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1.5.0 Release Candidate #7260

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trivialfis opened this issue Sep 26, 2021 · 54 comments
Closed
8 tasks done

1.5.0 Release Candidate #7260

trivialfis opened this issue Sep 26, 2021 · 54 comments

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@trivialfis
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trivialfis commented Sep 26, 2021

Roadmap #6846 . Draft of release note: #7271 .

We are about to release version 1.5.0 of XGBoost. In the next two weeks, we invite everyone to try out the release candidate (RC).

Feedback period: until the end of October 13, 2021. No new feature will be added to the release; only critical bug fixes will be added.

@dmlc/xgboost-committer

Available packages:

  • Python packages:
pip install xgboost==1.5.0rc1
R CMD INSTALL ./xgboost_r_gpu_linux.tar.gz
  • JVM packages
Show instructions (Maven/SBT)

Maven

<dependencies>
  ...
  <dependency>
      <groupId>ml.dmlc</groupId>
      <artifactId>xgboost4j_2.12</artifactId>
      <version>1.5.0-RC1</version>
  </dependency>
  <dependency>
      <groupId>ml.dmlc</groupId>
      <artifactId>xgboost4j-spark_2.12</artifactId>
      <version>1.5.0-RC1</version>
  </dependency>
</dependencies>

<repositories>
  <repository>
    <id>XGBoost4J Release Repo</id>
    <name>XGBoost4J Release Repo</name>
    <url>https://s3-us-west-2.amazonaws.com/xgboost-maven-repo/release/</url>
  </repository>
</repositories>

SBT

libraryDependencies ++= Seq(
  "ml.dmlc" %% "xgboost4j" % "1.5.0-RC1",
  "ml.dmlc" %% "xgboost4j-spark" % "1.5.0-RC1"
)
resolvers += ("XGBoost4J Release Repo"
              at "https://s3-us-west-2.amazonaws.com/xgboost-maven-repo/release/")

Starting from 1.2.0, XGBoost4J-Spark supports training with NVIDIA GPUs. To enable this capability, download artifacts suffixed with -gpu, as follows:

Show instructions (Maven/SBT)

Maven

<dependencies>
  ...
  <dependency>
      <groupId>ml.dmlc</groupId>
      <artifactId>xgboost4j-gpu_2.12</artifactId>
      <version>1.5.0-RC1</version>
  </dependency>
  <dependency>
      <groupId>ml.dmlc</groupId>
      <artifactId>xgboost4j-spark-gpu_2.12</artifactId>
      <version>1.5.0-RC1</version>
  </dependency>
</dependencies>

<repositories>
  <repository>
    <id>XGBoost4J Release Repo</id>
    <name>XGBoost4J Release Repo</name>
    <url>https://s3-us-west-2.amazonaws.com/xgboost-maven-repo/release/</url>
  </repository>
</repositories>

SBT

libraryDependencies ++= Seq(
  "ml.dmlc" %% "xgboost4j-gpu" % "1.5.0-RC1",
  "ml.dmlc" %% "xgboost4j-spark-gpu" % "1.5.0-RC1"
)
resolvers += ("XGBoost4J Release Repo"
              at "https://s3-us-west-2.amazonaws.com/xgboost-maven-repo/release/")

TO-DOs

  • Release pip rc package.
  • Test on R-hub.
  • Release R rc package.
  • Release jvm rc packages.

PRs to be backported

@trivialfis
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This time R-hub has Apple M1 instances. Let's wait for the test result. ;-)

@trivialfis
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trivialfis commented Sep 26, 2021

R-Hub

config.status: creating src/Makevars
 ** libs
Makevars:17: -DXGBOOST_STRICT_R_MODE=1
Makevars:17: -DDMLC_LOG_BEFORE_THROW=0
Makevars:17: -DDMLC_ENABLE_STD_THREAD=1
Makevars:17: -DDMLC_DISABLE_STDIN=1
Makevars:17: -DDMLC_LOG_CUSTOMIZE=1
Makevars:17: -DXGBOOST_CUSTOMIZE_LOGGER=1
Makevars:17: -DRABIT_CUSTOMIZE_MSG_
/opt/developerstudio12.6/bin/CC -std=c++14 -I"/opt/R/R-4.1.1/lib/R/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=1 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_  -I/opt/csw/include  -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread  -KPIC  -O -xlibmil -xtarget=native -xcache=generic -nofstore  -c xgboost_R.cc -o xgboost_R.o
CC: Warning: Option -pthread passed to ld, if ld is invoked, ignored otherwise

