Hi,

I was trying to install IlluminaHumanMethylation450k.db with biocLite, but I get an error on trying to install. Is there something else that I need to do?

Details are:

> biocLite("IlluminaHumanMethylation450k.db")

BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.1 (BiocInstaller 1.18.5), R version 3.2.0.
Installing package(s) ‘IlluminaHumanMethylation450k.db’
installing the source package ‘IlluminaHumanMethylation450k.db’

trying URL 'http://bioconductor.org/packages/3.1/data/annotation/src/contrib/IlluminaHumanMethylation450k.db_2.0.9.tar.gz'
Content type 'application/x-gzip' length 63268317 bytes (60.3 MB)
==================================================
downloaded 60.3 MB

* installing *source* package ‘IlluminaHumanMethylation450k.db’ ...

.

.

.

Warning in .recacheSubclasses(def@className, def, doSubclasses, env) :
  undefined subclass "externalRefMethod" of class "functionORNULL"; definition not updated
Error : .onLoad failed in loadNamespace() for 'IlluminaHumanMethylation450k.db', details:
  call: NULL
  error: 'fun' is defunct.
Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Defunct")
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/IlluminaHumanMethylation450k.db’

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] FDb.InfiniumMethylation.hg19_2.2.0                 org.Hs.eg.db_3.1.2                                 RSQLite_1.0.0                                     
 [4] DBI_0.3.1                                          TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2            GenomicFeatures_1.20.6                            
 [7] AnnotationDbi_1.30.1                               IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1 IlluminaHumanMethylation450kmanifest_0.4.0        
[10] minfi_1.14.0                                       bumphunter_1.8.0                                   locfit_1.5-9.1                                    
[13] iterators_1.0.8                                    foreach_1.4.3                                      Biostrings_2.36.4                                 
[16] XVector_0.8.0                                      lattice_0.20-33                                    Biobase_2.28.0                                    
[19] DESeq2_1.8.2                                       RcppArmadillo_0.6.100.0.0                          Rcpp_0.12.1                                       
[22] GenomicRanges_1.20.8                               GenomeInfoDb_1.4.3                                 IRanges_2.2.9                                     
[25] S4Vectors_0.6.6                                    BiocGenerics_0.14.0                                BiocInstaller_1.18.5                              

loaded via a namespace (and not attached):
 [1] nor1mix_1.2-1           splines_3.2.0           Formula_1.2-1           latticeExtra_0.6-26     doRNG_1.6               Rsamtools_1.20.5       
 [7] quadprog_1.5-5          limma_3.24.15           digest_0.6.8            RColorBrewer_1.1-2      colorspace_1.2-6        preprocessCore_1.30.0  
[13] plyr_1.8.3              GEOquery_2.34.0         siggenes_1.42.0         XML_3.98-1.3            biomaRt_2.24.1          genefilter_1.50.0      
[19] zlibbioc_1.14.0         xtable_1.7-4            scales_0.3.0            BiocParallel_1.2.22     annotate_1.46.1         beanplot_1.2           
[25] pkgmaker_0.22           ggplot2_1.0.1           nnet_7.3-11             proto_0.3-10            survival_2.38-3         magrittr_1.5           
[31] mclust_5.0.2            nlme_3.1-122            MASS_7.3-44             foreign_0.8-66          tools_3.2.0             registry_0.3           
[37] matrixStats_0.14.2      stringr_1.0.0           munsell_0.4.2           cluster_2.0.3           rngtools_1.2.4          base64_1.1             
[43] lambda.r_1.1.7          futile.logger_1.4.1     grid_3.2.0              RCurl_1.95-4.7          bitops_1.0-6            gtable_0.1.2           
[49] codetools_0.2-14        multtest_2.24.0         reshape_0.8.5           reshape2_1.4.1          illuminaio_0.10.0       GenomicAlignments_1.4.2
[55] gridExtra_2.0.0         rtracklayer_1.28.10     Hmisc_3.17-0            futile.options_1.0.0    stringi_0.5-5           geneplotter_1.46.0     
[61] rpart_4.1-10            acepack_1.3-3.3   

thanks!!

You should probably follow the recommendations given during the package install and use the FDb.InfiniumMethylation.hg19 package instead. The package you are attempting to install was deprecated (IIRC) two releases ago, in favor of the FDb versions.

James,

I was trying to use some of the functions in the IlluminaHumanMethylation450k.db package (e.g.IlluminaHumanMethylation450kALIAS2PROBE) that don't appear to be in the FDb.InfiniumMethylation.hg19 documentation. Is there a way that I can get gene to probe information in the new (or another) package?

thanks!