Session Info
## R version 4.1.1 (2021-08-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.3 LTS
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.8.so
##
## 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=C
## [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 stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] janitor_2.1.0 ggnewscale_0.4.5 ggrepel_0.9.1
## [4] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
## [7] purrr_0.3.4 readr_2.0.2 tidyr_1.1.4
## [10] tibble_3.1.5 ggplot2_3.3.5 tidyverse_1.3.1
## [13] rstatix_0.7.0 patchwork_1.1.1 copykit_0.1.0
## [16] DNAcopy_1.68.0 Rsubread_2.8.1 SingleCellExperiment_1.16.0
## [19] SummarizedExperiment_1.24.0 Biobase_2.54.0 GenomicRanges_1.46.0
## [22] GenomeInfoDb_1.30.0 IRanges_2.28.0 S4Vectors_0.32.2
## [25] BiocGenerics_0.40.0 MatrixGenerics_1.6.0 matrixStats_0.61.0
## [28] BiocParallel_1.28.0 bookdown_0.24 devtools_2.4.2
## [31] usethis_2.1.3
##
## loaded via a namespace (and not attached):
## [1] prabclus_2.3-2 semver_0.2.0 coda_0.19-4 clusterGeneration_1.3.7
## [5] knitr_1.36 irlba_2.3.3 DelayedArray_0.20.0 RCurl_1.98-1.5
## [9] doParallel_1.0.16 generics_0.1.1 callr_3.7.0 cowplot_1.1.1
## [13] lambda.r_1.2.4 combinat_0.0-8 tzdb_0.2.0 xml2_1.3.2
## [17] lubridate_1.8.0 httpuv_1.6.3 assertthat_0.2.1 viridis_0.6.2
## [21] amap_0.8-18 xfun_0.28 hms_1.1.1 jquerylib_0.1.4
## [25] evaluate_0.14 promises_1.2.0.1 DEoptimR_1.0-9 fansi_0.5.0
## [29] dbplyr_2.1.1 readxl_1.3.1 igraph_1.2.8 DBI_1.1.1
## [33] tmvnsim_1.0-2 futile.logger_1.4.3 ellipsis_0.3.2 RSpectra_0.16-0
## [37] backports_1.3.0 vctrs_0.3.8 ggalluvial_0.12.3 remotes_2.4.1
## [41] abind_1.4-5 cachem_1.0.6 withr_2.4.3 robustbase_0.93-9
## [45] treeio_1.18.0 prettyunits_1.1.1 mclust_5.4.7 mnormt_2.0.2
## [49] phytools_0.7-90 cluster_2.1.2 ape_5.5 segmented_1.3-4
## [53] lazyeval_0.2.2 crayon_1.4.2 versions_0.3 pkgconfig_2.0.3
## [57] labeling_0.4.2 nlme_3.1-153 vipor_0.4.5 pkgload_1.2.3
## [61] nnet_7.3-16 rlang_0.4.12 diptest_0.76-0 lifecycle_1.0.1
## [65] miniUI_0.1.1.1 dbscan_1.1-10 modelr_0.1.8 cellranger_1.1.0
## [69] rprojroot_2.0.2 shinyFiles_0.9.1 Matrix_1.3-4 aplot_0.1.1
## [73] phangorn_2.7.1 carData_3.0-4 boot_1.3-28 reprex_2.0.1
## [77] beeswarm_0.4.0 GlobalOptions_0.1.2 processx_3.5.2 png_0.1-7
## [81] viridisLite_0.4.0 rjson_0.2.20 bitops_1.0-7 shape_1.4.6
## [85] stevedore_0.9.4 gridGraphics_0.5-1 scales_1.1.1 memoise_2.0.0
## [89] magrittr_2.0.1 zlibbioc_1.40.0 compiler_4.1.1 RColorBrewer_1.1-2
## [93] plotrix_3.8-2 clue_0.3-60 snakecase_0.11.0 cli_3.1.0
## [97] XVector_0.34.0 ps_1.6.0 formatR_1.11 MASS_7.3-54
## [101] tidyselect_1.1.1 stringi_1.7.5 highr_0.9 yaml_2.2.1
## [105] grid_4.1.1 sass_0.4.0 fastmatch_1.1-3 tools_4.1.1
## [109] parallel_4.1.1 circlize_0.4.13 rstudioapi_0.13 bluster_1.4.0
## [113] foreach_1.5.1 gridExtra_2.3 scatterplot3d_0.3-41 farver_2.1.0
## [117] digest_0.6.28 FNN_1.1.3 shiny_1.7.1 quadprog_1.5-8
## [121] fpc_2.2-9 Rcpp_1.0.7 car_3.0-12 broom_0.7.10
## [125] later_1.3.0 httr_1.4.2 ComplexHeatmap_2.10.0 kernlab_0.9-29
## [129] colorspace_2.0-2 rvest_1.0.2 fs_1.5.0 splines_4.1.1
## [133] uwot_0.1.10 yulab.utils_0.0.4 tidytree_0.3.5 expm_0.999-6
## [137] ggplotify_0.1.0 flexmix_2.3-17 containerit_0.6.0.9004 sessioninfo_1.2.1
## [141] xtable_1.8-4 jsonlite_1.7.2 ggtree_3.2.0 futile.options_1.0.1
## [145] modeltools_0.2-23 ggfun_0.0.4 testthat_3.1.0 ggimage_0.3.0
## [149] R6_2.5.1 pillar_1.6.4 htmltools_0.5.2 mime_0.12
## [153] glue_1.4.2 fastmap_1.1.0 BiocNeighbors_1.12.0 class_7.3-19
## [157] codetools_0.2-18 maps_3.4.0 pkgbuild_1.2.0 utf8_1.2.2
## [161] lattice_0.20-45 bslib_0.3.1 mixtools_1.2.0 numDeriv_2016.8-1.1
## [165] curl_4.3.2 ggbeeswarm_0.6.0 gtools_3.9.2 magick_2.7.3
## [169] survival_3.2-13 rmarkdown_2.11 desc_1.4.0 munsell_0.5.0
## [173] GetoptLong_1.0.5 fastcluster_1.2.3 GenomeInfoDbData_1.2.7 iterators_1.0.13
## [177] haven_2.4.3 gtable_0.3.0
suppressPackageStartupMessages(library("containerit"))
my_dockerfile <- containerit::dockerfile(from = utils::sessionInfo(),
versioned_libs = TRUE,
versioned_packages = TRUE)
