Merge pull request #150 from bburns632/release/v0.3.0

Documentation for Release/v0.3.0

.Rbuildignore

@@ -50,6 +50,11 @@ vignettes/*\.pdf
 ^lib$
 ^coverage.html$
 
+# Readme files
+^readme_figures/.*
+^readme_figures
+
 # Stuff
 .Rbuildignore
 .*\.gitkeep
+

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pkgnet
 Type: Package
 Title: Get Network Representation of an R Package
-Version: 0.2.1.9000
+Version: 0.3.0
 Authors@R: c(
     person("Brian", "Burns", email = "brian.burns@uptake.com", role = c("aut", "cre")),
     person("James", "Lamb", email = "james.lamb@uptake.com", role = c("aut")),

NEWS.md

@@ -0,0 +1,22 @@
+# pkgnet 0.3.0
+
+## NEW FEATURES
+* `InheritanceReporter`, a reporter for R6, Reference, and S4 class inheritance relationships within a package. ([#14](https://github.com/UptakeOpenSource/pkgnet/issues/14), [#129](https://github.com/UptakeOpenSource/pkgnet/pull/129))
+* Dropdown menu in graph visualizations for selecting which node to highlight. ([#132](https://github.com/UptakeOpenSource/pkgnet/issues/132), [#143](https://github.com/UptakeOpenSource/pkgnet/pull/143))
+
+## CHANGES
+* Edge direction reversed to align with [UML dependency diagram](https://en.wikipedia.org/wiki/Dependency_(UML)) convention. Now, if A depends on B, then A->B. ([#131](https://github.com/UptakeOpenSource/pkgnet/issues/131), [#143](https://github.com/UptakeOpenSource/pkgnet/pull/143))
+* Reporters now support all layouts available in igraph. Use `grep("^layout_\\S", getNamespaceExports("igraph"), value = TRUE)` to see valid options. ([#143](https://github.com/UptakeOpenSource/pkgnet/pull/143))
+* `FunctionReporter` now utilizes graphopt layout by default. ([#143](https://github.com/UptakeOpenSource/pkgnet/pull/143))
+* `FunctionReporter` now supports non-exported functions and R6 class methods. ([#123](https://github.com/UptakeOpenSource/pkgnet/issues/123), [#128](https://github.com/UptakeOpenSource/pkgnet/pull/128))
+* Orphaned node clustering was removed in favor of using layout to better handle graphs with many orphaned nodes. ([#102](https://github.com/UptakeOpenSource/pkgnet/issues/102), [#143](https://github.com/UptakeOpenSource/pkgnet/pull/143))
+* Testing strategy with subpackages are now CRAN and TRAVIS compatible. ([#121](https://github.com/UptakeOpenSource/pkgnet/issues/121), [#139](https://github.com/UptakeOpenSource/pkgnet/pull/139), [#144](https://github.com/UptakeOpenSource/pkgnet/pull/144))
+* Test package `milne` created for unit testing of `InheritanceReporter` and R6 method support in `FunctionReporter`. ([#128](https://github.com/UptakeOpenSource/pkgnet/issues/128), [#129](https://github.com/UptakeOpenSource/pkgnet/pull/129))
+* Width of html reports now adjust to size of screen. ([#143](https://github.com/UptakeOpenSource/pkgnet/pull/143))
+* Default node colors are now colorblind accessible. ([#130](https://github.com/UptakeOpenSource/pkgnet/issues/130), [#141](https://github.com/UptakeOpenSource/pkgnet/pull/141))
+* Additional various improvements to UX for package reports. ([#143](https://github.com/UptakeOpenSource/pkgnet/pull/143))
+
+## BUG FIXES
+* Rendering of the table in Function Network tab. ([#136](https://github.com/UptakeOpenSource/pkgnet/issues/136), [#138](https://github.com/UptakeOpenSource/pkgnet/pull/138))
+
+<!--- Start of NEWS.md --->

R/testing_utils.R

@@ -31,6 +31,11 @@
     pkgnetSourcePath <- gsub('/pkgnet.Rcheck/tests_x64/testthat$', replacement = '/pkgnet.Rcheck/00_pkg_src/pkgnet', x = pkgnetSourcePath)
     pkgnetSourcePath <- gsub('/pkgnet.Rcheck/tests_x64$', replacement = '/pkgnet.Rcheck/00_pkg_src/pkgnet', x = pkgnetSourcePath)
 
+    # For R CMD check on some Linux machines that explicitly install i386 
+    pkgnetSourcePath <- gsub('/pkgnet.Rcheck/tests_i386/testthat$', replacement = '/pkgnet.Rcheck/00_pkg_src/pkgnet', x = pkgnetSourcePath)
+    pkgnetSourcePath <- gsub('/pkgnet.Rcheck/tests_i386$', replacement = '/pkgnet.Rcheck/00_pkg_src/pkgnet', x = pkgnetSourcePath)
+
+
     pkgnetSourcePath <- gsub('/pkgnet.Rcheck/vign_test/pkgnet$', replacement = '/pkgnet.Rcheck/00_pkg_src/pkgnet', x = pkgnetSourcePath)
     pkgnetSourcePath <- gsub('/pkgnet/vignettes$', replacement = '/pkgnet', x = pkgnetSourcePath)
     pkgnetSourcePath <- gsub('pkgnet/tests/testthat', replacement = 'pkgnet', x = pkgnetSourcePath)

