Prepare for Bioconductor submission

rformassspectrometry · Aug 21, 2024 · f46bfe0 · f46bfe0
1 parent e5a319c
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Showing 4 changed files with 13 additions and 15 deletions.
diff --git a/.github/workflows/check-bioc.yml b/.github/workflows/check-bioc.yml
@@ -53,8 +53,8 @@ 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: '4.4', bioc: '3.19'}
- - { os: windows-latest, r: '4.4', bioc: '3.19'}
+ - { 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
@@ -1,6 +1,6 @@
 Package: SpectraQL
 Title: MassQL support for Spectra
-Version: 0.98.6
+Version: 0.99.0
 Description: The Mass Spec Query Language (MassQL) is a domain-specific
  language enabling to express a query and retrieve mass spectrometry (MS)
  data in a more natural and understandable way for MS users. It is inspired
@@ -21,7 +21,7 @@ Authors@R: c(person(given = "Johannes", family = "Rainer",
  comment = c(ORCID = "0000-0001-7406-4443"))
  )
 Depends:
- R (>= 4.1.0),
+ R (>= 4.4.0),
  ProtGenerics (>= 1.25.1)
 Imports:
  Spectra (>= 1.5.6),

diff --git a/R/AllGenerics.R b/R/AllGenerics.R
@@ -1,2 +1,2 @@
 setGeneric("query", function(x, ...)
-  standardGeneric("query"))
+ standardGeneric("query"))
diff --git a/vignettes/SpectraQL.Rmd b/vignettes/SpectraQL.Rmd
@@ -37,9 +37,6 @@ for MS data represented by `Spectra` objects defined in Bioconductor's
 
 # Installation
 
-Until added to Bioconductor, the package can be installed with
-`devtools::install_github("RforMassSpectrometry/SpectraQL")`.
-
 The package can be installed with the `BiocManager` package. To
 install `BiocManager` use `install.packages("BiocManager")` and, after that,
 `BiocManager::install("SpectraQL")` to install this package.
@@ -309,9 +306,10 @@ We can also combine that with `"QUERY"` to restrict to a certain retention time
 range to generate an extracted ion chromatogram (XIC).
 
 ```{r}
-ic <- query(dda,
- paste0("query scansum(ms1data) where rtmin = 235 and rtmax = 250",
- " filter ms1mz = 219.095:tolerancemz=0.1"))
+ic <- query(
+ dda,
+ paste0("query scansum(ms1data) where rtmin = 235 and rtmax = 250",
+ " filter ms1mz = 219.095:tolerancemz=0.1"))
 plot(ic, type = "l", xlab = "scan index")
 ```
 
@@ -320,10 +318,10 @@ following combination of function calls:
 
 ```{r}
 res <- dda |>
-filterMsLevel(1L) |>
-filterRt(c(235, 250)) |>
-filterMzValues(219.095, tolerance = 0.1) |>
-ionCount()
+ filterMsLevel(1L) |>
+ filterRt(c(235, 250)) |>
+ filterMzValues(219.095, tolerance = 0.1) |>
+ ionCount()
 
 plot(res, type = "l", xlab = "scan index")
 ```