install IlluminaHumanMethylation450k.db error
Entering edit mode
tangming2005 ▴ 190
Last seen 4 months ago
United States

Hi, I just tried installing this package, but failed.

Using Bioconductor 3.3 (BiocInstaller 1.22.2), R 3.3.0 (2016-05-03).
Installing package(s) 'IlluminaHumanMethylation450k.db'
installing the source package 'IlluminaHumanMethylation450k.db'

trying URL ''
Content type 'application/x-gzip' length 63268317 bytes (60.3 MB)
downloaded 60.3 MB

* installing *source* package ‘IlluminaHumanMethylation450k.db’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
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/3.3/Resources/library/IlluminaHumanMethylation450k.db’

> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.5 (El Capitan)

[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] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BiocInstaller_1.22.2                    TCGAbiolinks_1.1.26                    
 [3] BSgenome.Hsapiens.UCSC.hg19_1.4.0       BSgenome_1.40.0                        
 [5] rtracklayer_1.32.0                      Biostrings_2.40.1                      
 [7] XVector_0.12.0                          ggplot2_2.1.0                          
 [9] tidyr_0.4.1                             dplyr_0.4.3                            
[11] GenomicInteractions_1.6.2               InteractionSet_1.0.0                   
[13] SummarizedExperiment_1.2.2              TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[15] GenomicFeatures_1.24.2                  AnnotationDbi_1.34.3                   
[17] Biobase_2.32.0                          GenomicRanges_1.24.1                   
[19] GenomeInfoDb_1.8.1                      IRanges_2.6.0                          
[21] S4Vectors_0.10.1                        BiocGenerics_0.18.0                    
[23] ChIPseeker_1.9.3                       

loaded via a namespace (and not attached):
  [1] circlize_0.3.6                Hmisc_3.17-4                  AnnotationHub_2.4.2          
  [4] aroma.light_3.2.0             plyr_1.8.3                    igraph_1.0.1                 
  [7] ConsensusClusterPlus_1.36.0   lazyeval_0.1.10               splines_3.3.0                
 [10] BiocParallel_1.6.2            gridBase_0.4-7                TH.data_1.0-7                
 [13] digest_0.6.9                  foreach_1.4.3                 ensembldb_1.4.5              
 [16] htmltools_0.3.5               gdata_2.17.0                  magrittr_1.5                 
 [19] memoise_1.0.0                 doParallel_1.0.10             cluster_2.0.4                
 [22] limma_3.28.0                  ComplexHeatmap_1.10.0         annotate_1.50.0              
 [25] matrixStats_0.50.2            R.utils_2.3.0                 sandwich_2.3-4               
 [28] colorspace_1.2-6              rvest_0.3.1                   ggrepel_0.5                  
 [31] haven_0.2.0                   hexbin_1.27.1                 RCurl_1.95-4.8               
 [34] graph_1.50.0                  genefilter_1.54.0             lme4_1.1-12                  
 [37] supraHex_1.10.0               iterators_1.0.8               ape_3.4                      
 [40] survival_2.39-3               VariantAnnotation_1.18.0      zoo_1.7-13                   
 [43] gtable_0.2.0                  zlibbioc_1.18.0               MatrixModels_0.4-1           
 [46] UpSetR_1.2.1                  GetoptLong_0.1.3              sjmisc_1.7                   
 [49] car_2.1-2                     Rgraphviz_2.16.0              shape_1.4.2                  
 [52] SparseM_1.7                   scales_0.4.0                  DESeq_1.24.0                 
 [55] mvtnorm_1.0-5                 edgeR_3.14.0                  DBI_0.4-1                    
 [58] GGally_1.0.1                  Rcpp_0.12.5                   plotrix_3.6-2                
 [61] xtable_1.8-2                  matlab_1.0.2                  foreign_0.8-66               
 [64] preprocessCore_1.34.0         Formula_1.2-1                 httr_1.1.0                   
 [67] gplots_3.0.1                  RColorBrewer_1.1-2            acepack_1.3-3.3              
 [70] modeltools_0.2-21             reshape_0.8.5                 XML_3.98-1.4                 
 [73] R.methodsS3_1.7.1             Gviz_1.16.1                   nnet_7.3-12                  
 [76] reshape2_1.4.1                labeling_0.3                  munsell_0.4.3                
 [79] tools_3.3.0                   downloader_0.4                RSQLite_1.0.0                
 [82] devtools_1.11.1               stringr_1.0.0                 knitr_1.12.3                 
 [85] caTools_1.17.1                dendextend_1.1.8              coin_1.1-2                   
 [88] EDASeq_2.5.1                  nlme_3.1-127                  quantreg_5.21                
 [91] whisker_0.3-2                 mime_0.4                      R.oo_1.20.0                  
 [94] xml2_0.1.2                    biomaRt_2.28.0                pbkrtest_0.4-6               
 [97] interactiveDisplayBase_1.10.3 affyio_1.42.0                 geneplotter_1.50.0           
[100] stringi_1.1.1                 lattice_0.20-33               Matrix_1.2-6                 
[103] psych_1.5.8                   nloptr_1.0.4                  effects_3.1-1                
[106] stringdist_0.9.4.1            GlobalOptions_0.0.10          data.table_1.9.6             
[109] cowplot_0.6.2                 bitops_1.0-6                  dnet_1.0.8                   
[112] httpuv_1.3.3                  R6_2.1.2                      latticeExtra_0.6-28          
[115] affy_1.50.0                   hwriter_1.3.2                 ShortRead_1.30.0             
[118] KernSmooth_2.23-15            gridExtra_2.2.1               codetools_0.2-14             
[121] dichromat_2.0-0               boot_1.3-18                   MASS_7.3-45                  
[124] gtools_3.5.0                  assertthat_0.1                chron_2.3-47                 
[127] rjson_0.2.15                  withr_1.0.1                   mnormt_1.5-4                 
[130] GenomicAlignments_1.8.1       Rsamtools_1.24.0              multcomp_1.4-5               
[133] mgcv_1.8-12                   sjPlot_1.9.4                  grid_3.3.0                   
[136] rpart_4.1-10                  minqa_1.2.4                   biovizBase_1.20.0            
[139] shiny_0.13.2  
illuminahumanmethylation450k.db • 1.2k views
Entering edit mode
Last seen 15 days ago
United States

The message is trying to say that the package is no longer supported, and you should use the alternatives in the message.

Use 'FDb.InfiniumMethylation.hg19' instead.
Use 'FDb.InfiniumMethylation.hg18' instead.
Use 'mapToGenome() function in minfi or methylumi' instead.
See help("Defunct")



Login before adding your answer.

Traffic: 987 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6