Entering edit mode
Hi, I just tried installing this package, but failed.
biocLite("IlluminaHumanMethylation450k.db")
BioC_mirror: https://bioconductor.org
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 'https://bioconductor.org/packages/3.3/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’ ...
** 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)
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] 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
