1.5.2 Patch Release.

[trivialfis]

This will be a bug fix release after 1.5.1. Please comment if you think there are commits that should be backported.
@dmlc/xgboost-committer

• [R] Fix single sample prediction with SHAP. #7524
• Fix num_boosted_rounds for linear model. #7538
• Fix index type for bitfield. #7541
• [dask] Fix with asyncio. #7508
• Fix early stopping with linear model. #7554
• Update setup.py. #7360

[trivialfis]

Test results from rhub and win-builder

Rhub

R version 3.6.3 (2020-02-29) -- "Holding the Windsock" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

library(rhub)
cran_prep <- check_for_cran(path = "./xgboost", email = "jm.yuan@outlook.com")
─ Building package
─ Uploading package
─ Preparing build, see status at
https://builder.r-hub.io/status/xgboost_1.5.2.1.tar.gz-9112bc028d224e1da29ac136be3bbea9
https://builder.r-hub.io/status/xgboost_1.5.2.1.tar.gz-2e87775819f94b57aba93592a34045e8
https://builder.r-hub.io/status/xgboost_1.5.2.1.tar.gz-f8772900cb944214b9f10cf5685ff4d4
https://builder.r-hub.io/status/xgboost_1.5.2.1.tar.gz-af160c56f6f747cd91b449cdb14bba51
─ Build started
─ Creating new user
─ Downloading and unpacking package file
─ Querying package dependencies
─ Installing package dependencies
─ Running R CMD check
setting R_CHECK_FORCE_SUGGESTS to false
setting R_COMPILE_AND_INSTALL_PACKAGES to never
setting R_REMOTES_STANDALONE to true
setting R_REMOTES_NO_ERRORS_FROM_WARNINGS to true
setting R_CHECK_FORCE_SUGGESTS to true
setting R_CHECK_CRAN_INCOMING_USE_ASPELL to true
'getOption("repos")' replaces Bioconductor standard repositories, see
'?repositories' for details

replacement repositories:
CRAN: https://cloud.r-project.org

─ using log directory 'C:/Users/USERkrXzntUWGv/xgboost.Rcheck'
─ using R Under development (unstable) (2021-12-17 r81389 ucrt)
─ using platform: x86_64-w64-mingw32 (64-bit)
─ using session charset: UTF-8 (801ms)
─ using option '--as-cran'
✔ checking for file 'xgboost/DESCRIPTION'
─ checking extension type ... Package
─ this is package 'xgboost' version '1.5.2.1' (805ms)
N checking CRAN incoming feasibility (18.5s)
Maintainer: 'Tong He hetong007@gmail.com'

Found the following (possibly) invalid URLs:
URL: https://research.fb.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/ (moved to https://research.facebook.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/)
From: man/xgb.create.features.Rd
Status: 200
Message: OK
URL: https://stats.idre.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/ (moved to https://stats.oarc.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/)
From: inst/doc/discoverYourData.html
Status: 200
Message: OK

