[R-package] miscellaneous changes to comply with CRAN requirements (#3338)

* [R-package] update DESCRIPTION per CRAN comments

* newlines

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* more fixes

* update Rbuildignore

* more changes

* more changes per CRAN response

* add email

* run examples in CI

* add newest CRAN response

* add Solaris patch

* update patch

* another attempt at ifaddrs patch

* fix unnecessary comment

* update configure

* comments

* bump version

* tabs

* fix address alignment, required by cran (#3415)

* fix dataset binary file alignment

* many fixes

* fix warnings

* fix bug

* Update file_io.cpp

* Update file_io.cpp

* simplify code

* Apply suggestions from code review

* general

* remove unneeded alignment

* Update file_io.h

* int32 to byte8 alignment

* Apply suggestions from code review

* Apply suggestions from code review

* [R-package] add new copyright holder in DESCRIPTION (#3409)

* [R-package] add new copyright holder in DESCRIPTION

* fix role

* fixing conflicts

* [R-package] add new copyright holder in DESCRIPTION (#3409)

* [R-package] add new copyright holder in DESCRIPTION

* fix role

* trying to fix conflicts

* more fixes

* this will work

* update cran-comments

* simplify solaris, add more testing docs

* stuff

* remove rchck docs

* Apply suggestions from code review
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* remove extra use of cat()

* change solaris check

* update docs

* remove testing code

* fix warning about cleanup not having execute permissions

* fix cmake builds

* remove blank line
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: Guolin Ke <guolin.ke@outlook.com>

R-package/R/removed.R

@@ -2,6 +2,7 @@
 #' @name lgb.prepare
 #' @description removed functions
 #' @param ... catch-all to match old calls
+#' @return Nothing. This function always raises an exception
 #' @export
 lgb.prepare <- function(...) {
     stop("lgb.prepare() was removed in LightGBM 3.0.0. Please use lgb.convert_with_rules()")
@@ -11,6 +12,7 @@ lgb.prepare <- function(...) {
 #' @name lgb.prepare2
 #' @description removed functions
 #' @param ... catch-all to match old calls
+#' @return Nothing. This function always raises an exception
 #' @export
 lgb.prepare2 <- function(...) {
     stop("lgb.prepare2() was removed in LightGBM 3.0.0. Please use lgb.convert_with_rules()")
@@ -20,6 +22,7 @@ lgb.prepare2 <- function(...) {
 #' @name lgb.prepare_rules
 #' @description removed functions
 #' @param ... catch-all to match old calls
+#' @return Nothing. This function always raises an exception
 #' @export
 lgb.prepare_rules <- function(...) {
     stop("lgb.prepare_rules() was removed in LightGBM 3.0.0. Please use lgb.convert_with_rules()")
@@ -29,6 +32,7 @@ lgb.prepare_rules <- function(...) {
 #' @name lgb.prepare_rules2
 #' @description removed functions
 #' @param ... catch-all to match old calls
+#' @return Nothing. This function always raises an exception
 #' @export
 lgb.prepare_rules2 <- function(...) {
     stop("lgb.prepare_rules2() was removed in LightGBM 3.0.0. Please use lgb.convert_with_rules()")

R-package/R/saveRDS.lgb.Booster.R

@@ -18,7 +18,7 @@
 #' @return NULL invisibly.
 #'
 #' @examples
-#' \dontrun{
+#' \donttest{
 #' library(lightgbm)
 #' data(agaricus.train, package = "lightgbm")
 #' train <- agaricus.train

