works

Dockerfile

@@ -1,4 +1,4 @@
-FROM rocker/r-ver:4.3.3 AS build
+FROM rocker/r-ver:4.4.0 AS build
 WORKDIR /src/dseqr
 
 # install required debian packages to install R packages
@@ -12,7 +12,7 @@ RUN echo ".libPaths(c('$RENV_LIB', .libPaths()))" >> $(R RHOME)/etc/Rprofile.sit
 
 # install dseqr dependencies from renv.lock file
 RUN R -e "install.packages('remotes', repos = c(CRAN = 'https://cloud.r-project.org'))" && \
-    R -e "remotes::install_github('rstudio/[email protected].5')" && \
+    R -e "remotes::install_github('rstudio/[email protected].7')" && \
     R -e "renv::init(bare = TRUE, settings = list(use.cache = FALSE))"
 
 # initial lockfile: sync periodically
@@ -54,7 +54,7 @@ RUN Rscript get_sysdeps_run.R
 # ----------
 # COMMON
 #-----------
-FROM rocker/r-ver:4.3.3 AS common
+FROM rocker/r-ver:4.4.0 AS common
 WORKDIR /src/dseqr
 
 # add conda to path

R/import_scseq.R

@@ -850,7 +850,7 @@ load_tx2gene <- function(species, tx2gene_dir) {
   fname <- paste0(ensdb_species, '_tx2gene.qs')
   fpath <- file.path(tx2gene_dir,  fname)
 
-  if (file.exists(fpath)) {
+  if (file_exists(fpath)) {
     tx2gene <- qs::qread(fpath)
   } else {
     tx2gene <- dseqr.data::load_tx2gene(species, release = NULL, with_hgnc = TRUE)
@@ -947,7 +947,7 @@ load_cellranger_counts <- function(data_dir) {
   ensids <- gsub('^[^_]+[_]+(ENS.+?)$', '\\1', row.names(counts))
 
   enids <- gsub('[.]\\d+', '', ensids)
-  row.names(counts) <- make.unique(enids)
+  row.names(counts) <- make_unique(enids)
 
   return(counts)
 }
@@ -1542,7 +1542,7 @@ run_symphony <- function(counts, logcounts, ref_name, batch, species, tx2gene_di
   uwot_name <- paste0(ref_name, '_uwot_model')
   dl_dir <- Sys.getenv('DSEQR_DATA_PATH')
   uwot_path <- file.path(dl_dir, uwot_name)
-  if (!file.exists(uwot_path)) dseqr.data::dl_data(uwot_name)
+  if (!file_exists(uwot_path)) dseqr.data::dl_data(uwot_name)
 
   # indicate model path for mapQuery
   reference$save_uwot_path <- uwot_path

R/merge_utils.R

@@ -97,7 +97,7 @@ merge_clusters <- function(data_dir, merge_list, resoln_dir = NULL) {
   annot <- pretty.unique(annot)
 
   orig_path <- file.path(data_dir, paste0(resoln_dir, '_orig'))
-  if (!dir.exists(orig_path)) {
+  if (!dir_exists(orig_path)) {
     # store original resolution
     file.rename(resoln_path, orig_path)
     dir.create(resoln_path)

R/modules-bulk-server.R

@@ -148,7 +148,7 @@ bulkMDS <- function(input, output, session, explore_eset, dataset_name, numsv, b
     req(eset)
 
     mds_path <- isolate(mds_path())
-    if (file.exists(mds_path)) {
+    if (file_exists(mds_path)) {
       mds <- qs::qread(mds_path)
 
     } else {
@@ -567,7 +567,7 @@ bulkDataset <- function(input, output, session, sc_dir, bulk_dir, tx2gene_dir, p
   observeEvent(input$up_raw, {
     prev <- uploads_table()
     new <- input$up_raw
-    new <- new[file.exists(new$datapath), ]
+    new <- new[file_exists(new$datapath), ]
 
     is.eset <- grep('[.]qs$|[.]rds$', new$name)
 
@@ -651,7 +651,7 @@ bulkDataset <- function(input, output, session, sc_dir, bulk_dir, tx2gene_dir, p
     if (is_eset()) return(FALSE)
 
     fastqs <- up_df$datapath
-    fastqs <- fastqs[file.exists(fastqs)]
+    fastqs <- fastqs[file_exists(fastqs)]
 
