9 Session Info
## R version 3.6.2 (2019-12-12)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Red Hat Enterprise Linux
##
## Matrix products: default
## BLAS: /usr/lib64/R/lib/libRblas.so
## LAPACK: /usr/lib64/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 grid parallel stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] scran_1.14.6 SingleCellExperiment_1.8.0 containerit_0.6.0.9003
## [4] fgsea_1.12.0 Rcpp_1.0.4.6 biomaRt_2.42.1
## [7] boot_1.3-25 janitor_2.0.1 jcolors_0.0.4
## [10] vcfR_1.12.0 conflicted_1.0.4 Homo.sapiens_1.3.1
## [13] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 org.Hs.eg.db_3.10.0 GO.db_3.10.0
## [16] OrganismDbi_1.28.0 DESeq2_1.26.0 SummarizedExperiment_1.16.1
## [19] DelayedArray_0.12.3 BiocParallel_1.20.1 matrixStats_0.56.0
## [22] jsonlite_1.7.0 AnnotationHub_2.18.0 BiocFileCache_1.10.2
## [25] dbplyr_1.4.4 GenomicFeatures_1.38.2 AnnotationDbi_1.48.0
## [28] Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.1
## [31] IRanges_2.20.2 S4Vectors_0.24.4 BiocGenerics_0.32.0
## [34] tximport_1.14.2 future.apply_1.7.0 future_1.21.0
## [37] ggtree_2.0.4 cowplot_1.0.0 amap_0.8-18
## [40] ComplexHeatmap_2.2.0 uwot_0.1.8 Matrix_1.2-18
## [43] phangorn_2.5.5 ape_5.4 ggbeeswarm_0.6.0
## [46] umap_0.2.5.0 patchwork_1.0.0 rstatix_0.6.0
## [49] paletteer_1.1.0 forcats_0.5.0 stringr_1.4.0
## [52] dplyr_1.0.0 purrr_0.3.4 readr_1.3.1
## [55] tidyr_1.0.2 tibble_3.0.3 ggplot2_3.2.1
## [58] tidyverse_1.3.0 here_0.1 bookdown_0.18
##
## loaded via a namespace (and not attached):
## [1] rsvd_1.0.3 Hmisc_4.4-1 Rsamtools_2.2.3 rprojroot_1.3-2
## [5] crayon_1.3.4 MASS_7.3-51.6 nlme_3.1-148 backports_1.1.6
## [9] reprex_0.3.0 rlang_0.4.7 XVector_0.26.0 readxl_1.3.1
## [13] irlba_2.3.3 limma_3.42.2 scater_1.14.6 rjson_0.2.20
## [17] bit64_4.0.2 glue_1.4.0 geiger_2.0.6.4 vipor_0.4.5
## [21] PNWColors_0.1.0 base64url_1.4 haven_2.3.1 tidyselect_1.1.0
## [25] rio_0.5.16 XML_3.99-0.3 packrat_0.5.0 GenomicAlignments_1.22.1
## [29] xtable_1.8-4 magrittr_1.5 evaluate_0.14 cli_2.0.2
## [33] zlibbioc_1.32.0 dbscan_1.1-5 rstudioapi_0.11 miniUI_0.1.1.1
## [37] rpart_4.1-15 fastmatch_1.1-0 lambda.r_1.2.4 treeio_1.10.0
## [41] maps_3.3.0 shiny_1.5.0 BiocSingular_1.2.2 xfun_0.16
## [45] askpass_1.1 clue_0.3-57 cluster_2.1.0 clusterGeneration_1.3.4
## [49] expm_0.999-5 interactiveDisplayBase_1.24.0 subplex_1.6 listenv_0.8.0
## [53] Biostrings_2.54.0 png_0.1-7 permute_0.9-5 withr_2.2.0
## [57] bitops_1.0-6 RBGL_1.62.1 cellranger_1.1.0 coda_0.19-3
## [61] dqrng_0.2.1 pillar_1.4.6 GlobalOptions_0.1.1 fs_1.5.0
## [65] scatterplot3d_0.3-41 GetoptLong_0.1.8 DelayedMatrixStats_1.8.0 vctrs_0.3.2
## [69] ellipsis_0.3.1 generics_0.0.2 tools_3.6.2 foreign_0.8-76
## [73] beeswarm_0.2.3 munsell_0.5.0 fastmap_1.0.1 compiler_3.6.2
## [77] abind_1.4-5 httpuv_1.5.4 rtracklayer_1.46.0 stevedore_0.9.3
## [81] rcartocolor_2.0.0 scico_1.2.0 animation_2.6 GenomeInfoDbData_1.2.2
## [85] gridExtra_2.3 edgeR_3.28.1 lattice_0.20-41 utf8_1.1.4
## [89] later_1.1.0.1 prismatic_0.2.0 semver_0.2.0 scales_1.1.1
## [93] graph_1.64.0 tidytree_0.3.3 carData_3.0-4 genefilter_1.68.0
## [97] lazyeval_0.2.2 promises_1.1.1 car_3.0-10 latticeExtra_0.6-29
## [101] brew_1.0-6 reticulate_1.16 checkmate_2.0.0 rmarkdown_2.3
## [105] openxlsx_4.1.5 statmod_1.4.34 dichromat_2.0-0 igraph_1.2.5
## [109] plotrix_3.7-8 numDeriv_2016.8-1.1 survival_3.2-3 yaml_2.2.1
## [113] versions_0.3 htmltools_0.5.1.1 memoise_1.1.0 locfit_1.5-9.4
## [117] batchtools_0.9.13 quadprog_1.5-8 memuse_4.1-0 viridisLite_0.3.0
## [121] digest_0.6.25 assertthat_0.2.1 mime_0.9 rappdirs_0.3.1
## [125] futile.options_1.0.1 palr_0.2.0 pals_1.6 RSQLite_2.2.0
## [129] debugme_1.1.0 mapproj_1.2.7 data.table_1.13.0 blob_1.2.1
## [133] vegan_2.5-6 futile.logger_1.4.3 deSolve_1.28 splines_3.6.2
## [137] Formula_1.2-3 labeling_0.3 rematch2_2.1.1 RCurl_1.98-1.2
## [141] broom_0.7.0 hms_0.5.3 modelr_0.1.8 colorspace_1.4-1
## [145] base64enc_0.1-3 mnormt_1.5-6 BiocManager_1.30.10 shape_1.4.4
## [149] evobiR_1.1 