R-package/README.md

@@ -338,6 +338,97 @@ mv \
     lightgbm-${LGB_VERSION}-r40-windows.zip
 ```
 
+### Testing the CRAN Package
+
+`{lightgbm}` is tested automatically on every commit, across many combinations of operating system, R version, and compiler. This section describes how to test the package locally while you are developing.
+
+#### Windows, Mac, and Linux
+
+```shell
+sh build-cran-package.sh
+R CMD check --as-cran lightgbm_*.tar.gz
+```
+
+#### Solaris
+
+All packages uploaded to CRAN must pass `R CMD check` on Solaris 10. To test LightGBM on this operating system, you can use the free service [R Hub](https://builder.r-hub.io/), a free service generously provided by the R Consortium.
+
+```shell
+sh build-cran-package.sh
+```
+
+```r
+package_tarball <- paste0("lightgbm_", readLines("VERSION.txt")[1], ".tar.gz")
+rhub::check(
+    path = package_tarball
+    , email = "your_email_here"
+    , check_args = "--as-cran"
+    , platform = c(
+        "solaris-x86-patched"
+        , "solaris-x86-patched-ods"
+    )
+    , env_vars = c(
+        "R_COMPILE_AND_INSTALL_PACKAGES" = "always"
+    )
+)
+```
+
+#### UBSAN
+
+All packages uploaded to CRAN must pass a build using `gcc` instrumented with two sanitizers: the Address Sanitizer (ASAN) and the Undefined Behavior Sanitizer (UBSAN). For more background, see [this blog post](http://dirk.eddelbuettel.com/code/sanitizers.html).
+
+You can replicate these checks locally using Docker.
+
+```shell
+docker run \
+    -v $(pwd):/opt/LightGBM \
+    -it rhub/rocker-gcc-san \
+    /bin/bash
+
+cd /opt/LightGBM
+Rscript -e "install.packages(c('R6', 'data.table', 'jsonlite', 'testthat'), repos = 'https://cran.rstudio.com')"
+
+sh build-cran-package.sh
+
+Rdevel CMD install lightgbm_*.tar.gz
+cd R-package/tests
+Rscriptdevel testthat.R
+```
+
+#### Valgrind
+
+All packages uploaded to CRAN must be built and tested without raising any issues from `valgrind`. `valgrind` is a profiler that can catch serious issues like memory leaks and illegal writes. For more information, see [this blog post](https://reside-ic.github.io/blog/debugging-and-fixing-crans-additional-checks-errors/).
+
+You can replicate these checks locally using Docker. Note that instrumented versions of R built to use `valgrind` run much slower, and these tests may take as long as 20 minutes to run.
+
+```shell
+docker run \
+    -v $(pwd):/opt/LightGBM \
+    -it \
+        wch1/r-debug
+
+cd /opt/LightGBM
+RDscriptvalgrind -e "install.packages(c('R6', 'data.table', 'jsonlite', 'testthat'), repos = 'https://cran.rstudio.com')"
+
+sh build-cran-package.sh
+
+RDvalgrind CMD INSTALL \
+    --preclean \
+    --install-tests \
+        lightgbm_*.tar.gz
+
+cd R-package/tests
+
+RDvalgrind \
+    --no-readline \
+    --vanilla \
+    -d valgrind \
+        -f testthat.R \
+2>&1 \
+| tee out.log \
+| cat
+```
+
 External (Unofficial) Repositories
 ----------------------------------
 

R-package/cran-comments.md

 # CRAN Submission History
 
+## v3.0.0.2 - Submission 1 - (September 29, 2020)
+
+### CRAN response
+
+First response was a message talking about failing checks on 3.0.0.
+
+```text
+package lightgbm_3.0.0.2.tar.gz has been auto-processed.
+The auto-check found additional issues for the last version released on CRAN:
+gcc-UBSAN <link>
+valgrind <link>
+CRAN incoming checks do not test for these additional issues and you will need an appropriately instrumented build of R to reproduce these.
+Hence please reply-all and explain: Have these been fixed?
+
+Please correct before 2020-10-05 to safely retain your package on CRAN.
+
+There is still a valgrind error. This did not happen when tested on
+submission, but the tests did run until timeout at 4 hours. When you
+write illegally, corruption is common.
+
+Illegal writes are serious errors.
+```
+
+Then in later responses to email correspondence with CRAN, CRAN expressed frustration with the number of failed submission and banned this package from new submissions for a month.
