I've just updated to the latest version of R (3.2.2) and Bioconductor and I am getting the following errors in minfi: 

Note: This code was working before with R version 3.1.1

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

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

When I try to use the estimateCellCounts function:

cellComposition <- estimateCellCounts(RGset)
[estimateCellCounts] Combining user data with reference (flow sorted) data.
Error in combine(pDataX, pDataY) : data.frames contain conflicting data:
        non-conforming colname(s): Slide

Any help appreciated.

Please add `sessionInfo` to your post.

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
 [2] IlluminaHumanMethylation450kmanifest_0.4.0
 [3] minfi_1.16.0
 [4] bumphunter_1.10.0
 [5] locfit_1.5-9.1
 [6] iterators_1.0.8
 [7] foreach_1.4.3
 [8] Biostrings_2.38.0
 [9] XVector_0.10.0
[10] SummarizedExperiment_1.0.1
[11] GenomicRanges_1.22.1
[12] GenomeInfoDb_1.6.0
[13] IRanges_2.4.1
[14] S4Vectors_0.8.1
[15] lattice_0.20-33
[16] Biobase_2.30.0
[17] BiocGenerics_0.16.1

loaded via a namespace (and not attached):
 [1] mclust_5.1              rgl_0.95.1367           base64_1.1
 [4] Rcpp_0.12.1             Rsamtools_1.22.0        digest_0.6.8
 [7] plyr_1.8.3              futile.options_1.0.0    ellipse_0.3-8
[10] RSQLite_1.0.0           ggplot2_1.0.1           zlibbioc_1.16.0
[13] GenomicFeatures_1.22.4  annotate_1.48.0         preprocessCore_1.32.0
[16] proto_0.3-10            splines_3.2.2           BiocParallel_1.4.0
[19] stringr_1.0.0           igraph_1.0.1            pheatmap_1.0.7
[22] RCurl_1.95-4.7          biomaRt_2.26.0          munsell_0.4.2
[25] rtracklayer_1.30.1      multtest_2.26.0         pkgmaker_0.22
[28] GEOquery_2.36.0         quadprog_1.5-5          codetools_0.2-14
[31] matrixStats_0.15.0      XML_3.98-1.3            reshape_0.8.5
[34] GenomicAlignments_1.6.1 MASS_7.3-44             bitops_1.0-6
[37] grid_3.2.2              nlme_3.1-122            xtable_1.8-0
[40] gtable_0.1.2            registry_0.3            DBI_0.3.1
[43] magrittr_1.5            scales_0.3.0            stringi_1.0-1
[46] reshape2_1.4.1          genefilter_1.52.0       doRNG_1.6
[49] limma_3.26.1            futile.logger_1.4.1     nor1mix_1.2-1
[52] lambda.r_1.1.7          RColorBrewer_1.1-2      mixOmics_5.1.2
[55] siggenes_1.44.0         tools_3.2.2             illuminaio_0.12.0
[58] rngtools_1.2.4          survival_2.38-3         colorspace_1.2-6
[61] AnnotationDbi_1.32.0    beanplot_1.2