nnet_7.3-14 mvtnorm_1.1-0 circlize_0.4.8
## [153] fansi_0.4.1 parallelly_1.23.0 R6_2.4.1 phytools_0.7-20
## [157] lifecycle_0.2.0 formatR_1.7 oompaBase_3.2.9 zip_2.1.0
## [161] curl_4.3 snakecase_0.11.0 fastcluster_1.1.25 desc_1.2.0
## [165] RcppAnnoy_0.0.16 pinfsc50_1.2.0 RColorBrewer_1.1-2 htmlwidgets_1.5.1
## [169] rvest_0.3.6 mgcv_1.8-31 globals_0.14.0 openssl_1.4.2
## [173] htmlTable_2.0.1 codetools_0.2-16 lubridate_1.7.8 gtools_3.8.2
## [177] prettyunits_1.1.1 RSpectra_0.16-0 gtable_0.3.0 DBI_1.1.0
## [181] httr_1.4.2 stringi_1.4.6 progress_1.2.2 farver_2.0.3
## [185] viridis_0.5.1 annotate_1.64.0 seqinr_3.6-1 combinat_0.0-8
## [189] xml2_1.3.2 rvcheck_0.1.8 shinyFiles_0.9.0 BiocNeighbors_1.4.2
## [193] ade4_1.7-15 geneplotter_1.64.0 BiocVersion_3.10.1 bit_1.1-15.2
## [197] jpeg_0.1-8.1 pkgconfig_2.0.3 knitr_1.29suppressPackageStartupMessages(library("containerit"))
my_dockerfile <- containerit::dockerfile(from = utils::sessionInfo(),
versioned_libs = TRUE,
versioned_packages = TRUE)## INFO [2021-03-21 16:25:37] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:37] Trying to determine system requirements for the package(s) 'amap' from sysreqs online DB
## INFO [2021-03-21 16:25:37] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:37] Trying to determine system requirements for the package(s) 'AnnotationDbi' from sysreqs online DB
## INFO [2021-03-21 16:25:37] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:37] Trying to determine system requirements for the package(s) 'AnnotationHub' from sysreqs online DB
## INFO [2021-03-21 16:25:38] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:38] Trying to determine system requirements for the package(s) 'ape' from sysreqs online DB
## INFO [2021-03-21 16:25:38] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:38] Trying to determine system requirements for the package(s) 'Biobase' from sysreqs online DB
## INFO [2021-03-21 16:25:39] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:39] Trying to determine system requirements for the package(s) 'BiocFileCache' from sysreqs online DB
## INFO [2021-03-21 16:25:39] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:39] Trying to determine system requirements for the package(s) 'BiocGenerics' from sysreqs online DB
## INFO [2021-03-21 16:25:40] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:40] Trying to determine system requirements for the package(s) 'BiocParallel' from sysreqs online DB
## INFO [2021-03-21 16:25:40] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:40] Trying to determine system requirements for the package(s) 'biomaRt' from sysreqs online DB
## INFO [2021-03-21 16:25:41] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:41] Trying to determine system requirements for the package(s) 'bookdown' from sysreqs online DB
## INFO [2021-03-21 16:25:41] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:41] Trying to determine system requirements for the package(s) 'boot' from sysreqs online DB
## INFO [2021-03-21 16:25:41] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:41] Trying to determine system requirements for the package(s) 'ComplexHeatmap' from sysreqs online DB
## INFO [2021-03-21 16:25:42] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:42] Trying to determine system requirements for the package(s) 'conflicted' from sysreqs online DB
## INFO [2021-03-21 16:25:42] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:42] Trying to determine system requirements for the package(s) 'cowplot' from sysreqs online DB
## INFO [2021-03-21 16:25:43] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:43] Trying to determine system requirements for the package(s) 'dbplyr' from sysreqs online DB
## INFO [2021-03-21 16:25:43] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:43] Trying to determine system requirements for the package(s) 'DelayedArray' from sysreqs online DB
## INFO [2021-03-21 16:25:43] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:43] Trying