Merge pull request #26 from jasenfinch/devel

v0.9.0

.Rbuildignore

@@ -6,3 +6,7 @@
 ^\.github$
 ^docs
 ^README\.Rmd$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^LICENSE\.md$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hrm
 Title: Install, Load and Update R Packages for High Resolution Metabolomics Analyses
-Version: 0.8.1
+Version: 0.9.0
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Easily install, load and update R packages for high resolution metabolomics analyses.
 URL: jasenfinch.github.io/hrm/
@@ -18,30 +18,18 @@ Imports: dplyr,
         rstudioapi,
         tidyverse,
         metaboData,
-        binneR,
-        metabolyseR,
-        profilePro,
-        mzAnnotation,
-        MFassign,
         construction,
         composition,
         riches,
         metaboMisc,
-        metaboWorkflows,
-        metaboReports
-License: GPL-3
+        metaboWorkflows
+License: GPL (>= 3)
 Encoding: UTF-8
 RoxygenNote: 7.1.2
 Suggests: testthat,
     covr
-Remotes: aberHRML/binneR,
-        jasenfinch/metabolyseR,
-        jasenfinch/profilePro,
-        jasenfinch/mzAnnotation,
-        jasenfinch/MFassign,
-        jasenfinch/construction,
+Remotes: jasenfinch/construction,
         jasenfinch/composition,
         jasenfinch/riches,
         jasenfinch/metaboMisc,
-        jasenfinch/metaboWorkflows,
-        jasenfinch/metaboReports
+        jasenfinch/metaboWorkflows

NAMESPACE

@@ -4,8 +4,6 @@ export(hrmAttach)
 export(hrmPackages)
 export(hrmUpdate)
 importFrom(BiocManager,install)
-importFrom(MFassign,assignmentParameters)
-importFrom(binneR,readFiles)
 importFrom(cli,rule)
 importFrom(cli,symbol)
 importFrom(composition,keggPathways)
@@ -21,11 +19,7 @@ importFrom(dplyr,bind_rows)
 importFrom(magrittr,"%>%")
 importFrom(metaboData,availableDataSets)
 importFrom(metaboMisc,preTreatModes)
-importFrom(metaboReports,report)
-importFrom(metaboWorkflows,workflowParameters)
-importFrom(metabolyseR,analysisData)
-importFrom(mzAnnotation,convert)
-importFrom(profilePro,profileParameters)
+importFrom(metaboWorkflows,defineWorkflow)
 importFrom(purrr,map_chr)
 importFrom(remotes,install_github)
 importFrom(riches,enrichmentParameters)

NEWS.md

@@ -1,3 +1,13 @@
+# 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.
+
+* Added dependency packages [`chunky`](https://jasenfinch.github.io/chunky/) and [`projecttemplates`](https://jasenfinch.github.io/projecttemplates/) of [`metaboWorkflows`](https://jasenfinch.github.io/metaboWorkflows) to ensure they can be updated using `hrm::hrmUpdate()`.
+
+* Reduced the number of package imports by removing those that are dependencies of other imported packages.
+
+* The loading of [`tidyverse`](https://www.tidyverse.org/) packages is now optional using the `tidyverse` argument in `hrm::hrmAttach()`.
+
 # hrm 0.8.1
 
 * Added a `NEWS.md` file to track changes to the package.

R/hrm.R

@@ -2,17 +2,11 @@ globalVariables('.')
 
 ## Suppress imports check notes
 #' @importFrom metaboData availableDataSets
-#' @importFrom binneR readFiles
-#' @importFrom metabolyseR analysisData
-#' @importFrom profilePro profileParameters
-#' @importFrom mzAnnotation convert
-#' @importFrom MFassign assignmentParameters
 #' @importFrom construction construction
 #' @importFrom composition keggPathways
 #' @importFrom riches enrichmentParameters
 #' @importFrom metaboMisc preTreatModes
-#' @importFrom metaboWorkflows workflowParameters
-#' @importFrom metaboReports report
+#' @importFrom metaboWorkflows defineWorkflow
 #' @importFrom tidyverse tidyverse_packages
 
 NULL

R/hrmAttach.R

@@ -1,5 +1,6 @@
 #' Load hrm packages
 #' @description Load hrm packages.
+#' @param tidyverse TRUE/FALSE also load the tidyverse package
 #' @importFrom stringr str_detect str_remove_all
 #' @importFrom purrr map_chr
 #' @importFrom magrittr %>%
@@ -8,7 +9,7 @@
 #' @importFrom utils packageVersion
 #' @export
 