     # auto-detect if paired
     fastq_id1s <- rkal::get_fastq_id1s(fastqs)
@@ -977,7 +977,7 @@ bulkDataset <- function(input, output, session, sc_dir, bulk_dir, tx2gene_dir, p
     svobj <- NULL
     svobj_path <- svobj_path()
 
-    if (file.exists(svobj_path)) {
+    if (file_exists(svobj_path)) {
       svobj <- qs::qread(svobj_path)
     }
 
@@ -996,7 +996,7 @@ bulkDataset <- function(input, output, session, sc_dir, bulk_dir, tx2gene_dir, p
     if (!is.null(svobj$n.sv)) maxsv <- svobj$n.sv
 
     numsv_path <- numsv_path()
-    if (file.exists(numsv_path)) numsv <- qs::qread(numsv_path)
+    if (file_exists(numsv_path)) numsv <- qs::qread(numsv_path)
     else qs::qsave(0, numsv_path)
 
     maxsv_r(maxsv)
@@ -1066,7 +1066,7 @@ bulkFormAnal <- function(input, output, session, project_dir, dataset_name, data
     prev_path <- file.path(dataset_dir(), 'pdata_explore_prev.qs')
     pdata_path <- file.path(dataset_dir(), 'pdata_explore.qs')
 
-    if (file.exists(prev_path)) {
+    if (file_exists(prev_path)) {
       prev <- qs::qread(prev_path)
       saved <- qs::qread(pdata_path)
       changed <- check_bulk_changed(prev, saved)
@@ -1349,7 +1349,7 @@ deconvForm <- function(input, output, session, show_deconv, new_dataset, sc_dir,
     # check if already have
     deconv_path <- deconv_path()
 
-    if (file.exists(deconv_path)) {
+    if (file_exists(deconv_path)) {
       new_deconv(deconv_path)
 
     } else {
@@ -1433,7 +1433,7 @@ deconv_bulk_dwls <- function(bulk_dataset_dir, scseq_dataset_dir, exclude_cluste
   # load markers
   resoln_dir <- load_resoln(scseq_dataset_dir)
   markers_path <- file.path(scseq_dataset_dir, resoln_dir, 'markers.qs')
-  have.markers <- file.exists(markers_path)
+  have.markers <- file_exists(markers_path)
 
   # need logs to get markers, counts for deconvolution
   scseq <- load_scseq_qs(scseq_dataset_dir, with_logs = !have.markers, with_counts = TRUE)
@@ -1634,7 +1634,7 @@ bulkExploreTable <- function(input, output, session, eset, up_annot, project_dir
     req(up)
 
 
-    if (file.exists(pdata_path)) {
+    if (file_exists(pdata_path)) {
       prev <- qs::qread(pdata_path)
       changed <- check_bulk_changed(prev, up)
 
@@ -1657,7 +1657,7 @@ bulkExploreTable <- function(input, output, session, eset, up_annot, project_dir
     req(pdata, pdata_path)
 
     # load pdata from previous if available
-    if (file.exists(pdata_path)) {
+    if (file_exists(pdata_path)) {
       pdata <- qs::qread(pdata_path)
 
       # TODO remove
@@ -1897,12 +1897,12 @@ bulkAnal <- function(input, output, session, pdata, dataset_name, eset, numsv, s
   })
 
   # do we have drug query results?
-  saved_drugs <- reactive(file.exists(drug_paths()$cmap))
+  saved_drugs <- reactive(file_exists(drug_paths()$cmap))
 
   # load lm_fit if saved or run limma
   lm_fit <- reactive({
 
-    if (file.exists(lmfit_path())) {
+    if (file_exists(lmfit_path())) {
       lm_fit <- qs::qread(lmfit_path())
 
     } else {
@@ -1986,7 +1986,7 @@ bulkAnal <- function(input, output, session, pdata, dataset_name, eset, numsv, s
     req(valid_contrast())
     goana_path <- goana_path()
 
-    if (file.exists(goana_path)) {
+    if (file_exists(goana_path)) {
       res <- qs::qread(goana_path)
 
     } else {

R/modules-bulk-utils.R

@@ -339,12 +339,12 @@ load_bulk_datasets <-function(data_dir, with.explore = FALSE) {
 
   dataset_names <- list.dirs(file.path(data_dir, 'bulk'), full.names = FALSE, recursive = FALSE)
 
