[R-package] miscellaneous changes to comply with CRAN requirements

.ci/test_r_package.sh

@@ -7,6 +7,10 @@ mkdir -p $R_LIB_PATH
 export R_LIBS=$R_LIB_PATH
 export PATH="$R_LIB_PATH/R/bin:$PATH"
 
+# hack to get around this:
+# https://stat.ethz.ch/pipermail/r-package-devel/2020q3/005930.html
+export _R_CHECK_SYSTEM_CLOCK_=0
+
 # Get details needed for installing R components
 #
 # NOTES:

.ci/test_r_package_windows.ps1

@@ -74,6 +74,10 @@ $env:CTAN_MIRROR = "https://ctan.math.illinois.edu/systems/win32/miktex"
 $env:CTAN_MIKTEX_ARCHIVE = "$env:CTAN_MIRROR/setup/windows-x64/"
 $env:CTAN_PACKAGE_ARCHIVE = "$env:CTAN_MIRROR/tm/packages/"
 
+# hack to get around this:
+# https://stat.ethz.ch/pipermail/r-package-devel/2020q3/005930.html
+$env:_R_CHECK_SYSTEM_CLOCK_ = 0
+
 if (($env:COMPILER -eq "MINGW") -and ($env:R_BUILD_TYPE -eq "cmake")) {
   $env:CXX = "$env:RTOOLS_MINGW_BIN/g++.exe"
   $env:CC = "$env:RTOOLS_MINGW_BIN/gcc.exe"

R-package/DESCRIPTION

@@ -9,7 +9,10 @@ Authors@R: c(
     person("Yachen", "Yan", role = c("ctb")),
     person("James", "Lamb", email="[email protected]", role = c("aut"))
     )
-Description: Tree based algorithms can be improved by introducing boosting frameworks. 'LightGBM' is one such framework, and this package offers an R interface to work with it.
+Description: Tree based algorithms can be improved by introducing boosting frameworks. 
+    'LightGBM' is one such framework, based on Ke, Guolin et al. (2017).
+    See the paper "LightGBM: a highly efficient gradient boosting decision tree", linked below.
+    This package offers an R interface to work with it.
     It is designed to be distributed and efficient with the following advantages:
         1. Faster training speed and higher efficiency.
         2. Lower memory usage.
@@ -20,7 +23,9 @@ Description: Tree based algorithms can be improved by introducing boosting frame
     Comparison experiments on public datasets suggest that 'LightGBM' can outperform existing boosting frameworks on both efficiency and accuracy, with significantly lower memory consumption. In addition, parallel experiments suggest that in certain circumstances, 'LightGBM' can achieve a linear speed-up in training time by using multiple machines.
 Encoding: UTF-8
 License: MIT + file LICENSE
-URL: https://github.com/Microsoft/LightGBM
+URL:
+    https://github.com/Microsoft/LightGBM,
+    https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision
 BugReports: https://github.com/Microsoft/LightGBM/issues
 NeedsCompilation: yes
 Biarch: true

R-package/LICENSE

@@ -1,21 +1,2 @@
-The MIT License (MIT)
-
-Copyright (c) Microsoft Corporation
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+YEAR: 2016
+COPYRIGHT HOLDER: Microsoft Corporation

R-package/cran-comments.md

@@ -1,5 +1,108 @@
 # CRAN Submission History
 
+## v3.0.0 - Submission 2 - (August 28, 2020)
+
+### CRAN response
+
+Failing pre-checks.
+
+### `R CMD check` results
+
+* Debian: 2 NOTEs
+
+    ```text
+    * checking CRAN incoming feasibility ... NOTE
+    Maintainer: 'Guolin Ke <[email protected]>'
+
+    New submission
+
+    Possibly mis-spelled words in DESCRIPTION:
+      Guolin (13:52)
+      Ke (13:48)
+      LightGBM (14:20)
+      al (13:62)
+      et (13:59)
+
+    * checking top-level files ... NOTE
+    Non-standard files/directories found at top level:
+      'docs' 'lightgbm-hex-logo.png' 'lightgbm-hex-logo.svg'
+    ```
+
+* Windows: 2 NOTEs
+
+    ```text
+    * checking CRAN incoming feasibility ... NOTE
+    Maintainer: 'Guolin Ke <[email protected]>'
+
+    New submission
+
+    Possibly mis-spelled words in DESCRIPTION:
+      Guolin (13:52)
+      Ke (13:48)
+      LightGBM (14:20)
+      al (13:62)
+      et (13:59)
+
+    * checking top-level files ... NOTE
+    Non-standard files/directories found at top level:
+      'docs' 'lightgbm-hex-logo.png' 'lightgbm-hex-logo.svg'
+    ```
+
+### Maintainer Notes
+
+We should tell them the misspellings note is a false positive.
+
+For the note about included files, that is my fault. I had extra files laying around when I generated the package. I'm surprised to see `docs/` in that list, since it is ignored in  `.Rbuildignore`. I even tested that with [the exact code Rbuildignore uses](https://github.com/wch/r-source/blob/9d13622f41cfa0f36db2595bd6a5bf93e2010e21/src/library/tools/R/build.R#L85). For now, I added `rm -r  docs/` to `build-cran-package.sh`. We can figure out what is happening with `.Rbuildignore` in the future, but it shouldn't block a release.
+
+## v3.0.0 - Submission 1 - (August 24, 2020)
+
+NOTE: 3.0.0-1 was never released to CRAN. CRAN was on vacation August 14-24, 2020, and in that time version 3.0.0-1 (a release candidate) became 3.0.0.
+
+### CRAN respoonse
+
+> Please only ship the CRAN template for the MIT license.
+
+> Is there some reference about the method you can add in the Description field in the form Authors (year) doi:.....?
+
+> Please fix and resubmit.
+
+### `R CMD check` results
+
+* Debian: 1 NOTE
+
+    ```text
+    * checking CRAN incoming feasibility ... NOTE
+    Maintainer: ‘Guolin Ke <[email protected]>’
+
+    New submission
+
+    License components with restrictions and base license permitting such:
+      MIT + file LICENSE
+    ```
+
+* Windows: 1 NOTE
+
+    ```text
+    * checking CRAN incoming feasibility ... NOTE
+    Maintainer: 'Guolin Ke <[email protected]>'
+
+    New submission
+
+    License components with restrictions and base license permitting such:
+      MIT + file LICENSE
+    ```
+
+### Maintainer Notes
+
+Tried updating `LICENSE` file to this template:
+
+```yaml
+YEAR: 2016
+COPYRIGHT HOLDER: Microsoft Corporation
+```
+
+Added a citation and link for [the main paper](https://papers.nips.cc/paper/6907-lightgbm-a-highly-efficient-gradient-boosting-decision) in `DESCRIPTION`.
+
 ## v3.0.0-1 - Submission 3 - (August 12, 2020)
 
 ### CRAN response

build-cran-package.sh

@@ -33,6 +33,7 @@ cd ${TEMP_R_DIR}
     # Remove files not needed for CRAN
     echo "Removing files not needed for CRAN"
     rm src/install.libs.R
+    rm -r docs/
     rm -r src/cmake/
     rm -r inst/
     rm -r pkgdown/