Fix for purityX example (failing build in bioconductor)

.github/workflows/check-bioc.yml

@@ -52,9 +52,9 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - { os: ubuntu-latest, r: 'latest', bioc: '3.17', cont: "bioconductor/bioconductor_docker:latest", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
-          - { os: macOS-latest, r: 'latest', bioc: '3.17'}
-          - { os: windows-latest, r: 'latest', bioc: '3.17'}
+          - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          #- { os: macOS-latest, r: 'next', bioc: '3.19'}
+          - { os: windows-latest, r: 'next', bioc: '3.19'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -141,6 +141,9 @@ jobs:
           ## For installing usethis's dependency gert
           brew install libgit2
 
+          ## Required for tcltk
+          brew install xquartz --cask
+
           ## required for ncdf4
           ## brew install netcdf ## Does not work as it is compiled with gcc
           ## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
@@ -188,14 +191,26 @@ jobs:
           gha_repos <- if(
               .Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
           ) c(
-              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.17/bioc",
+              "AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.19/bioc",
               BiocManager::repositories()
               ) else BiocManager::repositories()
 
-          # install suggested packages
-          BiocManager::install(c("MSnbase", "xcms", "BiocStyle", "msPurityData", "CAMERA"))
+          # Workaround for problems with cached S4objects in binary packages
+          BiocManager::install("GenomeInfoDb", force = TRUE, type = "source")
+          BiocManager::install("BiocParallel", force = TRUE, type = "source")
+          BiocManager::install("S4Vectors", force = TRUE, type = "source")
+          BiocManager::install("SummarizedExperiment", force = TRUE, type = "source")
+          ## install xcms with dependencies - to ensure dependencies are installed from source;
+          ## somehow install_local installs binary packages instead.
+          BiocManager::install("mzR", force = TRUE)
+          BiocManager::install("MSnbase", force = TRUE, type = "source")
+          BiocManager::install("xcms", force = TRUE, type = "source", dependencies = TRUE)
+          BiocManager::install("msPurityData", force = TRUE, type = "source", dependencies = TRUE)
+          BiocManager::install("CAMERA", force = TRUE, type = "source", dependencies = TRUE)
+          BiocManager::install(c("BiocStyle"))
           install.packages(c("rmarkdown", "RPostgres", "RMySQL"))
 
+
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
           install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)

DESCRIPTION

@@ -2,8 +2,8 @@ Package: msPurity
 Type: Package
 Title: Automated Evaluation of Precursor Ion Purity for Mass Spectrometry Based
     Fragmentation in Metabolomics
-Version: 1.27.1
-Date: 2023-08-30
+Version: 1.31.1
+Date: 2024-05-09
 Authors@R: c(
     person(given = "Thomas N.", family = "Lawson",
         email = "[email protected]", role = c("aut", "cre"),
@@ -61,7 +61,7 @@ Suggests:
     RPostgres,
     RMySQL
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Roxygen: list(markdown = TRUE)
 biocViews: MassSpectrometry, Metabolomics, Software
 Collate: 

NEWS

@@ -1,3 +1,6 @@
+CHANGES IN VERSION 1.30.1 / 1.31.1
++ Update example for purityX causing build error
+
 CHANGES IN VERSION 1.27.1
 + createMSP fix - now uses the median precursor MZ and precursor RT in the MSP file
 

R/purityX-constructor.R

@@ -54,14 +54,12 @@
 #'
 #' @return a purityX object containing a dataframe of predicted purity scores
 #' @examples
-#' msPths <- list.files(system.file("extdata", "lcms", "mzML",
-#'                     package="msPurityData"), full.names = TRUE,
-#'                     pattern = "LCMS_")
-#' xset <- xcms::xcmsSet(msPths)
-#' xset <- xcms::group(xset)
-#' xset <- xcms::retcor(xset)
-#' xset <- xcms::group(xset)
-#' ppLCMS <- purityX(xset, cores = 1, xgroups = c(1, 2))
+#'
+#' msPths <- list.files(system.file("extdata", "lcms", "mzML", package="msPurityData"), full.names = TRUE, pattern = "LCMS_")
+#' xset <- readRDS(system.file("extdata", "tests", "xcms", "ms_only_xset_OLD.rds", package="msPurity"))
+#' xset@filepaths[1] <- msPths[basename(msPths)=="LCMS_1.mzML"]
+#' xset@filepaths[2] <- msPths[basename(msPths)=="LCMS_2.mzML"]
+#' px <- purityX(xset, singleFile = 1)
 #'
 #' @export
 purityX <- function(xset, purityType="purityFWHMmedian", offsets=c(0.5, 0.5),