I have recently installed in the new version of R together with the new version of Bioconductor and minfi.  At the moment read.450k() is giving an error since the base directory is being duplicated in the Basname column.  I found a way around this by not specifying the base argument in read.450k.exp().  

Note this works well with R 3.1.1.

Please take note to fix this issue. 

Example:

RGset <- read.450k.exp(base=dataDir, targets=targets)

Error in read.450k(files, extended = extended, verbose = verbose) :
  The following specified files do not exist:/...

SessionInfo:

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.7 (Santiago)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] FlowSorted.Blood.450k_1.8.0 minfi_1.16.0
 [3] bumphunter_1.10.0           locfit_1.5-9.1
 [5] iterators_1.0.8             foreach_1.4.3
 [7] Biostrings_2.38.0           XVector_0.10.0
 [9] SummarizedExperiment_1.0.1  GenomicRanges_1.22.1
[11] GenomeInfoDb_1.6.1          IRanges_2.4.1
[13] S4Vectors_0.8.1             lattice_0.20-33
[15] Biobase_2.30.0              BiocGenerics_0.16.1
[17] BiocInstaller_1.20.0