"xgboost_R.cc", assertion failed in function pr_post_process_node() @ preopt.c:3862
assert(nd_eq_(scope_first_stmt_(node), first_s))

CC: ube failed for xgboost_R.cc
gmake: *** [/opt/R/R-4.1.1/lib/R/etc/Makeconf:175: xgboost_R.o] Error 2
ERROR: compilation failed for package ‘xgboost’
 * removing ‘/export/home/Xdub2Tz/R/xgboost’
 * restoring previous ‘/export/home/Xdub2Tz/R/xgboost’
14715docker rm xgboost_1.5.0.1.tar.gz-d66aa2b88da2a1ef57a0bd162afa617f-1

14716#> Error: No such container: xgboost_1.5.0.1.tar.gz-d66aa2b88da2a1ef57a0bd162afa617f-1

14717true

14718docker rm xgboost_1.5.0.1.tar.gz-d66aa2b88da2a1ef57a0bd162afa617f-2

@trivialfis
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Hi all, the RC packages are released to public repositories now. Please help test the new release and provide feedbacks. Enjoy!

@trivialfis
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Everything looks good. I will start preparing the stable release tomorrow.

@trivialfis
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Need to resolve #7294 first.

@trivialfis
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Hi @hetong007 @hcho3 I have made the 1.5 stable release and uploaded all Python packages to pypi. Could you please help upload the R package and JVM packages?

@hcho3 hcho3 unpinned this issue Oct 19, 2021
@hcho3
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hcho3 commented Oct 19, 2021

@trivialfis I've uploaded the JVM package to Maven Central.

@hcho3 hcho3 pinned this issue Oct 19, 2021
@hetong007
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I'm quite occupied these two days but I'll start submitting the R package later this week. Hope it'll go into cran smoothly.

@hetong007
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hetong007 commented Oct 25, 2021

The release branch consistently passes make Rcheck on my Ubuntu 16.04 and RHub's solaris test.

However, the pre-test via Win-Builder failed with R-devel, R-release and R-oldrelease consistently, due to too-large training errors from several checks in test_basic.R. A short sample from the log:

  Failure (test_basic.R:133:3): train and predict softprob
  bst$evaluation_log[, min(train_merror)] is not strictly less than 0.025. Difference: 0.588
  
  Failure (test_basic.R:144:3): train and predict softprob
  bst$evaluation_log[5, train_merror] not equal to `err`.
  1/1 mismatches
  [1] 0.613 - 0.667 == -0.0533
  
  Failure (test_basic.R:149:3): train and predict softprob
  bst$evaluation_log[1, train_merror] not equal to `err`.
  1/1 mismatches
  [1] 0.613 - 0.553 == 0.06
  
  Failure (test_basic.R:179:3): train and predict softmax
  bst$evaluation_log[, min(train_merror)] is not strictly less than 0.025. Difference: 0.588
  
  Failure (test_basic.R:396:3): colsample_bytree works
  nrow(xgb.importance(model = bst)) is not more than 30. Difference: -30

Full check logs (might be removed in 72 hours):

The error seems concerning to me as it indicates the model was not trained as expected in our test on Windows. Do we expect such behavior or have we observed similar issues? Also, please correct me if I made any mistakes in the pre-test.

@trivialfis
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Interesting, thanks for running the tests! I will look into it. Oddly, I ran the tests with R-hub #7260 (comment) and it worked fine there.

@trivialfis
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Might be an issue with the new prediction interface.

@trivialfis
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@hetong007 Do you know how to reproduce that particular environment locally? (or on platforms like AWS)

@hetong007
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@trivialfis Thanks for the effort! According to win-builder, the configuration is:

A Windows Server 2008 (64-bit) machine (2x Intel Xeon E5-2670, 8 cores each, 2.6 GHz, 32Gb RAM) builds and checks your source packages and makes the installation log, check log and the Windows binary available.

