiocInstaller_1.14.2 xcms_1.40.0         
[4] Biobase_2.24.0       BiocGenerics_0.10.0  mzR_1.10.7          
[7] Rcpp_0.11.3          rkward_0.6.1        

loaded via a namespace (and not attached):
[1] codetools_0.2-9 tools_3.1.1  

I would be tempted to say that the error you see has nothing to do with mzR, but is related to your IDE, RKWard. Anyway, could you edit your post and add the output of sessionInfo().