## INFO [2022-03-11 05:43:28] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:28] Trying to determine system requirements for the package(s) 'Biobase' from sysreqs online DB
## INFO [2022-03-11 05:43:28] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:28] Trying to determine system requirements for the package(s) 'BiocGenerics' from sysreqs online DB
## INFO [2022-03-11 05:43:29] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:29] Trying to determine system requirements for the package(s) 'BiocParallel' from sysreqs online DB
## INFO [2022-03-11 05:43:29] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:29] Trying to determine system requirements for the package(s) 'copykit' from sysreqs online DB
## INFO [2022-03-11 05:43:30] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:30] Trying to determine system requirements for the package(s) 'DNAcopy' from sysreqs online DB
## INFO [2022-03-11 05:43:30] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:30] Trying to determine system requirements for the package(s) 'GenomeInfoDb' from sysreqs online DB
## INFO [2022-03-11 05:43:31] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:31] Trying to determine system requirements for the package(s) 'GenomicRanges' from sysreqs online DB
## INFO [2022-03-11 05:43:31] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:31] Trying to determine system requirements for the package(s) 'IRanges' from sysreqs online DB
## INFO [2022-03-11 05:43:31] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:31] Trying to determine system requirements for the package(s) 'MatrixGenerics' from sysreqs online DB
## INFO [2022-03-11 05:43:32] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:32] Trying to determine system requirements for the package(s) 'remotes' from sysreqs online DB
## INFO [2022-03-11 05:43:32] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:32] Trying to determine system requirements for the package(s) 'Rsubread' from sysreqs online DB
## INFO [2022-03-11 05:43:33] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:33] Trying to determine system requirements for the package(s) 'S4Vectors' from sysreqs online DB
## INFO [2022-03-11 05:43:33] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:33] Trying to determine system requirements for the package(s) 'SingleCellExperiment' from sysreqs online DB
## INFO [2022-03-11 05:43:33] Going online? TRUE ... to retrieve system dependencies (sysreq-api)
## INFO [2022-03-11 05:43:33] Trying to determine system requirements for the package(s) 'SummarizedExperiment' from sysreqs online DB
## INFO [2022-03-11 05:43:34] Versioned packages enabled, installing 'versions'
## INFO [2022-03-11 05:43:34] Adding versioned CRAN packages: remotes
## WARN [2022-03-11 05:43:34] Adding versioned Bioconductor packages not supported: DNAcopy, Rsubread, SingleCellExperiment, SummarizedExperiment, Biobase, GenomicRanges, GenomeInfoDb, IRanges, S4Vectors, BiocGenerics, MatrixGenerics, BiocParallel
## INFO [2022-03-11 05:43:34] Adding Bioconductor packages: Biobase, BiocGenerics, BiocParallel, DNAcopy, GenomeInfoDb, GenomicRanges, IRanges, MatrixGenerics, Rsubread, S4Vectors, SingleCellExperiment, SummarizedExperiment
## INFO [2022-03-11 05:43:34] Adding GitHub packages: navinlabcode/copykit@f709a486c8e2d45bd46738067e2f60ca268d64b2
## INFO [2022-03-11 05:43:34] Created Dockerfile-Object based on sessionInfo
Dockerfile
## FROM rocker/r-ver:4.1.1
## LABEL maintainer="dminussi"
## RUN export DEBIAN_FRONTEND=noninteractive; apt-get -y update \
## && apt-get install -y git-core
## RUN ["install2.r", "versions"]
## RUN ["Rscript", "-e", "versions::install.versions('remotes', '1.1.1')"]
## RUN ["install2.r", "-r https://bioconductor.org/packages/3.14/bioc -r https://bioconductor.org/packages/3.14/data/annotation -r https://bioconductor.org/packages/3.14/data/experiment -r https://bioconductor.org/packages/3.14/workflows", "Biobase", "BiocGenerics", "BiocParallel", "DNAcopy", "GenomeInfoDb", "GenomicRanges", "IRanges", "MatrixGenerics", "Rsubread", "S4Vectors", "SingleCellExperiment", "SummarizedExperiment"]
## RUN ["installGithub.r", "navinlabcode/copykit@f709a486c8e2d45bd46738067e2f60ca268d64b2"]
## WORKDIR /payload/
## CMD ["R"]