+
+The content of that frustrated message was regrettable and it does not need to be preserved forever in this file.
+
+### Maintainer Notes
+
+The 3.0.0.x series is officially not making it to CRAN. We will wait until November, and try again.
+
+Detailed plan about what will be tried before November 2020 to increase the likelihood of success for that package: https://github.com/microsoft/LightGBM/pull/3338#issuecomment-702756840.
+
+## v3.0.0.1 - Submission 1 - (September 24, 2020)
+
+### CRAN response
+
+```text
+Thanks, we see:
+
+Still lots of alignment errors, such as
+
+lightgbm.Rcheck/tests/testthat.Rout:io/dataset_loader.cpp:340:59:
+runtime error: reference binding to misaligned address 0x7f51fefad81e for type 'const value_type', which requires 4 byte alignment
+lightgbm.Rcheck/tests/testthat.Rout:/usr/include/c++/10/bits/stl_vector.h:1198:21:
+runtime error: reference binding to misaligned address 0x7f51fefad81e for type 'const int', which requires 4 byte alignment lightgbm.Rcheck/tests/testthat.Rout:/usr/include/c++/10/bits/vector.tcc:449:28:runtime
+error: reference binding to misaligned address 0x7f51fefad81e for type 'const type', which requires 4 byte alignment
+lightgbm.Rcheck/tests/testthat.Rout:/usr/include/c++/10/bits/move.h:77:36:
+runtime error: reference binding to misaligned address 0x7f51fefad81e for type 'const int', which requires 4 byte alignment
+lightgbm.Rcheck/tests/testthat.Rout:/usr/include/c++/10/bits/alloc_traits.h:512:17:
+runtime error: reference binding to misaligned address 0x7f51fefad81e for type 'const type', which requires 4 byte alignment
+
+Please fix and resubmit.
+```
+
+### Maintainer Notes
+
+Ok, these are the notes from the UBSAN tests. Was able to reproduce them with https://github.com/microsoft/LightGBM/pull/3338#issuecomment-700399862, and they were fixed in https://github.com/microsoft/LightGBM/pull/3415.
+
+Struggling to replicate the valgrind result (running `R CMD check --use-valgrind` returns no issues), so trying submission again. Hoping that the fixes for mis-alignment fix the other errors too.
+
+## v3.0.0 - Submission 6 - (September 24, 2020)
+
+### CRAN response
+
+Failing pre-checks.
+
+### `R CMD check` results
+
+```text
+* checking CRAN incoming feasibility ... WARNING
+Maintainer: ‘Guolin Ke <guolin.ke@microsoft.com>’
+
+Insufficient package version (submitted: 3.0.0, existing: 3.0.0)
+
+Days since last update: 4
+```
+
+### Maintainer Notes
+
+Did not think the version needed to be incremented if submitting a package in response to CRAN saying "you are failing checks and will be kicked off if you don't fix it", but I guess you do!
+
+This can be fixed by just re-submitting but with the version changed from `3.0.0` to `3.0.0.1`.
+
+## v3.0.0 - Submission 5 - (September 11, 2020)
+
+### CRAN Response
+
+Accepted to CRAN!
+
+Please correct the problems below before 2020-10-05 to safely retain your package on CRAN:
+
+```text
+checking installed package size ... NOTE
+  installed size is 49.7Mb
+  sub-directories of 1Mb or more:
+    libs 49.1Mb
+
+"network/socket_wrapper.hpp", line 30: Error: Could not open include file<ifaddrs.h>.
+"network/socket_wrapper.hpp", line 216: Error: The type "ifaddrs" is incomplete.
+"network/socket_wrapper.hpp", line 217: Error: The type "ifaddrs" is incomplete.
+"network/socket_wrapper.hpp", line 220: Error: The type "ifaddrs" is incomplete.
+"network/socket_wrapper.hpp", line 222: Error: The type "ifaddrs" is incomplete.
+"network/socket_wrapper.hpp", line 214: Error: The function "getifaddrs" must have a prototype.
+"network/socket_wrapper.hpp", line 228: Error: The function "freeifaddrs" must have a prototype.
+"network/linkers_socket.cpp", line 76: Warning: A non-POD object of type "std::chrono::duration<double, std::ratio<1, 1000>>" passed as a variable argument to function "static LightGBM::Log::Info(const char*, ...)".
