Hi all, 

Yesterday I started having the following issue with retrieving HM450k manifest data via getAnnotation() in minfi:



> mset
MethylSet (storageMode: lockedEnvironment)
assayData: 484878 features, 78 samples
  element names: Meth, Unmeth
An object of class 'AnnotatedDataFrame'
  sampleNames: 5730192017_R01C01 5730192017_R03C01 ... 9344730111_R03C02 (78
    total)
  varLabels: DNA.soln Batch_ID ... filenames (19 total)
  varMetadata: labelDescription
Annotation
  array: IlluminaHumanMethylation450k
  annotation: ilmn12.hg19
Preprocessing
  Method: SWAN (based on a MethylSet preprocesses as 'Illumina, bg.correct = TRUE, normalize = controls, reference = 2'
  minfi version: 1.14.0
  Manifest version: 0.4.0
> head(getAnnotation(mset))
Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’
Error in head(getAnnotation(mset)) : 
  error in evaluating the argument 'x' in selecting a method for function 'head': Error in getAnnotationObject(object) : 
  cannot load annotation package IlluminaHumanMethylation450kanno.ilmn12.hg19

When attempting to install the annotation package manually, I am met with the following warning:

Warning message:
package ‘IlluminaHumanMethylation450kanno.ilmn.hg19’ is not available (for R version 3.2.2) 

Which doesn't make sense, as I have been using this R version for months, and only just had this problem yesterday. 

Thanks in advance for your help,

best,

Sean

sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

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

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

other attached packages:
 [1] BiocInstaller_1.20.0       minfi_1.16.0               bumphunter_1.10.0         
 [4] locfit_1.5-9.1             iterators_1.0.8            foreach_1.4.3             
 [7] Biostrings_2.38.0          XVector_0.10.0             SummarizedExperiment_1.0.1
[10] GenomicRanges_1.22.1       GenomeInfoDb_1.6.1         IRanges_2.4.1             
[13] S4Vectors_0.8.1            lattice_0.20-33            Biobase_2.30.0            
[16] 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         AnnotationDbi_1.32.0   
[61] colorspace_1.2-6        beanplot_1.2