-  has.eset <- file.exists(file.path(data_dir, 'bulk', dataset_names, 'eset.qs'))
+  has.eset <- file_exists(file.path(data_dir, 'bulk', dataset_names, 'eset.qs'))
   dataset_names <- dataset_names[has.eset]
 
   # for excluding datasets without a contrast
   if (with.explore) {
-    has.explore <- file.exists(file.path(data_dir, 'bulk', dataset_names, 'pdata_explore.qs'))
+    has.explore <- file_exists(file.path(data_dir, 'bulk', dataset_names, 'pdata_explore.qs'))
     dataset_names <- dataset_names[has.explore]
   }
 
@@ -798,7 +798,7 @@ add_vsd <- function(eset, vsd_path = NULL, rna_seq = TRUE) {
     # for microarray use exprs
     vsd <- Biobase::assayDataElement(eset, 'exprs')
 
-  } else if (!is.null(vsd_path) && file.exists(vsd_path)) {
+  } else if (!is.null(vsd_path) && file_exists(vsd_path)) {
     vsd <- qs::qread(vsd_path)
 
   } else {
@@ -812,7 +812,7 @@ add_vsd <- function(eset, vsd_path = NULL, rna_seq = TRUE) {
 
 add_adjusted <- function(eset, adj_path, svobj = list(sv = NULL), numsv = 0) {
 
-  if (file.exists(adj_path)) {
+  if (file_exists(adj_path)) {
     Biobase::assayDataElement(eset, 'adjusted') <- qs::qread(adj_path)
 
   } else {
@@ -826,7 +826,7 @@ add_adjusted <- function(eset, adj_path, svobj = list(sv = NULL), numsv = 0) {
 
 iqr_replicates <- function(eset, keep_path, annot = "SYMBOL", rm.dup = FALSE) {
 
-  if (file.exists(keep_path)) {
+  if (file_exists(keep_path)) {
     keep <- qs::qread(keep_path)
     eset <- eset[keep, ]
     Biobase::featureNames(eset) <- Biobase::fData(eset)[, annot]
@@ -1153,7 +1153,7 @@ handle_bulk_progress <- function(bgs, progs, new_dataset) {
 }
 
 file.move <- function(from, to) {
-  if (any(file.exists(to))) unlink(to)
+  if (any(file_exists(to))) unlink(to)
   tryCatch(
     file.rename(from, to),
     warning = function(w) {

R/modules-drugs-server.R

@@ -142,7 +142,7 @@ customQueryForm <- function(input, output, session, show_custom, is_custom, anal
   res_paths <- reactive({
     custom_name <- input$custom_name
     custom_dir <- file.path(project_dir(), 'custom_queries')
-    if (!dir.exists(custom_dir)) dir.create(custom_dir)
+    if (!dir_exists(custom_dir)) dir.create(custom_dir)
 
     res_paths <- get_drug_paths(custom_dir, custom_name)
     res_paths$query_genes <- file.path(custom_dir, 'drugs', paste0('query_genes_', custom_name, '.qs'))
@@ -691,7 +691,7 @@ selectedAnal <- function(input, output, session, project_dir, choices, new_custo
   numsv_path <- reactive(file.path(dataset_dir(), 'numsv.qs'))
   numsv <- reactive({
     numsv_path <- numsv_path()
-    if (!file.exists(numsv_path)) qs::qsave(0, numsv_path)
+    if (!file_exists(numsv_path)) qs::qsave(0, numsv_path)
     qs::qread(numsv_path)
   })
 
@@ -765,7 +765,7 @@ selectedAnal <- function(input, output, session, project_dir, choices, new_custo
     } else if (is_custom()) {
       custom_dir <- file.path(project_dir(), 'custom_queries')
       drug_paths <- get_drug_paths(custom_dir, sel_name)
-      drug_queries <- lapply(drug_paths, function(x) if (file.exists(x)) qs::qread(x))
+      drug_queries <- lapply(drug_paths, function(x) if (file_exists(x)) qs::qread(x))
 
     } else if (is_pert()) {
       drug_paths <- get_drug_paths(pert_query_dir, fs::path_sanitize(sel_name), ftype = '.rds')

