diff --git a/R/convenience.R b/R/convenience.R index 1f4a52bae..b531f7e1f 100644 --- a/R/convenience.R +++ b/R/convenience.R @@ -2633,7 +2633,7 @@ createArchRProj <- function(fragmentsPath, if(!requireNamespace('ArchR')) { wrap_msg('ArchR is needed. Install the package using remotes::install_github("GreenleafLab/ArchR")') - } else {require(ArchR)} + } ## Add reference genome wrap_msg('Loading reference genome') diff --git a/vignettes/ecosystem.Rmd b/vignettes/ecosystem.Rmd index beeca525d..578196ba9 100644 --- a/vignettes/ecosystem.Rmd +++ b/vignettes/ecosystem.Rmd @@ -79,7 +79,7 @@ The scripts used to create both the mini giotto objects and mini objects are ava ```{r, eval=FALSE} # Ensure Giotto Suite is installed if(!"Giotto" %in% installed.packages()) { - devtools::install_github("drieslab/Giotto@suite_modular") + devtools::install_github("drieslab/Giotto") } library(Giotto) @@ -117,9 +117,9 @@ sessionInfo() ```{r, eval=FALSE} -R version 4.3.1 (2023-06-16) +R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) -Running under: macOS Sonoma 14.1.2 +Running under: macOS Sonoma 14.2.1 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib @@ -128,7 +128,7 @@ LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlap locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 -time zone: America/New_York +time zone: America/Mexico_City tzcode source: internal attached base packages: @@ -136,36 +136,65 @@ attached base packages: [7] base other attached packages: -[1] GiottoData_0.2.6.1 Giotto_4.0.0 GiottoVisuals_0.1.0 -[4] GiottoClass_0.1.0 GiottoUtils_0.1.0 +[1] GiottoData_0.2.6.1 GiottoUtils_0.1.2 Giotto_4.0.2 +[4] GiottoClass_0.1.2 loaded via a namespace (and not attached): - [1] utf8_1.2.4 generics_0.1.3 - [3] lattice_0.22-5 digest_0.6.33 - [5] magrittr_2.0.3 evaluate_0.23 - [7] grid_4.3.1 fastmap_1.1.1 - [9] jsonlite_1.8.7 Matrix_1.6-4 -[11] backports_1.4.1 fansi_1.0.5 -[13] scales_1.3.0 codetools_0.2-19 -[15] cli_3.6.1 rlang_1.1.2 -[17] XVector_0.42.0 Biobase_2.60.0 -[19] munsell_0.5.0 withr_2.5.2 -[21] colorRamp2_0.1.0 tools_4.3.1 -[23] parallel_4.3.1 checkmate_2.3.0 -[25] dplyr_1.1.4 colorspace_2.1-0 -[27] ggplot2_3.4.4 BiocGenerics_0.48.1 -[29] reticulate_1.34.0 png_0.1-8 -[31] vctrs_0.6.5 R6_2.5.1 -[33] stats4_4.3.1 lifecycle_1.0.4 -[35] zlibbioc_1.48.0 S4Vectors_0.40.2 -[37] IRanges_2.36.0 pkgconfig_2.0.3 -[39] terra_1.7-55 pillar_1.9.0 -[41] gtable_0.3.4 data.table_1.14.8 -[43] glue_1.6.2 Rcpp_1.0.11 -[45] xfun_0.41 tibble_3.2.1 -[47] tidyselect_1.2.0 rstudioapi_0.15.0 -[49] knitr_1.45 igraph_1.5.1 -[51] htmltools_0.5.7 rmarkdown_2.25 -[53] compiler_4.3.1 - + [1] colorRamp2_0.1.0 DBI_1.2.0 + [3] bitops_1.0-7 