Merge pull request #270 from uptake/release/v0.4.1

release: v0.4.1

.Rbuildignore

@@ -1,14 +1,17 @@
 # Files currently checked into the repo
 ^docs$
 ^_pkgdown\.yml$
+^pkgdown$
 ^cran-comments\.md$
-^CONDUCT\.md$
+^CODE_OF_CONDUCT\.md$
 ^LICENSE\.MD$
 ^.travis\.yml$
 ^appveyor\.yml$
 ^coverage.sh$
 ^CONTRIBUTING\.md$
 ^test\.sh$
+^CODEOWNERS
+^vignettes.*
 
 # History files
 ^\.Rhistory*

.gitignore

@@ -8,6 +8,7 @@ tests/testthat/Rplots.pdf
 **/*.rds
 **/*.rda
 **/*.csv
+**/*.RData
 
 # Keep data files in testdata
 !/tests/testthat/testdata/*.csv

CONTRIBUTING.md

@@ -339,3 +339,7 @@ Add some notes explaining what has changed since the previous release.
 Now that everything is done, the last thing you have to do is move the repo ahead of the version you just pushed to CRAN.
 
 Make a PR that adds a `.9000` on the end of the version you just released. This is a common practice in open source software development. It makes it obvious that the code in source control is newer than what's available from package managers, but doesn't interfere with the [semantic versioning](https://semver.org/) components of the package version.
+
+### Update pkgnet gallery
+
+Currently, the pkgnet gallery is maintained in a seperate repository, [pkgnet-gallery](https://github.com/uptake/pkgnet-gallery).  Follow the README in that repository to update.  If you do not, the gallery page may look out of sync from the other website pages. 

DESCRIPTION

@@ -1,18 +1,18 @@
 Package: pkgnet
 Type: Package
 Title: Get Network Representation of an R Package
-Version: 0.4.0.9999
+Version: 0.4.1
 Authors@R: c(
-    person("Brian", "Burns", email = "brian.burns@uptake.com", role = c("aut", "cre")),
+    person("Brian", "Burns", email = "brian.burns.opensource@gmail.com", role = c("aut", "cre")),
     person("James", "Lamb", email = "jaylamb20@gmail.com", role = c("aut")),
-    person("Patrick", "Boueri", email = "patrick.boueri@uptake.com", role = c("ctb")),
     person("Jay", "Qi", email = "jayqi.opensource@gmail.com", role = c("aut"))
     )
-Maintainer: Brian Burns <brian.burns@uptake.com>
+Maintainer: Brian Burns <brian.burns.opensource@gmail.com>
 Description: Tools from the domain of graph theory can be used to quantify the complexity
              and vulnerability to failure of a software package. That is the guiding philosophy
              of this package. 'pkgnet' provides tools to analyze the dependencies between functions
-             in an R package and between its imported packages.
+             in an R package and between its imported packages.  See the pkgnet website for vignettes 
+             and other supplementary information.
 Imports:
     assertthat,
     covr,
@@ -31,11 +31,12 @@ Imports:
     visNetwork
 Suggests:
     devtools,
+    ggplot2,
     testthat,
+    webshot,
     withr
 License: BSD_3_clause + file LICENSE
 URL: https://github.com/uptake/pkgnet, https://uptake.github.io/pkgnet/
 BugReports: https://github.com/uptake/pkgnet/issues
 LazyData: TRUE
-RoxygenNote: 6.1.1
-VignetteBuilder: knitr
+RoxygenNote: 7.1.0

NEWS.md

@@ -1,9 +1,26 @@
 # pkgnet (dev)
 
+_No changes since latest release_
+
+# pkgnet 0.4.1
+
 ## NEW FEATURES
 
 * `CreatePackageReport()` now outputs an object of new class `PackageReport` (instead of a list of reporters). This object will let you interactively manipulate the included reporter objects to customize the report, and regenerate the report on demand. You can also instantiate and interact with a `PackageReport` object directly without `CreatePackageReport()`.
 
+## CHANGES
+* Rounding format within report tables improved.
+* Contact information updated throughout the package documentation.
+* Appveyor testing configured in order to test windows builds in CI process.
+* Package logos were created.  They are available within this repository at `./man/figures`.
+* Remove vignettes from CRAN hosted package.  They remain as articles on the website.
+
+## BUGFIXES
+* Error handling for erroneous colors within `AbstractGraphReporter$set_plot_node_color_scheme()`. ([#262](https://github.com/uptake/pkgnet/pull/262)
+* data.table osx install bug for Travis. ([#251](https://github.com/uptake/pkgnet/pull/251) Thanks @TylerGrantSmith
+* Single row data.table handling with R6 report code. ([#263](https://github.com/uptake/pkgnet/pull/263) Thanks @TylerGrantSmith
+* Jaccard similarity example in pkgnet-intro vignette. Thanks @marcpaterno
+
 # pkgnet 0.4.0
 