+7 Error(s) and 1 Warning(s) detected.
+*** Error code 2
+make: Fatal error: Command failed for target `network/linkers_socket.o'
+Current working directory /tmp/RtmpNfaavG/R.INSTALL40a84f70130a/lightgbm/src
+ERROR: compilation failed for package ‘lightgbm’
+* removing ‘/home/ripley/R/Lib32/lightgbm’
+```
+
+### Maintainer Notes
+
+Added a patch that `psutil` has used to fix missing `ifaddrs.h` on Solaris 10: https://github.com/microsoft/LightGBM/issues/629#issuecomment-665091451.
+
+## v3.0.0 - Submission 4 - (September 4, 2020)
+
+### CRAN Response
+
+> Thanks, if the running time is the only reason to wrap the examples in
+\donttest, please replace \donttest by \donttest (\donttest examples are
+not executed in the CRAN checks).
+
+> Please replace cat() by message() or warning() in your functions (except
+for print() and summary() functions). Messages and warnings can be
+suppressed if needed.
+
+> Missing Rd-tags:
+  lightgbm/man/dimnames.lgb.Dataset.Rd: \value
+  lightgbm/man/lgb.Dataset.construct.Rd: \value
+  lightgbm/man/lgb.prepare.Rd: \value
+  ...
+
+> Please add the tag and explain in detail the returned objects.
+
+### Maintainer Notes
+
+Responded to CRAN with the following:
+
+All examples have been wrapped with `\donttest` as requested. We have replied to Swetlana Herbrandt asking for clarification on the donttest news item in the R 4.0.2 changelog (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html).
+
+All uses of `cat()` have been replaced with `print()`. We chose `print()` over `message()` because it's important that they be written to stdout alongside all the other logs coming from the library's C++ code. `message()` and `warning()` write to stderr.
+
+All exported objects now have `\value{}` statements in their documentation files in `man/`.
+
+**We also replied directly to CRAN's feedback email**
+
+> Swetlana,
+
+> Thank you for your comments. I've just created a new submission that I believe addresses them.
+
+> Can you help us understand something? In your message you said "\donttest examples are
+not executed in the CRAN checks)", but in https://cran.r-project.org/doc/manuals/r-devel/NEWS.html  we see the following:
+
+> > "`R CMD check --as-cran` now runs \donttest examples (which are run by example()) instead of instructing the tester to do so. This can be temporarily circumvented during development by setting environment variable `_R_CHECK_DONTTEST_EXAMPLES_` to a false value."
+
+> Could you help us understand how both of those statements can be true?
+
+## v3.0.0 - Submission 3 - (August 29, 2020)
+
+### CRAN response
+
+* Please write references in the description of the DESCRIPTION file in
+the form
+  - authors (year) doi:...
+  - authors (year) arXiv:...
+  - authors (year, ISBN:...)
+* if those are not available: authors (year) https:... with no space after 'doi:', 'arXiv:', 'https:' and angle brackets for auto-linking.
+* (If you want to add a title as well please put it in quotes: "Title")
+
+* \donttest{} should only be used if the example really cannot be executed (e.g. because of missing additional software, missing API keys, ...) by the user. That's why wrapping examples in \donttest{} adds the comment ("# Not run:") as a warning for the user. Does not seem necessary. Please unwrap the examples if they are executable in < 5 sec, or replace
+\donttest{} with \donttest{}.
+
+* Please do not modify the global environment (e.g. by using <<-) in your
+functions. This is not allowed by the CRAN policies.
+
+* Please always add all authors, contributors and copyright holders in the Authors@R field with the appropriate roles. From CRAN policies you agreed to: "The ownership of copyright and intellectual property rights of all components of the package must be clear and unambiguous (including from the authors specification in the DESCRIPTION file). Where code is copied (or derived) from the work of others (including from R itself), care must be taken that any copyright/license statements are preserved and authorship is not misrepresented." e.g.: Microsoft Corporation, Dropbox Inc. Please explain in the submission comments what you did about this issue.