The Date field is over a month old.
✔ checking package namespace information
✔ checking package dependencies (800ms)
✔ checking if this is a source package
✔ checking if there is a namespace
✔ checking for executable files (2.4s)
✔ checking for hidden files and directories
✔ checking for portable file names
✔ checking serialization versions
✔ checking whether package 'xgboost' can be installed (2m 42.9s)
✔ checking installed package size
✔ checking package directory
✔ checking for future file timestamps (1.2s)
✔ checking 'build' directory
✔ checking DESCRIPTION meta-information
N checking top-level files
Non-standard file/directory found at top level:
'CMakeLists.txt'
✔ checking for left-over files
✔ checking index information
✔ checking package subdirectories (1.2s)
✔ checking R files for non-ASCII characters
✔ checking R files for syntax errors
✔ checking whether the package can be loaded (1.2s)
✔ checking whether the package can be loaded with stated dependencies (2.5s)
✔ checking whether the package can be unloaded cleanly (1.2s)
✔ checking whether the namespace can be loaded with stated dependencies (1.2s)
✔ checking whether the namespace can be unloaded cleanly (2.5s)
✔ checking loading without being on the library search path (1.3s)
✔ checking use of S3 registration (1.2s)
✔ checking dependencies in R code (3.8s)
✔ checking S3 generic/method consistency (1.4s)
✔ checking replacement functions (1.6s)
✔ checking foreign function calls (2.6s)
✔ checking R code for possible problems (16.7s)
✔ checking Rd files
✔ checking Rd metadata
✔ checking Rd line widths
✔ checking Rd cross-references (1.5s)
✔ checking for missing documentation entries (1.6s)
✔ checking for code/documentation mismatches (6.7s)
✔ checking Rd \usage sections (3.3s)
✔ checking Rd contents
✔ checking for unstated dependencies in examples (1.5s)
✔ checking contents of 'data' directory
✔ checking data for non-ASCII characters (2.7s)
✔ checking data for ASCII and uncompressed saves
✔ checking line endings in shell scripts
✔ checking line endings in C/C++/Fortran sources/headers
✔ checking line endings in Makefiles
✔ checking compilation flags in Makevars (1.5s)
N checking for GNU extensions in Makefiles
GNU make is a SystemRequirements.
✔ checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS)
✔ checking use of PKG_*FLAGS in Makefiles
✔ checking use of SHLIB_OPENMP_*FLAGS in Makefiles
✔ checking pragmas in C/C++ headers and code
✔ checking compilation flags used
✔ checking compiled code (48.2s)
N checking sizes of PDF files under 'inst/doc' (806ms)
Unable to find GhostScript executable to run checks on size reduction
✔ checking installed files from 'inst/doc'
✔ checking files in 'vignettes'
✔ checking examples (19.4s)
✔ checking for unstated dependencies in 'tests'
─ checking tests
✔ Running 'testthat.R' [76s] (1m 16.1s)
✔ checking for unstated dependencies in vignettes (1m 16.1s)
✔ checking package vignettes in 'inst/doc' (2s)
Build timed out (after 30 minutes). Marking the build as failed.
Build was aborted
Pinging https://builder.r-hub.io/build/FAILURE/xgboost_1.5.2.1.tar.gz-9112bc028d224e1da29ac136be3bbea9/2022-01-16T11:27:03Z
{"status":"ok"}
Finished: FAILURE

cran_prep

── xgboost 1.5.2.1: NOTE

Build ID: xgboost_1.5.2.1.tar.gz-9112bc028d224e1da29ac136be3bbea9
Platform: Windows Server 2022, R-devel, 64 bit
Submitted: 43m 27.9s ago
Build time: 43m 9.5s

❯ checking CRAN incoming feasibility ... NOTE
Maintainer: 'Tong He hetong007@gmail.com'

Found the following (possibly) invalid URLs:
URL: https://research.fb.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/ (moved to https://research.facebook.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/)
From: man/xgb.create.features.Rd
Status: 200
Message: OK
URL: https://stats.idre.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/ (moved to https://stats.oarc.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/)
From: inst/doc/discoverYourData.html
Status: 200
Message: OK

The Date field is over a month old.

❯ checking top-level files ... NOTE
Non-standard file/directory found at top level:
'CMakeLists.txt'

❯ checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.

❯ checking sizes of PDF files under 'inst/doc' ... NOTE
Unable to find GhostScript executable to run checks on size reduction

0 errors ✔ | 0 warnings ✔ | 4 notes ✖

── xgboost 1.5.2.1: NOTE

Build ID: xgboost_1.5.2.1.tar.gz-2e87775819f94b57aba93592a34045e8
Platform: Ubuntu Linux 20.04.1 LTS, R-release, GCC
Submitted: 43m 28s ago
Build time: 36m 32s

❯ checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Tong He hetong007@gmail.com’

Found the following (possibly) invalid URLs:
URL: https://research.fb.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/ (moved to https://research.facebook.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/)
From: man/xgb.create.features.Rd
Status: 200
Message: OK
URL: https://stats.idre.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/ (moved to https://stats.oarc.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/)
From: inst/doc/discoverYourData.html
Status: 200
Message: OK

The Date field is over a month old.

❯ checking installed package size ... NOTE
installed size is 64.7Mb
sub-directories of 1Mb or more:
libs 63.8Mb

❯ checking top-level files ... NOTE
Non-standard file/directory found at top level:
‘CMakeLists.txt’

❯ checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.

