Merge branch 'devel' into phili

.github/workflows/check-bioc.yml

@@ -54,8 +54,8 @@ jobs:
       matrix:
         config:
           - { 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: 'devel', bioc: '3.19'}
-          - { os: windows-latest, r: 'devel', bioc: '3.19'}
+          - { os: macOS-latest, r: 'next', bioc: '3.19'}
+          - { os: windows-latest, r: 'next', bioc: '3.19'}
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
@@ -160,12 +160,12 @@ jobs:
       - name: Install BiocManager
         run: |
           message(paste('****', Sys.time(), 'installing BiocManager ****'))
-          remotes::install_cran("BiocManager")
+          remotes::install_cran("BiocManager", type = "source")
         shell: Rscript {0}
 
       - name: Set BiocVersion
         run: |
-          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
+          BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, type = "source")
         shell: Rscript {0}
 
       - name: Install dependencies pass 1
@@ -177,45 +177,48 @@ jobs:
           ## https://github.com/r-lib/remotes/issues/296
           ## Ideally, all dependencies should get installed in the first pass.
 
+          ## 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("faahKO", type = "source")
+
           ## Pass #1 at installing dependencies
-          BiocManager::install(c("ncdf4", "mzR"))
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos =
-          BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, build_manual = FALSE, type = "source")
 
-          BiocManager::install(c("rmarkdown", "BiocStyle"))
+          BiocManager::install(c("rmarkdown", "BiocStyle"), type = "source")
         continue-on-error: true
         shell: Rscript {0}
 
       - name: Install dependencies pass 2
         run: |
           ## Pass #2 at installing dependencies
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, type = "source")
 
           ## Manually install packages that seem to be skipped.
           message(paste('****', Sys.time(), 'force installation of selected packages  ****'))
-          BiocManager::install(c("faahKO"))
-          BiocManager::install("ProtGenerics")
-          BiocManager::install("MSnbase")
-          BiocManager::install("mzR", type = "source", force = TRUE)
-          BiocManager::install("Spectra")
-          BiocManager::install("MsBackendMgf")
-          BiocManager::install("MetaboCoreUtils")
-          BiocManager::install("magick")
-          BiocManager::install("RforMassSpectrometry/MsExperiment")
+          BiocManager::install("RforMassSpectrometry/MsCoreUtils", force = TRUE)
+          BiocManager::install("magick", type = "source")
 
           ## For running the checks
           message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
-          remotes::install_cran("rcmdcheck")
-          BiocManager::install(c("BiocCheck", "DBI"))
+          remotes::install_cran("rcmdcheck", type = "source")
+          BiocManager::install("BiocCheck", type = "source")
         shell: Rscript {0}
 
       - name: Install BiocGenerics
         if:  env.has_RUnit == 'true'
         run: |
           ## Install BiocGenerics
-          BiocManager::install("BiocGenerics")
+          BiocManager::install("BiocGenerics", type = "source")
         shell: Rscript {0}
 
       - name: Install covr

DESCRIPTION

@@ -41,8 +41,8 @@ Authors@R: c(
 	   role = "ctb",
 	   comment = c(ORCID = "0000-0002-5492-6904")),
 	   person(given = "Carl", family = "Brunius",
-	   email = "[email protected]", 
-	   role = "ctb", 
+	   email = "[email protected]",
+	   role = "ctb",
 	   comment = c(ORCID = "0000-0003-3957-870X"))
 	   )
 Depends:
@@ -105,11 +105,11 @@ Collate:
     'MsExperiment-functions.R'
     'MsExperiment.R'
     'MzTabParam.R'
+    'XcmsExperiment.R'
     'PlainTextParam.R'
     'RDataParam.R'
     'XcmsExperiment-functions.R'
     'XcmsExperiment-plotting.R'
-    'XcmsExperiment.R'
     'c.R'
     'cwTools.R'
     'databases.R'

R/PlainTextParam.R

@@ -1,3 +1,5 @@
+#' @include XcmsExperiment.R
+
 #' @title Store contents of `MsExperiment` and `XcmsExperiment` objects as
 #' plain text files
 #'

R/methods-Params.R

@@ -1265,7 +1265,8 @@ setMethod("plot", signature(x = "LamaParama"),
                               zero_weight = x@zeroWeight,
                               bs = x@bs)
     datap <- x@rtMap[[index]]
-    plot(datap, type = "p", xlab = xlab, ylab = ylab, col = colPoints, ...)
+    plot(datap[, 2L], datap[, 1L], type = "p", xlab = xlab, ylab = ylab,
+         col = colPoints, ...)
     points(model, type = "l", col = colFit)
 })
 

tests/testthat.R

@@ -3,14 +3,10 @@ library(xcms)
 library(faahKO)
 library(MSnbase)
 library(msdata)
+library(BiocParallel)
+prm <- SerialParam()
 
-if (.Platform$OS.type == "unix") {
-    prm <- MulticoreParam(3)
-} else {
-    # prm <- SnowParam(3)
-    prm <- SerialParam()
-}
-register(bpstart(prm))
+register(SerialParam())
 
 ## Create some objects we can re-use in different tests:
 faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
@@ -19,7 +15,7 @@ faahko_3_files <- c(system.file('cdf/KO/ko15.CDF', package = "faahKO"),
 
 cwp <- CentWaveParam(noise = 10000, snthresh = 40, prefilter = c(3, 10000))
 faahko_od <- readMSData(faahko_3_files, mode = "onDisk")
-faahko_xod <- findChromPeaks(faahko_od, param = cwp)
+faahko_xod <- findChromPeaks(faahko_od, param = cwp, BPPARAM = SerialParam())
 od_x <- faahko_od
 mzr <- matrix(c(335, 335, 344, 344), ncol = 2, byrow = TRUE)
 od_chrs <- chromatogram(od_x, mz = mzr)
@@ -85,5 +81,3 @@ ref_mz_rt <- featureDefinitions(ref)[, c("mzmed","rtmed")]
 tst <- loadXcmsData("faahko_sub2")
 
 test_check("xcms")
-
-bpstop(prm)