+
+Please fix and resubmit
+
+### Maintainer Notes
+
+Responded to CRAN with the following:
+
+The paper citation has been adjusted as requested. We were using 'glmnet' as a  guide on how to include the URL but maybe they are no longer in compliance with CRAN policies: https://github.com/cran/glmnet/blob/b1a4b50de01e0cd24343959d7cf86452bac17b26/DESCRIPTION
+
+All authors from the original LightGBM paper have been added to Authors@R as `"aut"`. We have also added Microsoft and DropBox, Inc. as `"cph"` (copyright holders). These roles were chosen based on the guidance in https://journal.r-project.org/archive/2012-1/RJournal_2012-1_Hornik~et~al.pdf.
+
+lightgbm's code does use `<<-`, but it does not modify the global environment. The uses of `<<-` in R/lgb.interprete.R and R/callback.R are in functions which are called in an environment created by the lightgbm functions that call them, and this operator is used to reach one level up into the calling function's environment.
+
+We chose to wrap our examples in `\donttest{}` because we found, through testing on https://builder.r-hub.io/ and in our own continuous integration environments, that their run time varies a lot between platforms, and we cannot guarantee that all examples will run in under 5 seconds. We intentionally chose `\donttest{}` over `\donttest{}` because this item in the R 4.0.0 changelog (https://cran.r-project.org/doc/manuals/r-devel/NEWS.html) seems to indicate that \donttest will be ignored by CRAN's automated checks:
+
+> "`R CMD check --as-cran` now runs \donttest examples (which are run by example()) instead of instructing the tester to do so. This can be temporarily circumvented during development by setting environment variable `_R_CHECK_DONTTEST_EXAMPLES_` to a false value."
+
+We run all examples with `R CMD check --as-cran --run-dontrun` in our continuous integration tests on every commit to the package, so we have high confidence that they are working correctly.
+
+## 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 <guolin.ke@microsoft.com>'
+
+    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 <guolin.ke@microsoft.com>'
+
+    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 response
+
+> 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 <guolin.ke@microsoft.com>’
+
+    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 <guolin.ke@microsoft.com>'
+
+    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

R-package/man/dim.Rd

@@ -22,7 +22,7 @@ Note: since \code{nrow} and \code{ncol} internally use \code{dim}, they can also
 be directly used with an \code{lgb.Dataset} object.
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/dimnames.lgb.Dataset.Rd

@@ -15,6 +15,11 @@
 \item{value}{a list of two elements: the first one is ignored
 and the second one is column names}
 }
+\value{
+A list with the dimension names of the dataset
+
+A list with the dimension names of the dataset
+}
 \description{
 Only column names are supported for \code{lgb.Dataset}, thus setting of
              row names would have no effect and returned row names would be NULL.
@@ -24,7 +29,7 @@ Generic \code{dimnames} methods are used by \code{colnames}.
 Since row names are irrelevant, it is recommended to use \code{colnames} directly.
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/getinfo.Rd

@@ -17,6 +17,8 @@ getinfo(dataset, ...)
 \item{name}{the name of the information field to get (see details)}
 }
 \value{
+info data
+
 info data
 }
 \description{
@@ -33,7 +35,7 @@ The \code{name} field can be one of the following:
 }
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.Dataset.Rd