AFAIK, windows server 2008 is only available via "Community AMIs", but I'm not sure if that's critical to reproduce. I can also try later at home on my Windows 10 PC. If that doesn't reproduce, then maybe try an official Windows Server 2012 (the closest environment)?

Unfortunately, based on a few previous submissions, passing the win-builder check system has been a hard requirement to get into CRAN now. Thus we need to fix it eventually.

@trivialfis
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based on a few previous submissions, passing the win-builder check system has been a hard requirement to get into CRAN now

Yes. It's likely a bug in the R package. Just I need to reproduce it in order to fix it. So far neither the tests on GitHub action nor the one on R-hub show the error so I'm wondering where can I build that environment. On R-hub I tested Windows Server 2008 R2 SP1, R-release, 32/64 bit.

@hetong007
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Interestingly, I did the following on my Ubuntu 16.04 and observed a test failure:

  1. cd $PKG_ROOT/R-package/tests/testthat
  2. Add one line require(testthat) in the beginning of test_basic.R
  3. Rscript test_basic.R

And the message is:

Loading required package: xgboost
Loading required package: testthat
── Failure (???): train and predict binary classification ──────────────────────
`pred1` not equal to `pred2`.
6513/6513 mismatches (average diff: 0.0984)
[1] 0.847 - 0.9239 == -0.0768
[2] 0.154 - 0.2858 == -0.1314
[3] 0.154 - 0.2858 == -0.1314
[4] 0.847 - 0.9239 == -0.0768
[5] 0.126 - 0.0517 ==  0.0739
[6] 0.154 - 0.2858 == -0.1314
[7] 0.154 - 0.2858 == -0.1314
[8] 0.847 - 0.9239 == -0.0768
[9] 0.154 - 0.2858 == -0.1314
...

Error: Test failed
Execution halted

Hope that may help our debugging. But I'm not sure how it passes the local check though...

@trivialfis
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Unable to reproduce on Ubuntu 20.04. Let me spin up a 16.04 machine.

@hetong007
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Apologies! I messed up my environment thus didn't test with the latest release for the above results :(

Will still test on my Windows 10 though, and ping here about the results.

@trivialfis
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Just a quick note, I have tested with address and undefined sanitizers to eliminate some possible errors in libxgboost.so . The error is likely in R binding.

@hcho3
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hcho3 commented Oct 25, 2021

Hmm, I keep getting the error about xgb.ntree not being existent :(

@hcho3
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hcho3 commented Oct 25, 2021

After replacing xgb.ntree with xgboost:::xgb.ntree, all tests in test_basic.R are passing on my Windows machine. I could not reproduce the error reported by Win-Builder.

@trivialfis
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The evaluation log and feature importance are also different so it's not just the prediction function rewrite.

@trivialfis
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@hetong007 Did you reproduce it?

I tried to change the OMP_NUM_THREADS and see if anything flaky comes up. So far no avail.

@hetong007
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I couldn't reproduce it on my windows 10... I tried to either install the zip from our github release, or directly download the compiled zip from win-builder. They both passed the manual execution on test_basic.R and test_helpers.R with the namespace issue (like xgb.ntree) fixed.

@trivialfis
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@hetong007 Thanks for the help! I will test the package on win builder with the maintainer field changed to my email later today.

@trivialfis
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Hi @hetong007 @hcho3 I ran the test on the win builder. Here is the installation log: https://win-builder.r-project.org/Jujkkd7LoWF8/00install.out (also attached below).