biomaRt_2.58.0 + [5] rlang_1.1.2 magrittr_2.0.3 + [7] matrixStats_1.2.0 e1071_1.7-14 + [9] compiler_4.3.2 RSQLite_2.3.4 + [11] png_0.1-8 vctrs_0.6.5 + [13] stringr_1.5.1 pkgconfig_2.0.3 + [15] SpatialExperiment_1.12.0 crayon_1.5.2 + [17] fastmap_1.1.1 backports_1.4.1 + [19] dbplyr_2.4.0 magick_2.8.2 + [21] XVector_0.42.0 utf8_1.2.4 + [23] rmarkdown_2.25 purrr_1.0.2 + [25] bit_4.0.5 xfun_0.41 + [27] zlibbioc_1.48.0 cachem_1.0.8 + [29] jsonlite_1.8.8 GenomeInfoDb_1.38.5 + [31] progress_1.2.3 blob_1.2.4 + [33] rhdf5filters_1.14.1 gmp_0.7-3 + [35] DelayedArray_0.28.0 Rhdf5lib_1.24.1 + [37] terra_1.7-65 parallel_4.3.2 + [39] prettyunits_1.2.0 R6_2.5.1 + [41] stringi_1.8.3 reticulate_1.34.0 + [43] ClusterR_1.3.2 GenomicRanges_1.54.1 + [45] Rcpp_1.0.11 assertthat_0.2.1 + [47] SummarizedExperiment_1.32.0 knitr_1.45 + [49] IRanges_2.36.0 igraph_1.6.0 + [51] Matrix_1.6-4 tidyselect_1.2.0 + [53] yaml_2.3.8 rstudioapi_0.15.0 + [55] abind_1.4-5 codetools_0.2-19 + [57] curl_5.2.0 lattice_0.21-9 + [59] tibble_3.2.1 withr_2.5.2 + [61] Biobase_2.62.0 KEGGREST_1.42.0 + [63] evaluate_0.23 sf_1.0-15 + [65] units_0.8-5 proxy_0.4-27 + [67] BiocFileCache_2.10.1 xml2_1.3.6 + [69] Biostrings_2.70.1 pillar_1.9.0 + [71] filelock_1.0.3 MatrixGenerics_1.14.0 + [73] KernSmooth_2.23-22 checkmate_2.3.1 + [75] stats4_4.3.2 generics_0.1.3 + [77] RCurl_1.98-1.13 S4Vectors_0.40.2 + [79] hms_1.1.3 ggplot2_3.4.4 + [81] munsell_0.5.0 scales_1.3.0 + [83] class_7.3-22 glue_1.6.2 + [85] tools_4.3.2 GiottoVisuals_0.1.1 + [87] data.table_1.14.10 XML_3.99-0.16 + [89] cowplot_1.1.2 rhdf5_2.46.1 + [91] grid_4.3.2 AnnotationDbi_1.64.1 + [93] colorspace_2.1-0 SingleCellExperiment_1.24.0 + [95] GenomeInfoDbData_1.2.11 cli_3.6.2 + [97] rappdirs_0.3.3 fansi_1.0.6 + [99] S4Arrays_1.2.0 arrow_14.0.0.2 +[101] dplyr_1.1.4 gtable_0.3.4 +[103] digest_0.6.33 progressr_0.14.0 +[105] BiocGenerics_0.48.1 classInt_0.4-10 +[107] SparseArray_1.2.3 rjson_0.2.21 +[109] memoise_2.0.1 htmltools_0.5.7 +[111] lifecycle_1.0.4 httr_1.4.7 +[113] bit64_4.0.5 ``` diff --git a/vignettes/installation.Rmd b/vignettes/installation.Rmd index 79718bc57..16941f51b 100644 --- a/vignettes/installation.Rmd +++ b/vignettes/installation.Rmd @@ -29,7 +29,7 @@ if(!"devtools" %in% installed.packages()) { install.packages("devtools") } -devtools::install_github("drieslab/Giotto@suite_modular") +devtools::install_github("drieslab/Giotto") ``` @@ -57,36 +57,81 @@ sessionInfo() ```{r, eval=FALSE} - - R version 4.2.2 (2022-10-31 ucrt) - Platform: x86_64-w64-mingw32/x64 (64-bit) - Running under: Windows 10 x64 (build 22621) - - Matrix products: default - - locale: - [1] LC_COLLATE=English_United