I have recently begun using `minfi` for the analysis of 850K methylation data from the Illumina EPIC array. In following a fairly standard procedure (as in the the 2014 Bioconductor tutorial on using minfi for 450K data), I've encountered the following error, which arises anytime that `mapToGenome` is called:

"Error in out[wh, ] : incorrect number of dimensions"

This is the first time I've used minfi for analyzing EPIC data, but, in all previous instances in which I've used the tool to analyze 450K data, I've never encountered such an error.

Any help in diagnosing and/or resolving this issue would be much appreciated.

Output of traceback():

R >   genomeset <- mapToGenome(ratioset_raw)
Error in out[wh, ] : incorrect number of dimensions
R > traceback()
5: getAnnotation(object, what = what, dropNonMapping = TRUE, orderByLocation = orderByLocation,
       lociNames = lociNames)
4: getLocations(object, mergeManifest = mergeManifest, orderByLocation = TRUE)
3: .local(object, ...)
2: mapToGenome(ratioset_raw)
1: mapToGenome(ratioset_raw)

Output of biocValid():

* sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.8 (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 datasets  utils
[8] methods   base

other attached packages:
 [1] BiocInstaller_1.24.0
 [2] nima_0.4.0
 [3] IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0
 [4] IlluminaHumanMethylationEPICmanifest_0.3.0
 [5] minfi_1.20.2
 [6] bumphunter_1.14.0
 [7] locfit_1.5-9.1
 [8] iterators_1.0.8
 [9] foreach_1.4.3
[10] Biostrings_2.42.1
[11] XVector_0.12.0
[12] SummarizedExperiment_1.2.3
[13] GenomicRanges_1.24.2
[14] GenomeInfoDb_1.10.3
[15] IRanges_2.6.1
[16] S4Vectors_0.12.1
[17] lattice_0.20-34
[18] Biobase_2.34.0
[19] BiocGenerics_0.18.0
[20] here_0.0-5
[21] dtplyr_0.0.1
[22] data.table_1.10.4
[23] dplyr_0.5.0
[24] ggplot2_2.2.1
[25] devtools_1.12.0
[26] colorout_1.1-2

loaded via a namespace (and not attached):
 [1] nlme_3.1-131            bitops_1.0-6            matrixStats_0.51.0
 [4] RColorBrewer_1.1-2      httr_1.2.1              rprojroot_1.2
 [7] tools_3.3.2             backports_1.0.5         doRNG_1.6
[10] nor1mix_1.2-2           R6_2.1.2                DBI_0.4-1
[13] lazyeval_0.2.0          colorspace_1.3-2        withr_1.0.2
[16] gridExtra_2.2.1         base64_2.0              curl_2.3
[19] git2r_0.18.0            preprocessCore_1.36.0   pkgmaker_0.22
[22] rtracklayer_1.34.2      scales_0.4.1            genefilter_1.56.0
[25] quadprog_1.5-5          stringr_1.2.0           digest_0.6.10
[28] Rsamtools_1.26.1        illuminaio_0.16.0       siggenes_1.48.0
[31] GEOquery_2.40.0         limma_3.30.12           ggthemes_3.4.0
[34] RSQLite_1.0.0           mclust_5.2.2            BiocParallel_1.8.1
[37] gtools_3.5.0            RCurl_1.95-4.8          magrittr_1.5
[40] Matrix_1.2-7.1          Rcpp_0.12.8             munsell_0.4.3
[43] stringi_1.1.2           MASS_7.3-45             zlibbioc_1.20.0
[46] plyr_1.8.4              grid_3.3.2              splines_3.3.2
[49] multtest_2.30.0         GenomicFeatures_1.26.3  annotate_1.52.1
[52] beanplot_1.2            rngtools_1.2.4          codetools_0.2-15
[55] biomaRt_2.30.0          XML_3.98-1.5            gtable_0.2.0
[58] openssl_0.9.6           reshape_0.8.6           assertthat_0.1
[61] xtable_1.8-2            survival_2.40-1         tibble_1.2
[64] GenomicAlignments_1.8.4 AnnotationDbi_1.36.2    registry_0.3
[67] memoise_1.0.0