I noticed one weird thing, from this section:

d:/Compiler/rtools40/mingw32/bin/g++  -std=gnu++14 -I"D:/RCompile/recent/R-4.1.1/include" -DNDEBUG -I./include -I./dmlc-core/include -I./rabit/include -I. -DXGBOOST_STRICT_R_MODE=1 -DDMLC_LOG_BEFORE_THROW=0 -DDMLC_ENABLE_STD_THREAD=0 -DDMLC_DISABLE_STDIN=1 -DDMLC_LOG_CUSTOMIZE=1 -DXGBOOST_CUSTOMIZE_LOGGER=1 -DRABIT_CUSTOMIZE_MSG_ -DDMLC_CXX11_THREAD_LOCAL=0    -I"d:/Compiler/gcc-4.9.3/local330/include"  -fopenmp -DDMLC_CMAKE_LITTLE_ENDIAN=1 -pthread    -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c xgboost_R.cc -o xgboost_R.o
In file included from ./include/xgboost/logging.h:12,
                 from ./dmlc-core/include/../../src/common/threading_utils.h:13,
                 from xgboost_R.cc:13:

It's using rtools40, according to https://cran.microsoft.com/snapshot/2020-07-16/bin/windows/Rtools/ , it should be using gcc toolchains 8.3.0. But in the log somehow gcc-4.9.3 is in the include path.

00check.log.txt
00install.out.txt

@trivialfis
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Reproduced the error locally.

@hetong007
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Thanks, that's fantastic! Would you mind to leave a pointer to the exact commit?

There seems to be two ways to handle this:

  • Revert the commit in the CRAN submission. What would be the potential risk for CRAN users?
  • Bypass the relevant test. Is it easy to do so?

@trivialfis
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@hetong007 I opened a PR for the fix: #7390 .

@trivialfis
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trivialfis commented Nov 3, 2021

@hetong007
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Thanks a lot! I've submitted the latest release branch to CRAN. It passes the auto-check, however seems to break some dependencies. I'll need to look into these packages, and probably communicate with the maintainers before we can have it in CRAN.

Details are below:

Dear maintainer,

package xgboost_1.5.0.1.tar.gz has been auto-processed. The auto-check found problems when checking the first order strong reverse dependencies.
Please reply-all and explain: Is this expected or do you need to fix anything in your package? If expected, have all maintainers of affected packages been informed well in advance? Are there false positives in our results?

*** Changes to worse in reverse dependencies ***
Debian: <https://win-builder.r-project.org/incoming_pretest/xgboost_1.5.0.1_20211104_073948/reverseDependencies/summary.txt>

Log dir: <https://win-builder.r-project.org/incoming_pretest/xgboost_1.5.0.1_20211104_073948/>
The files will be removed after roughly 7 days.

Pretests:
Windows: <https://win-builder.r-project.org/incoming_pretest/xgboost_1.5.0.1_20211104_073948/Windows/00check.log>
Debian: <https://win-builder.r-project.org/incoming_pretest/xgboost_1.5.0.1_20211104_073948/Debian/00check.log>

Last published version on CRAN:

CRAN Web: <https://cran.r-project.org/package=xgboost>

Best regards,
CRAN teams' auto-check service
Package check result: OK

Changes to worse in reverse depends:

Package: EIX
Check: re-building of vignette outputs
New result: WARNING
  Error(s) in re-building vignettes:
    ...
  --- re-building ‘EIX.Rmd’ using rmarkdown
     [[ suppressing 19 column names 'satisfaction_level', 'last_evaluation', 'number_project' ... ]]
  Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider increasing max.overlaps
  Quitting from lines 157-165 (EIX.Rmd)
  Error: processing vignette ‘EIX.Rmd’ failed with diagnostics:
  non-numeric matrix extent
  --- failed re-building ‘EIX.Rmd’

  --- re-building ‘titanic_data.Rmd’ using rmarkdown
  Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider increasing max.overlaps
  Quitting from lines 81-86 (titanic_data.Rmd)
  Error: processing vignette ‘titanic_data.Rmd’ failed with diagnostics:
  non-numeric matrix extent
  --- failed re-building ‘titanic_data.Rmd’

  SUMMARY: processing the following files failed:
    ‘EIX.Rmd’ ‘titanic_data.Rmd’

  Error: Vignette re-building failed.
  Execution halted

Package: radiant.model
Check: tests
New result: ERROR
    Running ‘testthat.R’ [4s/4s]
  Running the tests in ‘tests/testthat.R’ failed.
  Complete output:
    > ## use shift-cmd-t to run all tests
    > library(testthat)
    > test_check("radiant.model")
    Loading required package: radiant.model
    Loading required package: radiant.data
    Loading required package: magrittr