 ## NEW FEATURES

R/AbstractGraphReporter.R

@@ -1,6 +1,7 @@
 #' @title Network Reporters for Packages
 #' @name NetworkReporters
 #' @keywords internal
+#' @concept Reporters
 #' @description \pkg{pkgnet} defines several package reporter R6 classes that model
 #'     a particular network aspect of a package as a graph. These network
 #'     reporter classes are extended from \code{AbstractGraphReporter}, which

R/AbstractPackageReporter.R

@@ -1,6 +1,7 @@
 #' @title Package Reporters
 #' @name PackageReporters
 #' @keywords internal
+#' @concept Reporters
 #' @description pkgnet defines several package reporter R6 classes that analyze
 #'     some particular aspect of a package. These reporters share common
 #'     functionality and interfaces defined by a base reporter class

R/CreatePackageReport.R

@@ -1,5 +1,6 @@
 #' @title Package Report
 #' @name PackageReport
+#' @concept Reporters
 #' @description pkgnet compiles one or more package reporters into a package
 #'     report for a specified package. \code{PackageReport} is an R6 class that
 #'     holds all of those reporters and has a method \code{render_report()}
@@ -276,6 +277,7 @@ PackageReport <- R6::R6Class(
 
 #' @title pkgnet Analysis Report for an R package
 #' @name CreatePackageReport
+#' @concept Main Functions
 #' @description Create a standalone HTML report about a package and its networks.
 #' @param pkg_name (string) name of a package
 #' @param pkg_path (string) The path to the package repository. If given, coverage

R/CreatePackageVignette.R

@@ -1,5 +1,6 @@
 #' @title pkgnet Report as Vignette
 #' @name CreatePackageVignette
+#' @concept Main Functions
 #' @description Create pkgnet package report as an R Markdown vignette. This
 #'    vignette can be rendered into a standard HTML vignette with the
 #'    \code{\link[knitr:vignette_engines]{knitr::rmarkdown}} vignette engine

R/DefaultReporters.R

@@ -1,5 +1,6 @@
 #' @title Default Reporters
 #' @name DefaultReporters
+#' @concept Reporters
 #' @description Instantiates a list of default reporters to feed into
 #'    \code{\link{CreatePackageReport}}.
 #' @return list of instantiated reporter objects

R/DependencyReporter.R

@@ -2,6 +2,7 @@
 #' @name DependencyReporter
 #' @family Network Reporters
 #' @family Package Reporters
+#' @concept Reporters
 #' @description This reporter looks at the recursive network of its dependencies
 #'    on other packages. This allows a developer to understand how individual
 #'    dependencies might lead to a much larger set of dependencies, potentially
@@ -23,8 +24,6 @@
 #' # Seed it with a package
 #' reporter$set_package("ggplot2")
 #'
-#' # plot it up
-#' reporter$plot_network()
 #' }
 NULL
 

R/FunctionReporter.R

@@ -2,6 +2,7 @@
 #' @name FunctionReporter
 #' @family Network Reporters
 #' @family Package Reporters
+#' @concept Reporters
 #' @description This reporter looks at the network of interdependencies of its
 #'    defined functions. Measures of centrality from graph theory can indicate
 #'    which function is most important to a package. Combined with unit test

R/GraphClasses.R

@@ -1,5 +1,7 @@
 #' @title Graph Classes for Network Modeling
 #' @name GraphClasses
+#' @concept Graph Classes
+#' @keywords internal
 #' @description pkgnet uses R6 classes to define and encapsulate the graph
 #'     models for representing package networks. These classes implement
 #'     different types of graphs and functionality to calculate their respective
@@ -116,7 +118,6 @@
 #'         }
 #'     }
 #' }
-#' @keywords internal
 NULL
 
 ## Base class for Graphs
@@ -293,6 +294,7 @@ AbstractGraph <- R6::R6Class(
 
 #' @title Directed Graph Network Model
 #' @name DirectedGraph
+#' @concept Graph Classes
 #' @description R6 class defining a directed graph model for representing a
 #'    network, including methods to calculate various measures from graph
 #'    theory. The \link[igraph:igraph-package]{igraph} package is used as a
@@ -536,6 +538,7 @@ DirectedGraph <- R6::R6Class(
 
 #' @title Measures for Directed Graph Class
 #' @name DirectedGraphMeasures
+#' @concept Graph Classes
 #' @keywords internal
 #' @description Descriptions for all available node and graph measures for
 #'    networks modeled by \link{DirectedGraph}.