* Out-of-date packages
                     Package
BiocGenerics         "BiocGenerics"
DBI                  "DBI"
dichromat            "dichromat"
digest               "digest"
GenomicAlignments    "GenomicAlignments"
GenomicRanges        "GenomicRanges"
gtools               "gtools"
IRanges              "IRanges"
labeling             "labeling"
locfit               "locfit"
munsell              "munsell"
R.methodsS3          "R.methodsS3"
R6                   "R6"
RColorBrewer         "RColorBrewer"
Rcpp                 "Rcpp"
RSQLite              "RSQLite"
                     LibPath
BiocGenerics         "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
DBI                  "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
dichromat            "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
digest               "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
GenomicAlignments    "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
GenomicRanges        "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
gtools               "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
IRanges              "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
labeling             "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
locfit               "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
munsell              "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
R.methodsS3          "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
R6                   "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
RColorBrewer         "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
Rcpp                 "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
RSQLite              "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
                     Installed Built   ReposVer
BiocGenerics         "0.18.0"  "3.3.0" "0.20.0"
DBI                  "0.4-1"   "3.3.0" "0.5-1"
dichromat            "2.0-0"   "3.2.3" "2.0-0"
digest               "0.6.10"  "3.3.2" "0.6.12"
GenomicAlignments    "1.8.4"   "3.3.1" "1.10.0"
GenomicRanges        "1.24.2"  "3.3.0" "1.26.3"
gtools               "3.5.0"   "3.2.3" "3.5.0"
IRanges              "2.6.1"   "3.3.0" "2.8.1"
labeling             "0.3"     "3.2.3" "0.3"
locfit               "1.5-9.1" "3.2.3" "1.5-9.1"
munsell              "0.4.3"   "3.2.3" "0.4.3"
R.methodsS3          "1.7.1"   "3.2.3" "1.7.1"
R6                   "2.1.2"   "3.3.0" "2.2.0"
RColorBrewer         "1.1-2"   "3.2.3" "1.1-2"
Rcpp                 "0.12.8"  "3.3.2" "0.12.9"
RSQLite              "1.0.0"   "3.2.3" "1.1-2"
                     Repository
BiocGenerics         "https://bioconductor.org/packages/3.4/bioc/src/contrib"
DBI                  "https://cran.rstudio.com/src/contrib"
dichromat            "https://cran.rstudio.com/src/contrib"
digest               "https://cran.rstudio.com/src/contrib"
GenomicAlignments    "https://bioconductor.org/packages/3.4/bioc/src/contrib"
GenomicRanges        "https://bioconductor.org/packages/3.4/bioc/src/contrib"
gtools               "https://cran.rstudio.com/src/contrib"
IRanges              "https://bioconductor.org/packages/3.4/bioc/src/contrib"
labeling             "https://cran.rstudio.com/src/contrib"
locfit               "https://cran.rstudio.com/src/contrib"
munsell              "https://cran.rstudio.com/src/contrib"
R.methodsS3          "https://cran.rstudio.com/src/contrib"
R6                   "https://cran.rstudio.com/src/contrib"
RColorBrewer         "https://cran.rstudio.com/src/contrib"
Rcpp                 "https://cran.rstudio.com/src/contrib"
RSQLite              "https://cran.rstudio.com/src/contrib"
 [ reached getOption("max.print") -- omitted 2 rows ]

update with biocLite()

* Packages too new for Bioconductor version '3.4'

            Version  LibPath
nima        "0.4.0"  "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
tmle.npvi   "0.11.2" "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"
wesanderson "0.3.4"  "/home/nhejazi/R/x86_64-pc-linux-gnu-library/3.3"

downgrade with biocLite(c("nima", "tmle.npvi", "wesanderson"))

Error: 18 package(s) out of date; 3 package(s) too new