States.utf8 - [2] LC_CTYPE=English_United States.utf8 - [3] LC_MONETARY=English_United States.utf8 - [4] LC_NUMERIC=C - [5] LC_TIME=English_United States.utf8 - - attached base packages: - [1] stats graphics grDevices utils datasets methods base - - other attached packages: - [1] Giotto_3.2.1 - - loaded via a namespace (and not attached): - [1] Rcpp_1.0.10 pillar_1.9.0 compiler_4.2.2 tools_4.2.2 - [5] digest_0.6.30 jsonlite_1.8.3 evaluate_0.20 lifecycle_1.0.3 - [9] tibble_3.2.1 gtable_0.3.3 lattice_0.20-45 pkgconfig_2.0.3 - [13] rlang_1.1.0 Matrix_1.5-1 cli_3.4.1 rstudioapi_0.14 - [17] parallel_4.2.2 yaml_2.3.7 xfun_0.38 fastmap_1.1.0 - [21] terra_1.7-18 dplyr_1.1.1 knitr_1.42 generics_0.1.3 - [25] vctrs_0.6.1 grid_4.2.2 tidyselect_1.2.0 glue_1.6.2 - [29] data.table_1.14.6 R6_2.5.1 fansi_1.0.4 rmarkdown_2.21 - [33] ggplot2_3.4.1 magrittr_2.0.3 scales_1.2.1 codetools_0.2-18 - [37] htmltools_0.5.4 colorspace_2.1-0 utf8_1.2.3 munsell_0.5.0 - +R version 4.3.2 (2023-10-31) +Platform: aarch64-apple-darwin20 (64-bit) +Running under: macOS Sonoma 14.2.1 + +Matrix products: default +BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib +LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 + +locale: +[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 + +time zone: America/Mexico_City +tzcode source: internal + +attached base packages: +[1] stats graphics grDevices utils datasets methods +[7] base + +other attached packages: +[1] Giotto_4.0.2 GiottoClass_0.1.2 + +loaded via a namespace (and not attached): + [1] colorRamp2_0.1.0 DBI_1.2.0 + [3] bitops_1.0-7 biomaRt_2.58.0 + [5] rlang_1.1.2 magrittr_2.0.3 + [7] GiottoUtils_0.1.2 matrixStats_1.2.0 + [9] e1071_1.7-14 compiler_4.3.2 + [11] RSQLite_2.3.4 png_0.1-8 + [13] vctrs_0.6.5 stringr_1.5.1 + [15] pkgconfig_2.0.3 SpatialExperiment_1.12.0 + [17] crayon_1.5.2 fastmap_1.1.1 + [19] backports_1.4.1 dbplyr_2.4.0 + [21] magick_2.8.2 XVector_0.42.0 + [23] utf8_1.2.4 rmarkdown_2.25 + [25] purrr_1.0.2 bit_4.0.5 + [27] xfun_0.41 zlibbioc_1.48.0 + [29] cachem_1.0.8 GenomeInfoDb_1.38.5 + [31] progress_1.2.3 blob_1.2.4 + [33] rhdf5filters_1.14.1 gmp_0.7-3 + [35] DelayedArray_0.28.0 Rhdf5lib_1.24.1 + [37] terra_1.7-65 parallel_4.3.2 + [39] prettyunits_1.2.0 R6_2.5.1 + [41] stringi_1.8.3 ClusterR_1.3.2 + [43] GenomicRanges_1.54.1 Rcpp_1.0.11 + [45] assertthat_0.2.1 SummarizedExperiment_1.32.0 + [47] knitr_1.45 IRanges_2.36.0 + [49] Matrix_1.6-4 tidyselect_1.2.0 + [51] yaml_2.3.8 rstudioapi_0.15.0 + [53] abind_1.4-5 codetools_0.2-19 + [55] curl_5.2.0 lattice_0.21-9 + [57] tibble_3.2.1 Biobase_2.62.0 + [59] KEGGREST_1.42.0 evaluate_0.23 + [61] sf_1.0-15 units_0.8-5 + [63] proxy_0.4-27 