❯ checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
xgb.plot.shap 8.138 0.056 2.017

0 errors ✔ | 0 warnings ✔ | 5 notes ✖

── xgboost 1.5.2.1: WARNING

Build ID: xgboost_1.5.2.1.tar.gz-f8772900cb944214b9f10cf5685ff4d4
Platform: Fedora Linux, R-devel, clang, gfortran
Submitted: 43m 28s ago
Build time: 25m 23.3s

❯ checking re-building of vignette outputs ... WARNING
Error(s) in re-building vignettes:
--- re-building ‘discoverYourData.Rmd’ using rmarkdown
Loading required package: xgboost
Loading required package: Matrix
Loading required package: data.table
Loading required package: vcd
Loading required package: grid
Warning in chisq.test(df$Age, output_vector) :
Chi-squared approximation may be incorrect
Warning in chisq.test(df$AgeDiscret, output_vector) :
Chi-squared approximation may be incorrect
Warning in chisq.test(df$AgeCat, output_vector) :
Chi-squared approximation may be incorrect
--- finished re-building ‘discoverYourData.Rmd’

--- re-building ‘xgboostPresentation.Rmd’ using rmarkdown
--- finished re-building ‘xgboostPresentation.Rmd’

--- re-building ‘xgboostfromJSON.Rmd’ using rmarkdown
--- finished re-building ‘xgboostfromJSON.Rmd’

--- re-building ‘xgboost.Rnw’ using knitr
Loading required package: knitr
Error: processing vignette 'xgboost.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'xgboost.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

Type X to quit or to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *>

l.30 \makeatletter
^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘xgboost.Rnw’

SUMMARY: processing the following file failed:
‘xgboost.Rnw’

Error: Vignette re-building failed.
Execution halted

❯ checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Tong He hetong007@gmail.com’

Found the following (possibly) invalid URLs:
URL: https://research.fb.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/ (moved to https://research.facebook.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/)
From: man/xgb.create.features.Rd
Status: 200
Message: OK
URL: https://stats.idre.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/ (moved to https://stats.oarc.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/)
From: inst/doc/discoverYourData.html
Status: 200
Message: OK

The Date field is over a month old.

❯ checking installed package size ... NOTE
installed size is 38.7Mb
sub-directories of 1Mb or more:
libs 37.8Mb

❯ checking top-level files ... NOTE
Non-standard file/directory found at top level:
‘CMakeLists.txt’

❯ checking for GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.

❯ checking examples ... NOTE
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
xgb.plot.shap 7.807 0.220 2.171
xgb.plot.deepness 6.141 0.137 2.182

0 errors ✔ | 1 warning ✖ | 5 notes ✖

── xgboost 1.5.2.1: IN-PROGRESS

Build ID: xgboost_1.5.2.1.tar.gz-af160c56f6f747cd91b449cdb14bba51
Platform: Debian Linux, R-devel, GCC ASAN/UBSAN
Submitted: 43m 28s ago

win-builder

* using log directory 'd:/RCompile/CRANguest/R-release/xgboost.Rcheck' * using R version 4.1.2 (2021-11-01) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * checking for file 'xgboost/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'xgboost' version '1.5.2.1' * checking CRAN incoming feasibility ... NOTE Maintainer: 'Jiaming Yuan '

New maintainer:
Jiaming Yuan jm.yuan@outlook.com
Old maintainer(s):
Tong He hetong007@gmail.com

Found the following (possibly) invalid URLs:
URL: https://research.fb.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/ (moved to https://research.facebook.com/publications/practical-lessons-from-predicting-clicks-on-ads-at-facebook/)
From: man/xgb.create.features.Rd
Status: 200
Message: OK
URL: https://stats.idre.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/ (moved to https://stats.oarc.ucla.edu/r/library/r-library-contrast-coding-systems-for-categorical-variables/)
From: inst/doc/discoverYourData.html
Status: 200
Message: OK

The Date field is over a month old.

• checking package namespace information ... OK

• checking package dependencies ... OK

• checking if this is a source package ... OK

• checking if there is a namespace ... OK

• checking for hidden files and directories ... OK

• checking for portable file names ... OK

• checking serialization versions ... OK

• checking whether package 'xgboost' can be installed ... OK

• checking installed package size ... OK

• checking package directory ... OK

• checking for future file timestamps ... OK

• checking 'build' directory ... OK

• checking DESCRIPTION meta-information ... NOTE
  Maintainer field differs from that derived from Authors@R
  Maintainer: 'Jiaming Yuan jm.yuan@outlook.com'
  Authors@R: 'Tong He hetong007@gmail.com'

• checking top-level files ... NOTE
  Non-standard file/directory found at top level:
  'CMakeLists.txt'

