I have not been able to install the package "mzR", which is one of the dependencies I need, recently on R (3.2.3) and Bioconductor (3.2). It seems that it has something to do with the conflict with the other package "Rcpp". The issue only occurs when I run R under windows 7, no issues under Linux.
Using Bioconductor 3.2 (BiocInstaller 1.20.1), R 3.2.3 (2015-12-10).
Installing package(s) ‘mzR’
Warning: dependencies ‘methods’, ‘utils’, ‘graphics’, ‘stats’, ‘parallel’ are not available
also installing the dependencies ‘Rcpp’, ‘Biobase’, ‘BiocGenerics’, ‘ProtGenerics’, ‘zlibbioc’
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.2/Rcpp_0.12.3.zip'
Content type 'application/zip' length 3197833 bytes (3.0 MB)
downloaded 3.0 MB
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/Biobase_2.30.0.zip'
Content type 'application/zip' length 4227858 bytes (4.0 MB)
downloaded 4.0 MB
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/BiocGenerics_0.16.1.zip'
Content type 'application/zip' length 962958 bytes (940 KB)
downloaded 940 KB
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/ProtGenerics_1.2.1.zip'
Content type 'application/zip' length 62396 bytes (60 KB)
downloaded 60 KB
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/zlibbioc_1.16.0.zip'
Content type 'application/zip' length 693613 bytes (677 KB)
downloaded 677 KB
trying URL 'https://bioconductor.org/packages/3.2/bioc/bin/windows/contrib/3.2/mzR_2.4.1.zip'
Content type 'application/zip' length 8395399 bytes (8.0 MB)
downloaded 8.0 MB
package ‘Rcpp’ successfully unpacked and MD5 sums checked
package ‘Biobase’ successfully unpacked and MD5 sums checked
package ‘BiocGenerics’ successfully unpacked and MD5 sums checked
package ‘ProtGenerics’ successfully unpacked and MD5 sums checked
package ‘zlibbioc’ successfully unpacked and MD5 sums checked
package ‘mzR’ successfully unpacked and MD5 sums checked
The downloaded binary packages are in
Loading required package: Rcpp
Error : .onLoad failed in loadNamespace() for 'mzR', details:
error: subscript out of bounds
In addition: Warning message:
In packageDescription(pkg, lib.loc = lib) : no package 'mzR' was found
Error: package or namespace load failed for ‘mzR’
R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 LC_TIME=English_United States.1252
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 Rcpp_0.12.3 BiocInstaller_1.20.1
loaded via a namespace (and not attached):
 ProtGenerics_1.2.1 parallel_3.2.3 tools_3.2.3 Biobase_2.30.0 BiocGenerics_0.16.1
Many thanks in advance,