BiocFileCache_2.10.1 + [65] xml2_1.3.6 Biostrings_2.70.1 + [67] pillar_1.9.0 filelock_1.0.3 + [69] MatrixGenerics_1.14.0 KernSmooth_2.23-22 + [71] checkmate_2.3.1 stats4_4.3.2 + [73] generics_0.1.3 RCurl_1.98-1.13 + [75] S4Vectors_0.40.2 hms_1.1.3 + [77] ggplot2_3.4.4 munsell_0.5.0 + [79] scales_1.3.0 class_7.3-22 + [81] glue_1.6.2 tools_4.3.2 + [83] GiottoVisuals_0.1.1 data.table_1.14.10 + [85] XML_3.99-0.16 cowplot_1.1.2 + [87] rhdf5_2.46.1 grid_4.3.2 + [89] AnnotationDbi_1.64.1 colorspace_2.1-0 + [91] SingleCellExperiment_1.24.0 GenomeInfoDbData_1.2.11 + [93] cli_3.6.2 rappdirs_0.3.3 + [95] fansi_1.0.6 S4Arrays_1.2.0 + [97] arrow_14.0.0.2 dplyr_1.1.4 + [99] gtable_0.3.4 digest_0.6.33 +[101] progressr_0.14.0 BiocGenerics_0.48.1 +[103] classInt_0.4-10 SparseArray_1.2.3 +[105] rjson_0.2.21 memoise_2.0.1 +[107] htmltools_0.5.7 lifecycle_1.0.4 +[109] httr_1.4.7 bit64_4.0.5 ``` diff --git a/vignettes/structure.Rmd b/vignettes/structure.Rmd index 7aee15f88..0757d9f9a 100644 --- a/vignettes/structure.Rmd +++ b/vignettes/structure.Rmd @@ -640,35 +640,92 @@ sessionInfo() ``` ```{r, eval=FALSE} - R version 4.2.1 (2022-06-23) - Platform: x86_64-apple-darwin17.0 (64-bit) - Running under: macOS Big Sur ... 10.16 - - Matrix products: default - BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib - LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib - - 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] stats graphics grDevices utils datasets methods base - - other attached packages: - [1] data.table_1.14.8 GiottoData_0.2.2 Giotto_3.3.1 - - loaded via a namespace (and not attached): - [1] Rcpp_1.0.11 pillar_1.9.0 compiler_4.2.1 tools_4.2.1 - [5] digest_0.6.31 jsonlite_1.8.4 evaluate_0.21 lifecycle_1.0.3 - [9] tibble_3.2.1 gtable_0.3.3 lattice_0.20-45 png_0.1-8 - [13] pkgconfig_2.0.3 rlang_1.1.1 igraph_1.4.2 Matrix_1.5-4 - [17] cli_3.6.1 rstudioapi_0.14 parallel_4.2.1 yaml_2.3.7 - [21] xfun_0.39 fastmap_1.1.1 terra_1.7-39 withr_2.5.0 - [25] dplyr_1.1.2 knitr_1.42 generics_0.1.3 vctrs_0.6.2 - [29] rprojroot_2.0.3 grid_4.2.1 tidyselect_1.2.0 here_1.0.1 - [33] reticulate_1.28 glue_1.6.2 R6_2.5.1 fansi_1.0.4 - [37] rmarkdown_2.21 ggplot2_3.4.2 magrittr_2.0.3 scales_1.2.1 - [41] codetools_0.2-18 htmltools_0.5.5 colorspace_2.1-0 utf8_1.2.3 - [45] munsell_0.5.0 - +R version 4.3.2 (2023-10-31) +Platform: aarch64-apple-darwin20 (64-bit) +Running under: macOS Sonoma 14.2.1 + +Matrix products: default +BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib +LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 + +locale: +[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 + +time zone: America/Mexico_City +tzcode source: internal + +attached base packages: +[1] stats graphics grDevices utils datasets methods +[7] base + +other attached packages: +[1] data.table_1.14.10 GiottoData_0.2.6.1 GiottoUtils_0.1.2 +[4] Giotto_4.0.2 GiottoClass_0.1.2 + +loaded via a namespace (and not attached): + [1] rstudioapi_0.15.0 jsonlite_1.8.8 + [3] magrittr_2.0.3 magick_2.8.2 + [5] rmarkdown_2.25 fs_1.6.3 + [7] zlibbioc_1.48.0 vctrs_0.6.5 + [9] memoise_2.0.1 RCurl_1.98-1.13 + [11] terra_1.7-65 usethis_2.2.2 + [13] htmltools_0.5.7 S4Arrays_1.2.0 + [15] progress_1.2.3 curl_5.2.0 + [17] Rhdf5lib_1.24.1 SparseArray_1.2.3 + [19] rhdf5_2.46.1 KernSmooth_2.23-22 + [21] htmlwidgets_1.6.4 cachem_1.0.8 + [23] igraph_1.6.0 mime_0.12 + [25] lifecycle_1.0.4 pkgconfig_2.0.3 + [27] Matrix_1.6-4 R6_2.5.1 + [29] fastmap_1.1.1 GenomeInfoDbData_1.2.11 + [31] MatrixGenerics_1.14.0 shiny_1.8.0 + [33] digest_0.6.33 colorspace_2.1-0 + [35] AnnotationDbi_1.64.1 S4Vectors_0.40.2 + [37] pkgload_1.3.3 GenomicRanges_1.54.1 + [39] RSQLite_2.3.4 filelock_1.0.3 + [41] progressr_0.14.0 fansi_1.0.6 + [43] httr_1.4.7 abind_1.4-5 + [45] compiler_4.3.2 proxy_0.4-27 + [47] remotes_2.4.2.1 bit64_4.0.5 + [49] withr_2.5.2 backports_1.4.1 + [51] DBI_1.2.0 pkgbuild_1.4.3 + [53] biomaRt_2.58.0 sessioninfo_1.2.2 + [55] rappdirs_0.3.3 DelayedArray_0.28.0 + [57] rjson_0.2.21 classInt_0.4-10 + [59] GiottoVisuals_0.1.1 tools_4.3.2 + [61] units_0.8-5 httpuv_1.6.13 + [63] glue_1.6.2 rhdf5filters_1.14.1 + [65] promises_1.2.1 grid_4.3.2 + [67] sf_1.0-15 checkmate_2.3.1 + [69] generics_0.1.3 gtable_0.3.4 + [71] class_7.3-22 hms_1.1.3 + [73] xml2_1.3.6 utf8_1.2.4 + [75] XVector_0.42.0 BiocGenerics_0.48.1 + [77] pillar_1.9.0 stringr_1.5.1 + [79] later_1.3.2 dplyr_1.1.4 + [81] BiocFileCache_2.10.1 lattice_0.21-9 + [83] gmp_0.7-3 bit_4.0.5 + [85] tidyselect_1.2.0 SingleCellExperiment_1.24.0 + [87] Biostrings_2.70.1 miniUI_0.1.1.1 + [89] knitr_1.45 IRanges_2.36.0 + [91] SummarizedExperiment_1.32.0 stats4_4.3.2 + [93] xfun_0.41 Biobase_2.62.0 + [95] devtools_2.4.5 matrixStats_1.2.0 + [97] stringi_1.8.3 yaml_2.3.8 + [99] evaluate_0.23 codetools_0.2-19 +[101] tibble_3.2.1 colorRamp2_0.1.0 +[103] cli_3.6.2 arrow_14.0.0.2 +[105] xtable_1.8-4 reticulate_1.34.0 +[107] munsell_0.5.0 Rcpp_1.0.11 +[109] GenomeInfoDb_1.38.5 dbplyr_2.4.0 +[111] png_0.1-8 XML_3.99-0.16 +[113] parallel_4.3.2 ellipsis_0.3.2 +[115] ggplot2_3.4.4 assertthat_0.2.1 +[117] blob_1.2.4 prettyunits_1.2.0 +[119] ClusterR_1.3.2 profvis_0.3.8 +[121] urlchecker_1.0.1 bitops_1.0-7 +[123] SpatialExperiment_1.12.0 scales_1.3.0 +[125] e1071_1.7-14 purrr_1.0.2 +[127] crayon_1.5.2 rlang_1.1.2 +[129] cowplot_1.1.2 KEGGREST_1.42.0 ```