to determine system requirements for the package(s) 'DESeq2' from sysreqs online DB
## INFO [2021-03-21 16:25:44] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:44] Trying to determine system requirements for the package(s) 'dplyr' from sysreqs online DB
## INFO [2021-03-21 16:25:44] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:44] Trying to determine system requirements for the package(s) 'fgsea' from sysreqs online DB
## INFO [2021-03-21 16:25:44] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:44] Trying to determine system requirements for the package(s) 'forcats' from sysreqs online DB
## INFO [2021-03-21 16:25:45] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:45] Trying to determine system requirements for the package(s) 'future' from sysreqs online DB
## INFO [2021-03-21 16:25:45] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:45] Trying to determine system requirements for the package(s) 'future.apply' from sysreqs online DB
## INFO [2021-03-21 16:25:46] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:46] Trying to determine system requirements for the package(s) 'GenomeInfoDb' from sysreqs online DB
## INFO [2021-03-21 16:25:46] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:46] Trying to determine system requirements for the package(s) 'GenomicFeatures' from sysreqs online DB
## INFO [2021-03-21 16:25:46] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:46] Trying to determine system requirements for the package(s) 'GenomicRanges' from sysreqs online DB
## INFO [2021-03-21 16:25:47] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:47] Trying to determine system requirements for the package(s) 'ggbeeswarm' from sysreqs online DB
## INFO [2021-03-21 16:25:47] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:47] Trying to determine system requirements for the package(s) 'ggplot2' from sysreqs online DB
## INFO [2021-03-21 16:25:48] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:48] Trying to determine system requirements for the package(s) 'ggtree' from sysreqs online DB
## INFO [2021-03-21 16:25:48] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:48] Trying to determine system requirements for the package(s) 'GO.db' from sysreqs online DB
## INFO [2021-03-21 16:25:49] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:49] Trying to determine system requirements for the package(s) 'here' from sysreqs online DB
## INFO [2021-03-21 16:25:49] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:49] Trying to determine system requirements for the package(s) 'Homo.sapiens' from sysreqs online DB
## INFO [2021-03-21 16:25:49] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:49] Trying to determine system requirements for the package(s) 'IRanges' from sysreqs online DB
## INFO [2021-03-21 16:25:50] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:50] Trying to determine system requirements for the package(s) 'janitor' from sysreqs online DB
## INFO [2021-03-21 16:25:50] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:50] Trying to determine system requirements for the package(s) 'jcolors' from sysreqs online DB
## INFO [2021-03-21 16:25:51] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:51] Trying to determine system requirements for the package(s) 'jsonlite' from sysreqs online DB
## INFO [2021-03-21 16:25:51] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:51] Trying to determine system requirements for the package(s) 'Matrix' from sysreqs online DB
## INFO [2021-03-21 16:25:51] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:51] Trying to determine system requirements for the package(s) 'matrixStats' from sysreqs online DB
## INFO [2021-03-21 16:25:52] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:52] Trying to determine system requirements for the package(s) 'org.Hs.eg.db' from sysreqs online DB
## INFO [2021-03-21 16:25:52] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:52] Trying to determine system