Merge pull request #27 from jasenfinch/devel

v0.9.1
jasenfinch · Oct 20, 2021 · 5c19510 · 5c19510
2 parents 17f57d6 + 81fb720
commit 5c19510
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -25,8 +25,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
+          #- {os: windows-latest, r: 'release'}
+          #- {os: macOS-latest, r: 'release'}
           - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
           - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
@@ -65,7 +65,7 @@ jobs:
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-          sudo apt-get install -y libopenbabel-dev libnetcdf-dev libglpk-dev texlive-base
+          sudo apt-get install -y libopenbabel-dev libnetcdf-dev libglpk-dev texlive-base libsodium-dev
 
       - name: Install dependencies
         run: |

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,35 +1,37 @@
 Package: hrm
 Title: Install, Load and Update R Packages for High Resolution Metabolomics Analyses
-Version: 0.9.0
+Version: 0.9.1
 Authors@R: person("Jasen", "Finch", email = "[email protected]", role = c("aut", "cre"))
 Description: Easily install, load and update R packages for high resolution metabolomics analyses.
 URL: jasenfinch.github.io/hrm/
 BugReports: https://github.com/jasenfinch/hrm/issues
 Depends: R (>= 3.5.0)
-Imports: dplyr,
-        magrittr,
-        purrr,
-        stringr,
-        tibble,
-        BiocManager,
-        remotes,
+Imports: BiocManager,
         cli,
+        composition,
+        construction,
         crayon,
-        rstudioapi,
-        tidyverse,
+        dplyr,
+        grover,
+        magrittr,
         metaboData,
-        construction,
-        composition,
-        riches,
         metaboMisc,
-        metaboWorkflows
+        metaboWorkflows,
+        purrr,
+        remotes,
+        riches,
+        rstudioapi,
+        stringr,
+        tibble,
+        tidyverse
 License: GPL (>= 3)
 Encoding: UTF-8
 RoxygenNote: 7.1.2
 Suggests: testthat,
     covr
-Remotes: jasenfinch/construction,
-        jasenfinch/composition,
-        jasenfinch/riches,
+Remotes: jasenfinch/composition,
+        jasenfinch/construction,
+        jasenfinch/grover,
         jasenfinch/metaboMisc,
-        jasenfinch/metaboWorkflows
+        jasenfinch/metaboWorkflows,
+        jasenfinch/riches
diff --git a/NAMESPACE b/NAMESPACE
@@ -16,6 +16,7 @@ importFrom(crayon,col_nchar)
 importFrom(crayon,green)
 importFrom(crayon,white)
 importFrom(dplyr,bind_rows)
+importFrom(grover,readGrover)
 importFrom(magrittr,"%>%")
 importFrom(metaboData,availableDataSets)
 importFrom(metaboMisc,preTreatModes)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# hrm 0.9.1
+
+* Added the [`grover`](https://jasenfinch.github.io/grover) package.
+
 # hrm 0.9.0
 
 * Temporarily removed [`metaboReports`](https://github.com/jasenfinch/metaboReports) due to breaking changes in [`metaboWorkflows`](https://jasenfinch.github.io/metaboWorkflows/) v0.9.0.

diff --git a/R/hrm.R b/R/hrm.R
@@ -8,5 +8,6 @@ globalVariables('.')
 #' @importFrom metaboMisc preTreatModes
 #' @importFrom metaboWorkflows defineWorkflow
 #' @importFrom tidyverse tidyverse_packages
+#' @importFrom grover readGrover
 
 NULL
diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/README.Rmd b/README.Rmd
@@ -26,6 +26,7 @@ Easily install, load and update an R package ecosystem for performing analyses o
 `hrm` packages include:
 
 * [metaboData](https://aberHRML.github.io/metaboData) - Example data sets for metabolomics analyses
+* [grover](https://jasenfinch.github.io/grover) - Web API Framework for Mass Spectrometry Data Transfer
 * [binneR](https://aberHRML.github.io/binneR) - Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
 * [metabolyseR](https://jasenfinch.github.io/metabolyseR) - A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data
 * [profilePro](https://jasenfinch.github.io/profilePro) - Unified Input and Output for Processing of Metabolomic Profiling Experiments

diff --git a/README.md b/README.md
@@ -20,6 +20,8 @@ analyses of high resolution metabolomics data.
 
