1.5.2 Patch Release. - Githubissues

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 ' 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 ' 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 ’ 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. 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 ’ 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 Old maintainer(s): Tong He 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 ' Authors@R: 'Tong He ' * 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

dmlc / xgboost

1.5.2 Patch Release. #7557