R/modules-drugs-utils.R

@@ -187,10 +187,10 @@ load_custom_results <- function(res_paths, is_pert) {
     res_name <- names(res_paths)[i]
 
     # download requested pert result
-    if (!file.exists(res_path) && is_pert && !grepl('diff_expr_symbol_.+?.rds$', res_path))
+    if (!file_exists(res_path) && is_pert && !grepl('diff_expr_symbol_.+?.rds$', res_path))
       dl_pert_result(res_path)
 
-    if (file.exists(res_path))
+    if (file_exists(res_path))
       res[[res_name]] <- readRDS(res_path)
   }
   return(res)
@@ -211,7 +211,7 @@ load_custom_results <- function(res_paths, is_pert) {
 #'
 dl_pert_result <- function(res_path) {
   # name of the file being requested
-  if (file.exists(res_path)) return(NULL)
+  if (file_exists(res_path)) return(NULL)
   dl_url <- paste0('https://s3.us-east-2.amazonaws.com/dseqr/pert_query_dir/', basename(res_path))
   dl_url <- utils::URLencode(dl_url)
   dl_url <- gsub('+', '%2B', dl_url, fixed = TRUE)
@@ -229,7 +229,7 @@ load_custom_anals <- function(data_dir) {
   custom_dir <- file.path(data_dir, 'custom_queries', 'drugs')
 
   anals <- NULL
-  if (dir.exists(custom_dir)) {
+  if (dir_exists(custom_dir)) {
     custom_names <- list.files(custom_dir, pattern = '^cmap_res_.+?.qs')
     custom_names <- gsub('^cmap_res_(.+?).qs$', '\\1', custom_names)
 

R/modules-path-utils.R

@@ -10,13 +10,13 @@
 load_pert_signature <- function(pert, pert_type, pert_signature_dir, pvals = FALSE) {
   sig <- NULL
   type_dir <- file.path(pert_signature_dir, pert_type)
-  if (!file.exists(type_dir)) dir.create(type_dir)
+  if (!file_exists(type_dir)) dir.create(type_dir)
 
 
   fname <- paste0(pert, '.rds')
   sig_path <- file.path(type_dir, fs::path_sanitize(fname))
-  if (!file.exists(sig_path)) dl_pert_signature(sig_path, pert_type)
-  if (file.exists(sig_path)) sig <- readRDS(sig_path)
+  if (!file_exists(sig_path)) dl_pert_signature(sig_path, pert_type)
+  if (file_exists(sig_path)) sig <- readRDS(sig_path)
   return(sig)
 }
 
@@ -209,7 +209,7 @@ get_cluster_markers <- function(selected_clusters, dataset_dir) {
   fname <- paste0("markers_", clusters_name, '.qs')
   fpath <- file.path(dataset_dir, fname)
 
-  if (file.exists(fpath)) {
+  if (file_exists(fpath)) {
     cluster_markers <- qs::qread(fpath)
 
   }
@@ -293,12 +293,12 @@ get_genego <- function(species = 'Hs', gs_dir = NULL) {
   PathwayID <- GeneID <- SYMBOL <- NULL
 
   persist <- !is.null(gs_dir)
-  if (persist && !dir.exists(gs_dir)) dir.create(gs_dir)
+  if (persist && !dir_exists(gs_dir)) dir.create(gs_dir)
 
   fname <- paste('genego', species, 'qs', sep = '.')
   genego_path <- file.path(gs_dir, fname)
 
-  if (file.exists(genego_path)) {
+  if (file_exists(genego_path)) {
     genego <- qs::qread(genego_path)
 
   } else {
@@ -350,12 +350,12 @@ get_genego <- function(species = 'Hs', gs_dir = NULL) {
 #'
 get_gonames <- function(genego, gs_dir = NULL) {
   persist <- !is.null(gs_dir)
-  if (persist && !dir.exists(gs_dir)) dir.create(gs_dir)
+  if (persist && !dir_exists(gs_dir)) dir.create(gs_dir)
 
   fname <- paste('genego.names', 'qs', sep = '.')
   gonames_path <- file.path(gs_dir, fname)
 
-  if (file.exists(gonames_path)) {
+  if (file_exists(gonames_path)) {
     gonames <- qs::qread(gonames_path)
 
   } else {