R/InheritanceReporter.R

@@ -2,6 +2,7 @@
 #' @name InheritanceReporter
 #' @family Network Reporters
 #' @family Package Reporters
+#' @concept Reporters
 #' @description This reporter takes a package and traces the class inheritance
 #'   structure. Currently the following object-oriented systems are supported:
 #'   \itemize{

R/SummaryReporter.R

@@ -1,6 +1,7 @@
 #' @title Package Summary Reporter
 #' @name SummaryReporter
 #' @family Package Reporters
+#' @concept Reporters
 #' @description This reporter provides a high-level overview of a package via
 #'    its package DESCRIPTION file.
 #' @section Class Constructor:

_pkgdown.yml

@@ -28,6 +28,12 @@ navbar:
      href: https://github.com/uptake/pkgnet
 
 reference:
-- title: All Functions
+- title: Main Functions
   contents:
-  - -matches("doc_shared") 
+  - has_concept("Main Functions")
+- title: Reporter Objects and Supporting Functions
+  contents:
+  - has_concept("Reporters")
+- title: Graph Classes
+  contents:
+  - has_concept("Graph Classes")

cran-comments.md

@@ -1,5 +1,46 @@
 # CRAN Submission History
 
+## v 0.4.1
+
+### Submission on March 29th, 2020
+This is a patch release that includes a number of bug fixes and minor backwards compatible changes.  Please see `NEWS.md` for details.
+
+Please note that the maintainer of this package has not changed, just his email address.  Specifically, "brian.burns@uptake.com" has changed to "brian.burns.opensource@gmail.com".  If you would like further verification of this change, please email Dennis Lee at dennis.lee@uptake.com.  Dennis is a member of the Open Source Software Committee at Uptake as well as legal counsel.  He can confirm this change. 
+
+As always, issues are tracked and source code is maintained at https://github.com/uptake/pkgnet.
+
+### CRAN Response on March 29th, 2020 
+
+In short, one warning building the vignettes on windows. 
+
+### Resubmission on April 1st, 2020
+
+This is a second submission for version 0.4.1 of pkgnet.  It corrects an error in vignettte build on CRAN windows r-devel server in the original submission. This build has passed both rocker/r-devel linux tests as well as those on https://win-builder.r-project.org/. 
+
+As always, issues are tracked and source code is maintained at https://github.com/uptake/pkgnet.  This is a patch release that includes a number of bug fixes and minor backwards compatible changes.  Please see `NEWS.md` for details.
+
+Please note that the maintainer of this package has not changed, just his email address.  Specifically, "brian.burns@uptake.com" has changed to "brian.burns.opensource@gmail.com".  If you would like further verification of this change, please email Dennis Lee at dennis.lee@uptake.com.  Dennis is a member of the Open Source Software Committee at Uptake as well as legal counsel.  He can confirm this change. 
+
+### CRAN Response/Discussion on April 1st, 2020
+
+CRAN robot: Does not pass tests
+
+Me: This one note is the maintainer email change I mentioned in the submission note.  This is fine.  Please upload. 
+
+CRAN person: But the problem is: "Package has a VignetteBuilder field but no prebuilt vignette index." Please fix and resubmit.
+
+Me: Is it possible to proceed with that as is?  I would like to use vignettes to build the website articles but not host them on CRAN (because issues).  It would be easier if I could keep the DESCRIPTION file the same for both processes. 
+
+CRAN person: No, if you have the field all our checks assume there is also a vignette.
+
+### Resubmission on April 2nd, 2020
+
+This is a third submission for version 0.4.1 of pkgnet.  It corrects the issue with the "VignetteBuilder" field in the DESCRIPTION file. 
+
+As always, issues are tracked and source code is maintained at https://github.com/uptake/pkgnet.  This is a patch release that includes a number of bug fixes and minor backwards compatible changes.  Please see `NEWS.md` for details.
+
+Please note that the maintainer of this package has not changed, just his email address.  Specifically, "brian.burns@uptake.com" has changed to "brian.burns.opensource@gmail.com".  If you would like further verification of this change, please email Dennis Lee at dennis.lee@uptake.com.  Dennis is a member of the Open Source Software Committee at Uptake as well as legal counsel.  He can confirm this change. 
+
 ## v 0.4.0
 
 ### Submission on April 1st, 2019
@@ -47,7 +88,7 @@ BUG FIXES
 
 ## v 0.3.1
 
-### CRAN Notiifcation on January 6th, 2019
+### CRAN Notification on January 6th, 2019
 >Dear maintainer,
 >
 >Please see the problems shown on the pkgnet check test results page. 
@@ -147,7 +188,7 @@ Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
 CRAN teams' auto-check service
 Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
 Check: CRAN incoming feasibility, Result: Note_to_CRAN_maintainers
-  Maintainer: 'Brian Burns <brian.burns@uptake.com>'
+  Maintainer: 'Brian Burns <brian.burns.opensource@gmail.com>'
 
 ---
 
@@ -190,4 +231,3 @@ during vignette build or package testing.
 * Need to use CRAN recognized LICENSE format
 * Need to single-quote `pkgnet` in `DESCRIPTION` file
 
-