_pkgdown.yml

@@ -12,6 +12,8 @@ navbar:
       href: reference/index.html
     - text: "Articles"
       href: articles/index.html
+    - text: "News"
+      href: news/index.html
 
   right:
    - icon: fa-github

cran-comments.md

@@ -1,30 +1,128 @@
 # CRAN Submission History
 
-## v 0.2.1 - Submission 3 - (November 1st, 2018)
+## v 0.3.0  
 
-This is a minor release to address a bug with the `report_path` parameter of `CreatePackageReport`.  Prior to this fix, reports would continue to be saved to a default location rather than the file path supplied by the user.  
+### Submission on December 19th, 2018
+> This is a major release with several improvements to 
+> R package diagnostics, report layout, and testing 
+> strategy.  New features and changes are now being 
+> tracked in NEWS.md.  
+>
+> This NEWS.md file and all 
+> source code is maintained at https://github.com/UptakeOpenSource/pkgnet.
+  
+### CRAN Response on December 20th, 2018 (Paraphrased)
 
-Other items in this release are typo corrections, some additional parameter checks, and more verbose error and info messages. 
+> Dear maintainer,
+>
+> package pkgnet_0.3.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests: Windows (2 ERRORs) & Debian (1 ERROR)
+>
+> ...
+>
+> Please fix all problems and resubmit a fixed version via the webform.
+>
+> ...
+>
+> Best regards,
+> CRAN teams' auto-check service
 
-## v 0.2.0 - Submission 2 - (April 30th, 2018)
+See [#154](https://github.com/UptakeOpenSource/pkgnet/pull/154) for the issue description and fix. 
+
+### Resubmission on December 20th, 2018
+> The attached package addresses issues found earlier today in the CRAN teams' auto-check service.  It has been checked (via R CMD check --as-cran) on both R-core and R-devel versions today. 
+>
+> This NEWS.md file and all source code is maintained at https://github.com/UptakeOpenSource/pkgnet.
+
+### CRAN response on December 21st (Paraphrased)
+>Dear maintainer,
+>
+>package pkgnet_0.3.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
+Windows: ...
+Status: 1 ERROR
+...
+Warning: invalid package 'd:/RCompile/CRANincoming/R-devel/pkgnet.Rcheck/tests_i386'
+...
+Best regards,
+CRAN teams' auto-check service
+Flavor: r-devel-linux-x86_64-debian-gcc, r-devel-windows-ix86+x86_64
+
+### Resubmission on January 2nd, 2019
+>Hello, 
+>
+>I hope you had a refreshing holiday break. 
+>
+>Apologies for the past issues with this build.  I believe we have remedied the functionality that did not pass i386 tests.  However, I cannot confirm this as the last submission alsopassed R CMD check on R-devel without issue.  Is there a separate docker container I can use to check i386 compatibility?   
+>
+>This submission passes R CMD check tests on r-devel with two warnings regarding URLs that fail within the container but have been confirmed valid and pass on R CMD check on R-core outside the container. 
+>
+>Here is the version info: 
+```
+> RD CMD check --as-cran pkgnet_0.3.0.tar.gz
+* using log directory ‘/RPackage/pkgnet.Rcheck’
+* using R Under development (unstable) (2018-12-21 r75875)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+...
+```
+>
+>The exact procedure I followed is outlined here: https://alexandereckert.com/post/testing-r-packages-with-latest-r-devel/
+>
+>All source code is maintained at https://github.com/UptakeOpenSource/pkgnet.
+>
+>Sincerely, 
+>
+>Brian Burns (current pkgnet maintainer)
+
+### Response on January 2nd, 2019
+
+>Dear maintainer,
+>
+>thanks, package pkgnet_0.3.0.tar.gz is on its way to CRAN.
+>
+>Best regards,
+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>'
+
+---
+
+## v 0.2.1
+
+### Submission on November 1st, 2018
+
+>This is a minor release to address a bug with the `report_path` parameter of `CreatePackageReport`.  Prior to this fix, reports would continue to be saved to a default location rather than the file path supplied by the user.  
+
+>Other items in this release are typo corrections, some additional parameter checks, and more verbose error and info messages. 
+
+---
+
+## v 0.2.0
+
+### Submission on April 30th, 2018
 * Resubmitted to CRAN without test folder or source vigette code.
 * This was to ensure nothing is written outside of the temp folder 
 during vignette build or package testing.  
 * Future versions will handle this issue more directly. 
 
-## v0.1.0 - Submission 1 - (April 11, 2018)
+----
+
+## v0.1.0
+
+### Submission on April 12, 2018
 
-### R CMD check results
+#### R CMD check results
+* No issues
+
+#### CRAN Response
+* accepted and available on CRAN
+
+### Submission on April 11, 2018
+
+#### R CMD check results
 * One NOTE about license file, will see what they say
 
-### CRAN Response
+#### CRAN Response
 * Need to use CRAN recognized LICENSE format
 * Need to single-quote `pkgnet` in `DESCRIPTION` file
 
-## v0.1.0 - Submission 2 - (April 12, 2018)
 
-### R CMD check results
-* No issues
-
-### CRAN Response
-* accepted and available on CRAN