 -   [metaboData](https://aberHRML.github.io/metaboData) - Example data
     sets for metabolomics analyses
+-   [grover](https://jasenfinch.github.io/grover) - Web API Framework
+    for Mass Spectrometry Data Transfer
 -   [binneR](https://aberHRML.github.io/binneR) - Spectral Processing
     for High Resolution Flow Infusion Mass Spectrometry
 -   [metabolyseR](https://jasenfinch.github.io/metabolyseR) - A tool kit
@@ -61,14 +63,14 @@ Loading the `hrm` packages will load the included R packages.
 library(hrm)
 #> Warning in .recacheSubclasses(def@className, def, env): undefined subclass
 #> "numericVector" of class "Mnumeric"; definition not updated
-#> ── Attaching packages ───────────────────────────────────────────── hrm 0.9.0 ──
+#> ── Attaching packages ───────────────────────────────────────────── hrm 0.9.1 ──
 #> ✓ chunky           0.1.0   ✓ projecttemplates 0.5.1 
-#> ✓ metaboData       0.6.2   ✓ binneR           2.6.0 
-#> ✓ metabolyseR      0.14.3  ✓ profilePro       0.7.0 
-#> ✓ mzAnnotation     1.7.5   ✓ MFassign         0.7.10
-#> ✓ construction     0.2.10  ✓ composition      0.1.4 
-#> ✓ riches           0.2.1   ✓ metaboMisc       0.5.7 
-#> ✓ metaboWorkflows  0.9.0
+#> ✓ metaboData       0.6.2   ✓ grover           1.0.7 
+#> ✓ binneR           2.6.0   ✓ metabolyseR      0.14.3
+#> ✓ profilePro       0.7.0   ✓ mzAnnotation     1.7.5 
+#> ✓ MFassign         0.7.10  ✓ construction     0.2.10
+#> ✓ composition      0.1.4   ✓ riches           0.2.1 
+#> ✓ metaboMisc       0.5.7   ✓ metaboWorkflows  0.9.0
 #> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
 #> ✓ tibble  3.1.5     ✓ dplyr   1.0.7
 #> ✓ tidyr   1.1.4     ✓ stringr 1.4.0
@@ -99,10 +101,10 @@ A vector of the current `hrm` packages can be found by:
 
 ``` r
 hrmPackages()
-#>  [1] "chunky"           "projecttemplates" "metaboData"       "binneR"          
-#>  [5] "metabolyseR"      "profilePro"       "mzAnnotation"     "MFassign"        
-#>  [9] "construction"     "composition"      "riches"           "metaboMisc"      
-#> [13] "metaboWorkflows"
+#>  [1] "chunky"           "projecttemplates" "metaboData"       "grover"          
+#>  [5] "binneR"           "metabolyseR"      "profilePro"       "mzAnnotation"    
+#>  [9] "MFassign"         "construction"     "composition"      "riches"          
+#> [13] "metaboMisc"       "metaboWorkflows"
 ```
 
 `hrm` associated packages can be updated using:

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 2.11.4
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2021-10-07T12:44Z
+last_built: 2021-10-20T12:55Z
 urls:
   reference: https://jasenfinch.github.io/hrm//reference
   article: https://jasenfinch.github.io/hrm//articles

diff --git a/docs/reference/hrmAttach.html b/docs/reference/hrmAttach.html
diff --git a/docs/reference/hrmPackages.html b/docs/reference/hrmPackages.html
diff --git a/docs/reference/hrmUpdate.html b/docs/reference/hrmUpdate.html
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/tests/testthat/test-hrm.R b/tests/testthat/test-hrm.R
@@ -8,5 +8,5 @@ test_that('hrmAttach works',{
 })
 
 test_that('hrmPackages works',{
-    expect_length(hrmPackages(),13)
+    expect_length(hrmPackages(),14)
 })