requirements for the package(s) 'OrganismDbi' from sysreqs online DB
## INFO [2021-03-21 16:25:52] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:53] Trying to determine system requirements for the package(s) 'paletteer' from sysreqs online DB
## INFO [2021-03-21 16:25:53] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:53] Trying to determine system requirements for the package(s) 'patchwork' from sysreqs online DB
## INFO [2021-03-21 16:25:53] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:53] Trying to determine system requirements for the package(s) 'phangorn' from sysreqs online DB
## INFO [2021-03-21 16:25:54] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:54] Trying to determine system requirements for the package(s) 'purrr' from sysreqs online DB
## INFO [2021-03-21 16:25:54] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:54] Trying to determine system requirements for the package(s) 'Rcpp' from sysreqs online DB
## INFO [2021-03-21 16:25:54] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:54] Trying to determine system requirements for the package(s) 'readr' from sysreqs online DB
## INFO [2021-03-21 16:25:55] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:55] Trying to determine system requirements for the package(s) 'rstatix' from sysreqs online DB
## INFO [2021-03-21 16:25:55] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:55] Trying to determine system requirements for the package(s) 'S4Vectors' from sysreqs online DB
## INFO [2021-03-21 16:25:56] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:56] Trying to determine system requirements for the package(s) 'scran' from sysreqs online DB
## INFO [2021-03-21 16:25:56] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:56] Trying to determine system requirements for the package(s) 'SingleCellExperiment' from sysreqs online DB
## INFO [2021-03-21 16:25:57] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:57] Trying to determine system requirements for the package(s) 'stringr' from sysreqs online DB
## INFO [2021-03-21 16:25:57] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:57] Trying to determine system requirements for the package(s) 'SummarizedExperiment' from sysreqs online DB
## INFO [2021-03-21 16:25:58] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:58] Trying to determine system requirements for the package(s) 'tibble' from sysreqs online DB
## INFO [2021-03-21 16:25:58] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:58] Trying to determine system requirements for the package(s) 'tidyr' from sysreqs online DB
## INFO [2021-03-21 16:25:58] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:58] Trying to determine system requirements for the package(s) 'tidyverse' from sysreqs online DB
## INFO [2021-03-21 16:25:59] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:59] Trying to determine system requirements for the package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene' from sysreqs online DB
## INFO [2021-03-21 16:25:59] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:25:59] Trying to determine system requirements for the package(s) 'tximport' from sysreqs online DB
## INFO [2021-03-21 16:26:00] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:26:00] Trying to determine system requirements for the package(s) 'umap' from sysreqs online DB
## INFO [2021-03-21 16:26:00] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:26:00] Trying to determine system requirements for the package(s) 'uwot' from sysreqs online DB
## INFO [2021-03-21 16:26:00] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2021-03-21 16:26:00] Trying to determine system requirements for the package(s) 'vcfR' from sysreqs online DB
## INFO [2021-03-21 16:26:01] Versioned packages enabled, installing 'versions'
## INFO [2021-03-21 16:26:01] Adding versioned CRAN packages: Rcpp, boot, janitor, jcolors, vcfR, conflicted, matrixStats, jsonlite, dbplyr, future.apply, future, cowplot, amap, uwot, Matrix, phangorn, ape, ggbeeswarm, umap, patchwork, rstatix, paletteer, forcats, stringr, dplyr, purrr, readr, tidyr, tibble, ggplot2, tidyverse, here, bookdown
## WARN [2021-03-21 16:26:01] Adding versioned Bioconductor packages not supported: scran, SingleCellExperiment, fgsea, biomaRt, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, GO.db, OrganismDbi, DESeq2, SummarizedExperiment, DelayedArray, BiocParallel, AnnotationHub, BiocFileCache, GenomicFeatures, AnnotationDbi, Biobase, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, BiocGenerics, tximport, ggtree, ComplexHeatmap
## INFO [2021-03-21 16:26:01] Adding Bioconductor packages: AnnotationDbi, AnnotationHub, Biobase, BiocFileCache, BiocGenerics, BiocParallel, biomaRt, ComplexHeatmap, DelayedArray, DESeq2, fgsea, GenomeInfoDb, GenomicFeatures, GenomicRanges, ggtree, GO.db, Homo.sapiens, IRanges, org.Hs.eg.db, OrganismDbi, S4Vectors, scran, SingleCellExperiment, SummarizedExperiment, TxDb.Hsapiens.UCSC.hg19.knownGene, tximport
## INFO [2021-03-21 16:26:01] Created Dockerfile-Object based on sessionInfo9.1 Dockerfile
## FROM rocker/r-ver:3.6.2
## LABEL maintainer="dminussi"
## RUN export DEBIAN_FRONTEND=noninteractive; apt-get -y update \
## && apt-get install -y pandoc \
## pandoc-citeproc
## RUN ["install2.r", "versions"]
## RUN ["Rscript", "-e", "versions::install.versions('Rcpp', '1.0.4.6')", "-e", "versions::install.versions('boot', '1.3-25')", "-e", "versions::install.versions('janitor', '2.0.1')", "-e", "versions::install.versions('jcolors', '0.0.4')", "-e", "versions::install.versions('vcfR', '1.12.0')", "-e", "versions::install.versions('conflicted', '1.0.4')", "-e", "versions::install.versions('matrixStats', '0.56.0')", "-e", "versions::install.versions('jsonlite', '1.7.0')", "-e", "versions::install.versions('dbplyr', '1.4.4')", "-e", "versions::install.versions('future.apply', '1.7.0')", "-e", "versions::install.versions('future', '1.21.0')", "-e", "versions::install.versions('cowplot', '1.0.0')", "-e", "versions::install.versions('amap', '0.8-18')", "-e", "versions::install.versions('uwot', '0.1.8')", "-e", "versions::install.versions('Matrix', '1.2-18')", "-e", "versions::install.versions('phangorn', '2.5.5')", "-e", "versions::install.versions('ape', '5.4')", "-e", "versions::install.versions('ggbeeswarm', '0.6.0')", "-e", "versions::install.versions('umap', '0.2.5.0')", "-e", "versions::install.versions('patchwork', '1.0.0')", "-e", "versions::install.versions('rstatix', '0.6.0')", "-e", "versions::install.versions('paletteer', '1.1.0')", "-e", "versions::install.versions('forcats', '0.5.0')", "-e", "versions::install.versions('stringr', '1.4.0')", "-e", "versions::install.versions('dplyr', '1.0.0')", "-e", "versions::install.versions('purrr', '0.3.4')", "-e", "versions::install.versions('readr', '1.3.1')", "-e", "versions::install.versions('tidyr', '1.0.2')", "-e", "versions::install.versions('tibble', '3.0.3')", "-e", "versions::install.versions('ggplot2', '3.2.1')", "-e", "versions::install.versions('tidyverse', '1.3.0')", "-e", "versions::install.versions('here', '0.1')", "-e", "versions::install.versions('bookdown', '0.18')"]
## RUN ["install2.r", "-r https://bioconductor.org/packages/3.10/bioc -r https://bioconductor.org/packages/3.10/data/annotation -r https://bioconductor.org/packages/3.10/data/experiment -r https://bioconductor.org/packages/3.10/workflows", "AnnotationDbi", "AnnotationHub", "Biobase", "BiocFileCache", "BiocGenerics", "BiocParallel", "biomaRt", "ComplexHeatmap", "DelayedArray", "DESeq2", "fgsea", "GenomeInfoDb", "GenomicFeatures", "GenomicRanges", "ggtree", "GO.db", "Homo.sapiens", "IRanges", "org.Hs.eg.db", "OrganismDbi", "S4Vectors", "scran", "SingleCellExperiment", "SummarizedExperiment", "TxDb.Hsapiens.UCSC.hg19.knownGene", "tximport"]
## WORKDIR /payload/
## CMD ["R"]This repository contains the scripts used for in the manuscript: Breast Tumors Maintain a Reservoir of Subclonal Diversity During Primary Expansion