-hrmAttach <- function(){
+hrmAttach <- function(tidyverse = TRUE){
   isAttached <- search() %>%
     .[str_detect(.,'package:')] %>%
     str_remove_all('package:')
@@ -43,16 +44,21 @@ hrmAttach <- function(){
     )
 
     if (length(packages_load) %% 2 == 1) {
-      packages_load <- append(packages_load, "")
+      packages_load <- append(packages_load, " ")
     }
 
-    col1 <- seq_len(length(p) / 2)
-    info <- paste0(packages_load[col1], "     ", packages_load[-col1])  %>%
+    column_odd <- seq(1,length(packages_load),2)
+    column_even <- seq(2,length(packages_load),2)
+
+    info <- paste0(packages_load[column_odd], "  ", packages_load[column_even]) %>% 
       paste0(collapse = '\n')
 
     message(info)
   }
-  do.call('library',list('tidyverse'))
+
+  if (isTRUE(tidyverse)){
+    do.call('library',list('tidyverse')) 
+  }
 
   invisible()
 }
@@ -74,4 +80,4 @@ text_colour <- function(x) {
 
   if (isTRUE(theme$dark)) white(x) else black(x)
 
-}
+}

README.Rmd

@@ -16,7 +16,7 @@ knitr::opts_chunk$set(
 # hrm
 
 <!-- badges: start -->
-[![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
+[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![R build status](https://github.com/jasenfinch/hrm/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/hrm/actions)
 [![Coverage Status](https://img.shields.io/codecov/c/github/jasenfinch/hrm/master.svg)](https://codecov.io/github/jasenfinch/hrm?branch=master)
 <!-- badges: end -->
@@ -25,19 +25,17 @@ Easily install, load and update an R package ecosystem for performing analyses o
 
 `hrm` packages include:
 
-* [metaboData](https://github.com/aberHRML/metaboData)
-* [binneR](https://github.com/aberHRML/binneR)
-* [metabolyseR](https://github.com/jasenfinch/metabolyseR)
-* [profilePro](https://github.com/jasenfinch/profilePro)
-* [mzAnnotation](https://github.com/jasenfinch/mzAnnotation)
-* [MFassign](https://github.com/jasenfinch/MFassign)
-* [construction](https://github.com/jasenfinch/construction)
-* [composition](https://github.com/jasenfinch/composition)
-* [riches](https://github.com/jasenfinch/riches)
-* [metaboMisc](https://github.com/jasenfinch/metaboMisc)
-* [metaboWorkflows](https://github.com/jasenfinch/metaboWorkflows)
-* [metaboReports](https://github.com/jasenfinch/metaboReports)
-
+* [metaboData](https://aberHRML.github.io/metaboData) - Example data sets for metabolomics analyses
+* [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
+* [mzAnnotation](https://jasenfinch.github.io/mzAnnotation) -  Tools for putative annotation of accurate m/z from electrospray ionisation mass spectrometry data
+* [MFassign](https://github.com/jasenfinch/MFassign) - Molecular formula assignment for high resolution ESI metabolomics
+* [construction](https://github.com/jasenfinch/construction) - Consensus structural classifications for putative molecular formula assignments
+* [composition](https://github.com/jasenfinch/composition) - Compositional analyses for metabolomics data
+* [riches](https://jasenfinch.github.io/riches) - Structural and functional enrichment for metabolomics data
+* [metaboMisc](https://jasenfinch.github.io/metaboMisc) - A collection of miscellaneous helper and linker functions for metabolomics analyses
+* [metaboWorkflows](https://jasenfinch.github.io/metaboWorkflows) - Workflow Project Templates for Metabolomics Analyses
 
 ## Installation
 

README.md

@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![Lifecycle:
-maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/#maturing)
+stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
 [![R build
 status](https://github.com/jasenfinch/hrm/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/hrm/actions)
 [![Coverage
@@ -18,18 +18,32 @@ analyses of high resolution metabolomics data.
 
