Preparation for release

XiaoyangSu · Sep 13, 2023 · d79e534 · d79e534
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diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# accucor 0.3.1
+
+* Minor fix to package documentation (@lparsons)
+
 # accucor 0.3.0
 
 * Added reference to package description

diff --git a/R/accucor_lib.R b/R/accucor_lib.R
@@ -642,7 +642,7 @@ nitrogen_isotope_correction <- function(formula,
 #' intensities of isotopically labeled mass spectrometry data. It was designed
 #' to work with input data from
 #' \href{https://elucidatainc.github.io/ElMaven/}{El-MAVEN} and
-#' \href{http://maven.princeton.edu}{MAVEN} software.
+#' \href{https://github.com/eugenemel/maven}{MAVEN} software.
 #'
 #' C13, H2, and N15 isotopes are supported. The isotopes are detected from the
 #' \code{isotopeLabel} column of the input file. The expected label text is

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,16 +1,10 @@
-## Test environments
-
-Testing via R CMD checks using GitHub Actions with following matrix:
-* os: windows-latest, r: 'release'
-* os: macOS-latest, r: 'release'
-* os: ubuntu-latest, r: 'release'
-* os: ubuntu-latest, r: 'devel', http-user-agent: 'release'
-* os: ubuntu-latest, r: 'oldrel-1'
-
 ## R CMD check results
 
-There were no ERRORs, WARNINGs, or NOTEs.
+0 errors | 0 warnings | 0 notes
+
+## revdepcheck results
 
-## Downstream dependencies
+We checked 1 reverse dependencies (0 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
-There are currently no downstream dependencies for this package.
+ * We saw 0 new problems
+ * We failed to check 0 packages
diff --git a/man/carbon_isotope_correction.Rd b/man/carbon_isotope_correction.Rd
diff --git a/man/deuterium_isotope_correction.Rd b/man/deuterium_isotope_correction.Rd
diff --git a/man/natural_abundance_correction.Rd b/man/natural_abundance_correction.Rd
diff --git a/man/nitrogen_isotope_correction.Rd b/man/nitrogen_isotope_correction.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,64 +1,65 @@
 # Platform
 
-|field    |value                                |
-|:--------|:------------------------------------|
-|version  |R version 4.1.2 (2021-11-01)         |
-|os       |Ubuntu 20.04.3 LTS                   |
-|system   |x86_64, linux-gnu                    |
-|ui       |RStudio                              |
-|language |(EN)                                 |
-|collate  |en_US.UTF-8                          |
-|ctype    |en_US.UTF-8                          |
-|tz       |America/New_York                     |
-|date     |2021-11-16                           |
-|rstudio  |2021.09.1+372 Ghost Orchid (desktop) |
-|pandoc   |2.5 @ /usr/bin/pandoc                |
+|field    |value                                      |
+|:--------|:------------------------------------------|
+|version  |R version 4.3.1 (2023-06-16)               |
+|os       |Ubuntu 22.04.3 LTS                         |
+|system   |x86_64, linux-gnu                          |
+|ui       |RStudio                                    |
+|language |(EN)                                       |
+|collate  |en_US.UTF-8                                |
+|ctype    |en_US.UTF-8                                |
+|tz       |America/New_York                           |
+|date     |2023-09-13                                 |
+|rstudio  |2023.06.2+561 Mountain Hydrangea (desktop) |
+|pandoc   |NA                                         |
 