• checking for left-over files ... OK

• checking index information ... OK

• checking package subdirectories ... OK

• checking R files for non-ASCII characters ... OK

• checking R files for syntax errors ... OK

• loading checks for arch 'i386'
  ** checking whether the package can be loaded ... OK
  ** checking whether the package can be loaded with stated dependencies ... OK
  ** checking whether the package can be unloaded cleanly ... OK
  ** checking whether the namespace can be loaded with stated dependencies ... OK
  ** checking whether the namespace can be unloaded cleanly ... OK
  ** checking loading without being on the library search path ... OK
  ** checking use of S3 registration ... OK

• loading checks for arch 'x64'
  ** checking whether the package can be loaded ... OK
  ** checking whether the package can be loaded with stated dependencies ... OK
  ** checking whether the package can be unloaded cleanly ... OK
  ** checking whether the namespace can be loaded with stated dependencies ... OK
  ** checking whether the namespace can be unloaded cleanly ... OK
  ** checking loading without being on the library search path ... OK
  ** checking use of S3 registration ... OK

• checking dependencies in R code ... OK

• checking S3 generic/method consistency ... OK

• checking replacement functions ... OK

• checking foreign function calls ... OK

• checking R code for possible problems ... [11s] OK

• checking Rd files ... [1s] OK

• checking Rd metadata ... OK

• checking Rd line widths ... OK

• checking Rd cross-references ... OK

• checking for missing documentation entries ... OK

• checking for code/documentation mismatches ... OK

• checking Rd \usage sections ... OK

• checking Rd contents ... OK

• checking for unstated dependencies in examples ... OK

• checking contents of 'data' directory ... OK

• checking data for non-ASCII characters ... OK

• checking data for ASCII and uncompressed saves ... OK

• checking line endings in shell scripts ... OK

• checking line endings in C/C++/Fortran sources/headers ... OK

• checking line endings in Makefiles ... OK

• checking compilation flags in Makevars ... OK

• checking for GNU extensions in Makefiles ... OK

• checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK

• checking use of PKG_*FLAGS in Makefiles ... OK

• checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK

• checking pragmas in C/C++ headers and code ... OK

• checking compiled code ... OK

• checking sizes of PDF files under 'inst/doc' ... OK

• checking installed files from 'inst/doc' ... OK

• checking files in 'vignettes' ... OK

• checking examples ...
  ** running examples for arch 'i386' ... [14s] OK
  ** running examples for arch 'x64' ... [15s] OK

• checking for unstated dependencies in 'tests' ... OK

• checking tests ...
  ** running tests for arch 'i386' ... [49s] OK
  Running 'testthat.R' [49s]
  ** running tests for arch 'x64' ... [49s] OK
  Running 'testthat.R' [49s]

• checking for unstated dependencies in vignettes ... OK

• checking package vignettes in 'inst/doc' ... OK

• checking re-building of vignette outputs ... [17s] OK

• checking PDF version of manual ... OK

• checking for detritus in the temp directory ... OK

• DONE
  Status: 3 NOTEs

[trivialfis]

I have uploaded the Python packages.

Friendly ping. ;-)
@hetong007 Could you please help with the R package? I ran cran tests on rhub. But win builder hasn't responded to me yet for some reason.

@hcho3 Could you please help with maven packages?

[hcho3]

@trivialfis Acknowledged. I'll get to it soon.

[trivialfis]

Thank you!

[hcho3]

@trivialfis Done.

[hetong007]

Thanks for managing this @trivialfis !

The 'invalid URLs' issue can be fixed directly by using the new move-to address. The error in vignette build should be fine for the official CRAN check environment.

Since the maintainer has been changed, you could go ahead and directly submit it at https://cran.r-project.org/submit.html :D

[trivialfis]

@hetong007 The maintainer is only changed for testing so that I can receive emails about test results, I did not include that into the repository here.

I'm happy to start maintaining the R package, however, R is not my day-to-day language, would be great to have you oversee the release process.

[trivialfis]

I will try to submit the package tomorrow.

[hetong007]

Sorry I'm busy with ICML deadline this week and was absent in this thread. It would be great that you could try to submit the package! On the other hand, I can also take care of it this weekend (after the deadline).

[trivialfis]

@hetong007 I have submitted the package and need confirmation from you due to the changed maintainer. Could you please check your inbox when you are available? Thank you!

[hetong007]

I have just replied. Good luck with the submission!

[trivialfis]

Closing this now, will continue to monitor https://cran.r-project.org/web/checks/check_results_xgboost.html .

@hetong007 Thank you for the support!