 `hrm` packages include:
 
--   [metaboData](https://github.com/aberHRML/metaboData)
--   [binneR](https://github.com/aberHRML/binneR)
--   [metabolyseR](https://github.com/jasenfinch/metabolyseR)
--   [profilePro](https://github.com/jasenfinch/profilePro)
--   [mzAnnotation](https://github.com/jasenfinch/mzAnnotation)
--   [MFassign](https://github.com/jasenfinch/MFassign)
--   [construction](https://github.com/jasenfinch/construction)
--   [composition](https://github.com/jasenfinch/composition)
--   [riches](https://github.com/jasenfinch/riches)
--   [metaboMisc](https://github.com/jasenfinch/metaboMisc)
--   [metaboWorkflows](https://github.com/jasenfinch/metaboWorkflows)
--   [metaboReports](https://github.com/jasenfinch/metaboReports)
+-   [metaboData](https://aberHRML.github.io/metaboData) - Example data
+    sets for metabolomics analyses
+-   [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
+-   [mzAnnotation](https://jasenfinch.github.io/mzAnnotation) - Tools
+    for putative annotation of accurate m/z from electrospray ionisation
+    mass spectrometry data
+-   [MFassign](https://github.com/jasenfinch/MFassign) - Molecular
+    formula assignment for high resolution ESI metabolomics
+-   [construction](https://github.com/jasenfinch/construction) -
+    Consensus structural classifications for putative molecular formula
+    assignments
+-   [composition](https://github.com/jasenfinch/composition) -
+    Compositional analyses for metabolomics data
+-   [riches](https://jasenfinch.github.io/riches) - Structural and
+    functional enrichment for metabolomics data
+-   [metaboMisc](https://jasenfinch.github.io/metaboMisc) - A collection
+    of miscellaneous helper and linker functions for metabolomics
+    analyses
+-   [metaboWorkflows](https://jasenfinch.github.io/metaboWorkflows) -
+    Workflow Project Templates for Metabolomics Analyses
 
 ## Installation
 
@@ -47,24 +61,26 @@ 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 0.8.0 ──
-#> ✓ metaboData      0.6.2      ✓ construction    0.2.10
-#> ✓ binneR          2.5.3      ✓ composition     0.1.4 
-#> ✓ metabolyseR     0.14.2     ✓ riches          0.2.1 
-#> ✓ profilePro      0.7.0      ✓ metaboMisc      0.5.5 
-#> ✓ mzAnnotation    1.7.5      ✓ metaboWorkflows 0.8.10
-#> ✓ MFassign        0.7.10     ✓ metaboReports   0.8.6
+#> ── Attaching packages ───────────────────────────────────────────── hrm 0.9.0 ──
+#> ✓ 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
 #> ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──
-#> ✓ tibble  3.1.4     ✓ dplyr   1.0.7
-#> ✓ tidyr   1.1.3     ✓ stringr 1.4.0
-#> ✓ readr   2.0.1     ✓ forcats 0.5.1
+#> ✓ tibble  3.1.5     ✓ dplyr   1.0.7
+#> ✓ tidyr   1.1.4     ✓ stringr 1.4.0
+#> ✓ readr   2.0.2     ✓ forcats 0.5.1
 #> ✓ purrr   0.3.4
 #> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
 #> x dplyr::collect()    masks xcms::collect()
 #> x dplyr::combine()    masks MSnbase::combine(), Biobase::combine(), BiocGenerics::combine()
 #> x tidyr::expand()     masks S4Vectors::expand()
 #> x dplyr::filter()     masks stats::filter()
 #> x dplyr::first()      masks S4Vectors::first()
+#> x dplyr::glimpse()    masks tibble::glimpse(), metaboWorkflows::glimpse()
 #> x dplyr::groups()     masks xcms::groups()
 #> x dplyr::lag()        masks stats::lag()
 #> x ggplot2::Position() masks BiocGenerics::Position(), base::Position()
@@ -83,9 +99,10 @@ A vector of the current `hrm` packages can be found by:
 
 ``` r
 hrmPackages()
-#>  [1] "metaboData"      "binneR"          "metabolyseR"     "profilePro"     
-#>  [5] "mzAnnotation"    "MFassign"        "construction"    "composition"    
-#>  [9] "riches"          "metaboMisc"      "metaboWorkflows" "metaboReports"
+#>  [1] "chunky"           "projecttemplates" "metaboData"       "binneR"          
+#>  [5] "metabolyseR"      "profilePro"       "mzAnnotation"     "MFassign"        
+#>  [9] "construction"     "composition"      "riches"           "metaboMisc"      
+#> [13] "metaboWorkflows"
 ```
 
 `hrm` associated packages can be updated using:

_pkgdown.yml

@@ -0,0 +1 @@
+url: https://jasenfinch.github.io/hrm/