 # Dependencies
 
 |package     |old    |new    |Δ  |
 |:-----------|:------|:------|:--|
-|accucor     |0.2.4  |0.3.0  |*  |
-|bit         |4.0.4  |4.0.4  |   |
-|bit64       |4.0.5  |4.0.5  |   |
-|cellranger  |1.1.0  |1.1.0  |   |
-|CHNOSZ      |1.4.1  |1.4.1  |   |
-|cli         |3.1.0  |3.1.0  |   |
-|clipr       |0.7.1  |0.7.1  |   |
-|cpp11       |0.4.1  |0.4.1  |   |
-|crayon      |1.4.2  |1.4.2  |   |
-|dplyr       |1.0.7  |1.0.7  |   |
-|ellipsis    |0.3.2  |0.3.2  |   |
-|fansi       |0.5.0  |0.5.0  |   |
-|generics    |0.1.1  |0.1.1  |   |
-|glue        |1.5.0  |1.5.0  |   |
-|gsubfn      |0.7    |NA     |*  |
-|hms         |1.1.1  |1.1.1  |   |
-|lifecycle   |1.0.1  |1.0.1  |   |
-|magrittr    |2.0.1  |2.0.1  |   |
-|nnls        |1.4    |1.4    |   |
-|pillar      |1.6.4  |1.6.4  |   |
-|pkgconfig   |2.0.3  |2.0.3  |   |
-|prettyunits |1.1.1  |1.1.1  |   |
-|progress    |1.2.2  |1.2.2  |   |
-|proto       |1.0.0  |NA     |*  |
-|purrr       |0.3.4  |0.3.4  |   |
-|R6          |2.5.1  |2.5.1  |   |
-|Rcpp        |1.0.7  |1.0.7  |   |
-|readr       |2.1.0  |2.1.0  |   |
-|readxl      |1.3.1  |1.3.1  |   |
-|rematch     |1.0.1  |1.0.1  |   |
-|rlang       |0.4.12 |0.4.12 |   |
-|stringi     |1.7.5  |1.7.5  |   |
-|stringr     |1.4.0  |1.4.0  |   |
-|tibble      |3.1.6  |3.1.6  |   |
-|tidyselect  |1.1.1  |1.1.1  |   |
-|tzdb        |0.2.0  |0.2.0  |   |
-|utf8        |1.2.2  |1.2.2  |   |
-|vctrs       |0.3.8  |0.3.8  |   |
-|vroom       |1.5.6  |1.5.6  |   |
-|withr       |2.4.2  |2.4.2  |   |
-|writexl     |1.4.0  |1.4.0  |   |
+|accucor     |0.3.0  |0.3.0  |NA |
+|bit         |4.0.5  |4.0.5  |NA |
+|bit64       |4.0.5  |4.0.5  |NA |
+|cellranger  |1.1.0  |1.1.0  |NA |
+|CHNOSZ      |2.0.0  |2.0.0  |NA |
+|cli         |3.6.1  |3.6.1  |NA |
+|clipr       |0.8.0  |0.8.0  |NA |
+|cpp11       |0.4.6  |0.4.6  |NA |
+|crayon      |1.5.2  |1.5.2  |NA |
+|dplyr       |1.1.3  |1.1.3  |NA |
+|fansi       |1.0.4  |1.0.4  |NA |
+|generics    |0.1.3  |0.1.3  |NA |
+|glue        |1.6.2  |1.6.2  |NA |
+|hms         |1.1.3  |1.1.3  |NA |
+|lifecycle   |1.0.3  |1.0.3  |NA |
+|magrittr    |2.0.3  |2.0.3  |NA |
+|nnls        |1.5    |1.5    |NA |
+|pillar      |1.9.0  |1.9.0  |NA |
+|pkgconfig   |2.0.3  |2.0.3  |NA |
+|prettyunits |1.1.1  |1.1.1  |NA |
+|progress    |1.2.2  |1.2.2  |NA |
+|R6          |2.5.1  |2.5.1  |NA |
+|readr       |2.1.4  |2.1.4  |NA |
+|readxl      |1.4.3  |1.4.3  |NA |
+|rematch     |2.0.0  |2.0.0  |NA |
+|rlang       |1.1.1  |1.1.1  |NA |
+|stringi     |1.7.12 |1.7.12 |NA |
+|stringr     |1.5.0  |1.5.0  |NA |
+|tibble      |3.2.1  |3.2.1  |NA |
+|tidyselect  |1.2.0  |1.2.0  |NA |
+|tzdb        |0.4.0  |0.4.0  |NA |
+|utf8        |1.2.3  |1.2.3  |NA |
+|vctrs       |0.6.3  |0.6.3  |NA |
+|vroom       |1.6.3  |1.6.3  |NA |
+|withr       |2.5.0  |2.5.0  |NA |
+|writexl     |1.4.2  |1.4.2  |NA |
 
 # Revdeps
 
+## Failed to check (1)
+
+|package |version |error |warning |note |
+|:-------|:-------|:-----|:-------|:----|
+|FAMetA  |?       |      |        |     |
+
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,6 +1,6 @@
 ## revdepcheck results
 
-We checked 0 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 1 reverse dependencies (0 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
  * We failed to check 0 packages

diff --git a/revdep/failures.md b/revdep/failures.md
@@ -1 +1,33 @@
-*Wow, no problems at all. :)*
+# FAMetA
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/XiaoyangSu/AccuCor
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+
+
+
+
+
+```
+### CRAN
+
+```
+
+
+
+
+
+
+```