@@ -40,7 +40,7 @@ Construct \code{lgb.Dataset} object from dense matrix, sparse matrix
              or local file (that was created previously by saving an \code{lgb.Dataset}).
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.Dataset.construct.Rd

@@ -9,11 +9,14 @@ lgb.Dataset.construct(dataset)
 \arguments{
 \item{dataset}{Object of class \code{lgb.Dataset}}
 }
+\value{
+constructed dataset
+}
 \description{
 Construct Dataset explicitly
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.Dataset.create.valid.Rd

@@ -22,7 +22,7 @@ constructed dataset
 Construct validation data according to training data
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.Dataset.save.Rd

@@ -12,14 +12,14 @@ lgb.Dataset.save(dataset, fname)
 \item{fname}{object filename of output file}
 }
 \value{
-passed dataset
+the dataset you passed in
 }
 \description{
 Please note that \code{init_score} is not saved in binary file.
              If you need it, please set it again after loading Dataset.
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.Dataset.set.categorical.Rd

@@ -14,14 +14,14 @@ names or an integer vector with the indices of the features (e.g.
 \code{c(1L, 10L)} to say "the first and tenth columns").}
 }
 \value{
-passed dataset
+the dataset you passed in
 }
 \description{
 Set the categorical features of an \code{lgb.Dataset} object. Use this function
              to tell LightGBM which features should be treated as categorical.
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.Dataset.set.reference.Rd

@@ -12,13 +12,13 @@ lgb.Dataset.set.reference(dataset, reference)
 \item{reference}{object of class \code{lgb.Dataset}}
 }
 \value{
-passed dataset
+the dataset you passed in
 }
 \description{
 If you want to use validation data, you should set reference to training data
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package ="lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.convert_with_rules.Rd

@@ -34,7 +34,7 @@ Attempts to prepare a clean dataset to prepare to put in a \code{lgb.Dataset}.
              NOTE: In previous releases of LightGBM, this function was called \code{lgb.prepare_rules2}.
 }
 \examples{
-\dontrun{
+\donttest{
 data(iris)
 
 str(iris)

R-package/man/lgb.cv.Rd

@@ -149,7 +149,7 @@ Cross validation logic used by LightGBM
 }
 
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.dump.Rd

@@ -18,7 +18,7 @@ json format of model
 Dump LightGBM model to json
 }
 \examples{
-\dontrun{
+\donttest{
 library(lightgbm)
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train

R-package/man/lgb.get.eval.result.Rd

@@ -25,14 +25,14 @@ lgb.get.eval.result(
 \item{is_err}{TRUE will return evaluation error instead}
 }
 \value{
-vector of evaluation result
+numeric vector of evaluation result
 }
 \description{
 Given a \code{lgb.Booster}, return evaluation results for a
              particular metric on a particular dataset.
 }
 \examples{
-\dontrun{
+\donttest{
 # train a regression model
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train

R-package/man/lgb.importance.Rd

@@ -24,7 +24,7 @@ For a tree model, a \code{data.table} with the following columns:
 Creates a \code{data.table} of feature importances in a model.
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)

R-package/man/lgb.interprete.Rd

@@ -29,7 +29,7 @@ For regression, binary classification and lambdarank model, a \code{list} of \co
 Computes feature contribution components of rawscore prediction.
 }
 \examples{
-\dontrun{
+\donttest{
 Logit <- function(x) log(x / (1.0 - x))
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train

R-package/man/lgb.load.Rd

@@ -19,7 +19,7 @@ Load LightGBM takes in either a file path or model string.
               If both are provided, Load will default to loading from file
 }
 \examples{
-\dontrun{
+\donttest{
 data(agaricus.train, package = "lightgbm")
 train <- agaricus.train
 dtrain <- lgb.Dataset(train$data, label = train$label)