Updated docker versions

smped · Apr 24, 2024 · e7a09e0 · e7a09e0
1 parent 477779f
commit e7a09e0
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Showing 3 changed files with 16 additions and 11 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -51,9 +51,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'next', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
-          - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3', bioc: '3.18'}
+          - { os: ubuntu-latest, r: '4.4', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
+          - { os: macOS-latest, r: '4.4', bioc: 'devel'}
+          - { os: windows-latest, r: '4.4', bioc: 'devel'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: extraChIPs
-Version: 1.7.8
+Version: 1.7.9
 Title: Additional functions for working with ChIP-Seq data
 Authors@R: person("Stevie", "Pederson", 
   email = "[email protected]", 

diff --git a/R/mergeByHMP.R b/R/mergeByHMP.R
@@ -163,22 +163,27 @@ setMethod(
         ## If keyval = "merged" (as opposed to "min")
         if (keyval == "merged") { ## Reform the keyvalue range by merging
             df$range <- as.character(x)
+            ## If a blank prefix has been passed ref_p & ref_hmp will be the same &
+            ## the subsequent left_join will add suffixes causing a failure
             df <- left_join(
-                df, ret_df[c("subjectHits", new_cols)], by = "subjectHits"
+                df, ret_df[c("subjectHits", new_cols)], by = "subjectHits",
+                suffix = c("_raw", "_hmp")
             )
+            if (ref_p == ref_hmp) {
+                ref_p <- paste0(ref_p, "_raw")
+                ref_hmp <- paste0(ref_hmp, "_hmp")
+            }
             df <- dplyr::filter(
                 df,
-                (
-                    !!sym(ref_p) <= !!sym(ref_hmp) |
-                     !!sym(ref_p) == min(!!sym(ref_p))
-                ),
+                (!!sym(ref_p) <= !!sym(ref_hmp) | !!sym(ref_p) == min(!!sym(ref_p))),
                 .by = !!sym("subjectHits")
             )
-            kv_gr <- colToRanges(df, "range")
-            kv_grl <- splitAsList(kv_gr, kv_gr$subjectHits)
+            kv_gr <- granges(colToRanges(df, "range"))
+            kv_grl <- splitAsList(kv_gr, df$subjectHits)
             kv_grl <- range(kv_grl)
             kv_gr <- unlist(kv_grl)
             mcols(kv_gr)[["subjectHits"]] <- as.integer(names(kv_gr))
+            names(kv_gr) <- NULL
             kv_df <- as_tibble(kv_gr, name = "keyval_range")
             inc_df <- inc_df[names(inc_df) != "keyval_range"]
             inc_df <- left_join(