    Attaching package: 'magrittr'

    The following objects are masked from 'package:testthat':

        equals, is_less_than, not

    Loading required package: ggplot2
    Loading required package: lubridate

    Attaching package: 'lubridate'

    The following objects are masked from 'package:base':

        date, intersect, setdiff, union

    Loading required package: tidyr

    Attaching package: 'tidyr'

    The following object is masked from 'package:magrittr':

        extract

    The following object is masked from 'package:testthat':

        matches

    Loading required package: dplyr

    Attaching package: 'dplyr'

    The following object is masked from 'package:testthat':

        matches

    The following objects are masked from 'package:stats':

        filter, lag

    The following objects are masked from 'package:base':

        intersect, setdiff, setequal, union


    Attaching package: 'radiant.data'

    The following objects are masked from 'package:lubridate':

        month, wday

    The following object is masked from 'package:ggplot2':

        diamonds

    The following object is masked from 'package:magrittr':

        set_attr

    The following object is masked from 'package:testthat':

        describe

    The following object is masked from 'package:base':

        date

    SI1     9 114304.420 104924.680 123684.159  9379.739
    sex|male    0.080 -92.0%      -2.522     0.163 -15.447  < .001 ***
    2nd female      0.779 0.712 0.833
    1st female      0.896 0.856 0.926
    1st female 29.000      0.919 0.880 0.945
    ══ Failed tests ════════════════════════════════════════════════════════════════
    ── Failure (test_stats.R:160:3): Gradient Boosting - NoLD test ─────────────────
    `res1` not equal to `res2`.
    3/3 mismatches (average diff: 0.062)
    [1] 0.847 - 0.758 ==  0.089
    [2] 0.117 - 0.210 == -0.093
    [3] 0.036 - 0.032 ==  0.004

    [ FAIL 1 | WARN 0 | SKIP 0 | PASS 25 ]
    Error: Test failures
    Execution halted

@trivialfis
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It shouldn't have breaking change (but has new deprecation) I will look into it.

@hetong007
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From the above log, the error from EIX doesn't seem directly relevant, while the error from radiant.model seems to be relevant, as our new version might train the model differently and lead to different prediction values.

@trivialfis
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Building that package now. Might take some time to debug, I'm working on other things at the moment. Will keep you posted.

@trivialfis
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663136a is the commit to blame.

@trivialfis
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trivialfis commented Nov 4, 2021

Okay, I get the issue now. I re-implemented the global feature importance in C++ to eliminate the text parsing. But there's a subtle difference between the original Python and R implmentation. For Python there were "total_gain" and "gain", the latter is just the former divided by split count (or "frequency" in R). But for R this should not occur.

@trivialfis
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Opened a PR for the fix #7394 . Sorry about the inconvenience and thanks for all the help!

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trivialfis commented Nov 5, 2021

Ran tests on R-hub and win-builder

Passing:

Failing:

The windows instance on R-hub failed during "download and unpack files", which doesn't seem to be related to XGBoost:

 106#> windows_tracing_logfile C:\BVTBin\Tests\installpackage\csilogfile.log
 107#> setting _R_CHECK_FORCE_SUGGESTS_ to false
 108#> setting R_COMPILE_AND_INSTALL_PACKAGES to never
 109#> setting _R_CHECK_THINGS_IN_CHECK_DIR_ to false
 110#> setting R_REMOTES_STANDALONE to true
 111#> setting R_REMOTES_NO_ERRORS_FROM_WARNINGS to true
 112#> Exception calling "Start" with "0" argument(s): "The system cannot find the
 113#> file specified"
 114#> At C:\Users\USERdQIgyZGwrB\slave.ps1:124 char:5
 115#> + [void]$Process.Start()
 116#> + ~~~~~~~~~~~~~~~~~~~~~~
 117#> + CategoryInfo : NotSpecified: (:) [], MethodInvocationException
 118#> + FullyQualifiedErrorId : Win32Exception
 119#>
 120#> Exception calling "BeginOutputReadLine" with "0" argument(s): "StandardOut has
 121#> not been redirected or the process hasn't started yet."
 122#> At C:\Users\USERdQIgyZGwrB\slave.ps1:127 char:5
 123#> + $Process.BeginOutputReadLine()
 124#> + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 125#> + CategoryInfo : NotSpecified: (:) [], MethodInvocationException
 126#> + FullyQualifiedErrorId : InvalidOperationException
 127#>
 128#> Exception calling "BeginErrorReadLine" with "0" argument(s): "StandardError
 129#> has not been redirected."
 130#> At C:\Users\USERdQIgyZGwrB\slave.ps1:128 char:5
 131#> + $Process.BeginErrorReadLine()
 132#> + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 133#> + CategoryInfo : NotSpecified: (:) [], MethodInvocationException
 134#> + FullyQualifiedErrorId : InvalidOperationException
 135#>
 136#> Build timed out (after 30 minutes). Marking the build as failed.
 137#> Build was aborted
 138#> Pinging https://builder.r-hub.io/build/FAILURE/xgboost_1.5.0.1.tar.gz-7611c479e76f26550e3d61dc98388a5e

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trivialfis commented Nov 5, 2021

2 failures caused by timeout. The tests have passed, but timeout at building doc.

This on centos is concerning:

14037#> * checking compiled code ... WARNING
14038#> File ‘xgboost/libs/xgboost.so’:
14039#> Found ‘abort’, possibly from ‘abort’ (C)
14040#> Objects: ‘./xgboost_R.o’, ‘./amalgamation/xgboost-all0.o’,
14041#> ‘./amalgamation/dmlc-minimum0.o’, ‘./rabit/src/allreduce_base.o’
14042#> Found ‘printf’, possibly from ‘printf’ (C)
14043#> Objects: ‘./xgboost_R.o’, ‘./amalgamation/xgboost-all0.o’,
14044#> ‘./amalgamation/dmlc-minimum0.o’, ‘./rabit/src/allreduce_base.o’
14045#> Compiled code should not call entry points which might terminate R nor

Other tests don't have this note.

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trivialfis commented Nov 5, 2021

Doesn't make sense, I checked the binary locally, there's only __snprintf_chk. I couldn't download the artifacts from R-hub due to not found error.

@hetong007
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@trivialfis Thanks a ton for digging into this! It has successfully passed the reverse dependency test, and on its way to CRAN. Let's hope it'll pass the real tests across all platforms :)

@trivialfis
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@hetong007 Do you have the bandwidth to review R PRs? My experience with R is very limited and would be great to have an expert at supervising. ;-)

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No problem. I can still handle the R part, but not familiar with things that touch low-level source now.

@trivialfis
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Excellent!

@hetong007
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There might be some warnings we need to fix:

Please see the problems shown on
https://cran.r-project.org/web/checks/check_results_xgboost.html.

Please correct before 2021-11-22 to safely retain your package on CRAN.

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Opened a PR: #7404 I did not reproduce the warning using the development version of clang though.

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trivialfis commented Nov 19, 2021

Running tests on R-hub and win-builder. I will update this comment accordingly:

** DONE EIX
CLOSED: [2021-11-19 Fri 18:02]
** DONE radiant.model
CLOSED: [2021-11-19 Fri 18:02]

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@hetong007 Should I bump the version to 1.5.0.2 or 1.5.1? We are preparing the 1.5.1 for Python and JVM and it would be great to have some consistency. But I'm not entirely sure about the CRAN policy. Right now, the other 2 packages use <major, minor, patch> release naming format.

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Do we plan 1.5.1 to include ONLY the incremental fixes for CRAN submission?

If so, we can bump to 1.5.1, otherwise I think it is better to use 1.5.0.2.

@trivialfis
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Got it, I will keep it as 1.5.0.2. Opened a PR for incrementing the version number: #7452 .

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All tests have passed.

@trivialfis
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Closing as all 1.5.0 packages are submitted. Thank you all!

@trivialfis trivialfis unpinned this issue Nov 23, 2021
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