CRAN version 1.0.1

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.0
-Date: 2023-03-15 22:17:16 UTC
-SHA: 8d50a65715738db529e0dba756b6f5924f4453ec
+Version: 1.0.1
+Date: 2023-08-08 14:32:43 UTC
+SHA: 3ec72261a9c7e1b99b1ab8aedacd3fc94097e314

R/LCMSQA-package.R

@@ -35,7 +35,7 @@
 ##' - Set m/z and retention time of interest
 ##'   + compound (or m/z) with a ppm tolerance
 ##'   + retention time in second (min, max)
-##' - Peak picking using the centWave method (see [xcms::CentWaveParam])
+##' - Peak picking using the centWave method (see xcms::CentWaveParam)
 ##'   + ppm: the maximal tolerated m/z deviation in consecutive scans in ppm for
 ##'   the initial region of interest (ROI) definition
 ##'   + peak width: the expected approximate peak width in chromatographic space
@@ -51,7 +51,7 @@
 ##'   chromatographic peaks
 ##'   + integration: whether or not peak limits are found through descent on the
 ##'   Mexican Hat filtered data
-##' - Peak grouping using the peak density method (see [xcms::PeakDensityParam])
+##' - Peak grouping using the peak density method (see xcms::PeakDensityParam)
 ##'   + bandwidth: the bandwidth (standard deviation of the smoothing kernel) to
 ##'   be used
 ##'   + min fraction: the minimum fraction of samples in which the peaks has to

cran-comments.md

@@ -1,32 +1,14 @@
-## (Update) Reviewer's comments on the new submission
-
-* Please always write package names, software names and API (application
-  programming interface) names in single quotes in title and description. Note
-  that package names are case sensitive
-  - We checked case-sensitivity of package names and added single quotes
-
-* Please always explain all acronyms in the description text.
-  - We spelled out fully LC/MS in the text (liquid chromatography/mass spectrometry)
-
-* Please add small executable examples in your Rd-files
-  - Our reviewer confirmed that case examples not need for this package; we
-    included the package vignette to illustrate how to use the shiny app.
-
 ## Test environments
 
-* Ubuntu 22.04 LTS: R 4.2.2
-* GitHub Actions (Ubuntu-lastest): devel, release, oldrel-1
-* GitHub Actions (Windows-lastest): release
-* GitHub Actions (macOS-lastest): release
-* Win-builder: devel, release, oldrelease
+* Ubuntu 22.04 LTS: devel, release
+* macOS-lastest: release
+* Win-builder: devel, release
 
 ## R CMD check results
 
 0 errors | 0 warnings | 1 note
 
-* This is a new submission.
+* Packages suggested but not available for checking: 'xcms', 'MSnbase'
 
-* Possibly misspelled words in DESCRIPTION: BPC, LCMSQA, XIC, and chromatogram
-  - BPC, XIC, and chromatogram: technical terms in the field of metabolomics
-  - LCMSQA: the name of package
+xcms and MSnbase are BioC packages