I am new to all this! I can download DESeq2 using
source("https://bioconductor.org/biocLite.R")
biocLite("DESeq2")
but when I go to load the libraries I get this error:
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) :
there is no package called ‘data.table’
Error: package or namespace load failed for ‘DESeq2’
Can anyone help?
Venessa.
SessionInfo:
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3
locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
attached base packages:
[1] stats4 parallel stats graphics grDevices utils
[7] datasets methods base
other attached packages:
[1] BiocInstaller_1.24.0 SummarizedExperiment_1.4.0
[3] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3
[5] IRanges_2.8.1 S4Vectors_0.12.1
[7] edgeR_3.16.5 limma_3.30.12
[9] Biobase_2.34.0 BiocGenerics_0.20.0
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 splines_3.3.2 lattice_0.20-34
[4] colorspace_1.3-2 htmltools_0.3.5 base64enc_0.1-3
[7] survival_2.40-1 foreign_0.8-67 BiocParallel_1.8.1
[10] RColorBrewer_1.1-2 plyr_1.8.4 stringr_1.2.0
[13] zlibbioc_1.20.0 munsell_0.4.3 gtable_0.2.0
[16] htmlwidgets_0.8 latticeExtra_0.6-28 knitr_1.15.1
[19] htmlTable_1.9 Rcpp_0.12.9 acepack_1.4.1
[22] scales_0.4.1 backports_1.0.5 checkmate_1.8.2
[25] XVector_0.14.0 gridExtra_2.2.1 ggplot2_2.2.1
[28] digest_0.6.12 stringi_1.1.2 grid_3.3.2
[31] tools_3.3.2 bitops_1.0-6 magrittr_1.5
[34] lazyeval_0.2.0 RCurl_1.95-4.8 tibble_1.2
[37] Formula_1.2-1 cluster_2.0.5 Matrix_1.2-8
[40] assertthat_0.1 rpart_4.1-10 nnet_7.3-12
I'm having a similar error, but different package:
Installing Hmisc as suggested above did not solve the issue.
sessionInfo() R version 3.6.3 (2020-02-29) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS Catalina 10.15.3
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale: [1] enUS.UTF-8/enUS.UTF-8/enUS.UTF-8/C/enUS.UTF-8/en_US.UTF-8
attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] RCurl1.98-1.1 SummarizedExperiment1.16.1 DelayedArray0.12.2
[4] BiocParallel1.20.1 matrixStats0.56.0 Biobase2.46.0
[7] GenomicRanges1.38.0 GenomeInfoDb1.22.0 IRanges2.20.2
[10] S4Vectors0.24.3 BiocGenerics0.32.0 reshape21.4.3
[13] ggplot23.3.0 car3.0-7 carData3.0-3
[16] phyloseq1.30.0
loaded via a namespace (and not attached): [1] jsonlite1.6.1 splines3.6.3 foreach1.4.8 assertthat0.2.1
[5] BiocManager1.30.10 GenomeInfoDbData1.2.2 cellranger1.1.0 pillar1.4.3
[9] lattice0.20-40 glue1.3.2 digest0.6.25 XVector0.26.0
[13] colorspace1.4-1 Matrix1.2-18 plyr1.8.6 pkgconfig2.0.3
[17] haven2.2.0 zlibbioc1.32.0 purrr0.3.3 scales1.1.0
[21] openxlsx4.1.4 rio0.5.16 tibble2.1.3 mgcv1.8-31
[25] farver2.0.3 withr2.1.2 survival3.1-11 magrittr1.5
[29] crayon1.3.4 readxl1.3.1 nlme3.1-145 MASS7.3-51.5
[33] forcats0.5.0 foreign0.8-76 vegan2.5-6 tools3.6.3
[37] data.table1.12.8 hms0.5.3 lifecycle0.2.0 stringr1.4.0
[41] Rhdf5lib1.8.0 munsell0.5.0 cluster2.1.0 zip2.0.4
[45] Biostrings2.54.0 ade41.7-15 compiler3.6.3 rlang0.4.5
[49] rhdf52.30.1 grid3.6.3 iterators1.0.12 biomformat1.14.0
[53] rstudioapi0.11 igraph1.2.5 bitops1.0-6 labeling0.3
[57] gtable0.3.0 codetools0.2-16 multtest2.42.0 abind1.4-5
[61] curl4.3 R62.4.1 dplyr0.8.5 permute0.9-5
[65] ape5.3 stringi1.4.6 Rcpp1.0.4 vctrs0.2.4
[69] tidyselect_1.0.0
Any ideas are welcome!
If you don’t post the error in question (why you can’t install Hmisc) no one can help answer your question.
No, when you install Hmisc.