[R-pkg-devel] CRAN Submission xgboost 1.7.11.1

Mon May 12 21:49:43 CEST 2025

Hi Uwe,

Please help take a look into reproducing the failure if possible. We 
really appreciate your help. Thanks to Ivan, we managed to reproduce the 
memory protection error. But we haven't reproduced other test failures.

Cheers!

Jiaming

On 5/12/25 17:23, Uwe Ligges wrote:
> We realized this has already been answered by Ivan Krylov on the 
> r-packages-devel list.
>
> Best,
> Uwe Ligges
>
>
> On 12.05.2025 11:07, Uwe Ligges wrote:
>> I'll try to reproduce this locally.
>>
>>
>>
>> On 09.05.2025 06:22, jiaming yuan wrote:
>>> Hi CRAN,
>>>
>>> May I ask if someone has tried to reproduce the openblas test 
>>> environment from CRAN? We are trying to resolve the test failures of 
>>> XGBoost but so far no one has managed to reproduce them locally. 
>>> https://github.com/dmlc/xgboost/issues/11431
>>>
>>> Would be great if you can share some guidance on how to reproduce 
>>> that exact environment.
>>>
>>> Cheers
>>> Jiaming
>>> ________________________________
>>> From: jiaming yuan <jm.yuan using outlook.com>
>>> Sent: Friday, May 9, 2025 12:04:45 PM
>>> To: Uwe Ligges <ligges using statistik.tu-dortmund.de>; CRAN <cran- 
>>> submissions using r-project.org>
>>> Cc: CRAN Package Submission Form <cransubmit using xmbombadil.wu.ac.at>
>>> Subject: Re: CRAN Submission xgboost 1.7.11.1
>>>
>>> Hi,
>>>
>>> Others kindly provided help to reproduce the failure but so far no 
>>> one has managed to do so.
>>>
>>> Please see  https://github.com/dmlc/xgboost/ 
>>> issues/11431#issuecomment-2864947065  and related discussions the 
>>> thread. Would be great if you can share something more precise.
>>>
>>>
>>> Cheers
>>> Jiaming
>>>
>>> ________________________________
>>> From: Uwe Ligges <ligges using statistik.tu-dortmund.de>
>>> Sent: Wednesday, May 7, 2025 9:48:56 PM
>>> To: jiaming yuan <jm.yuan using outlook.com>; CRAN <cran-submissions using r- 
>>> project.org>
>>> Cc: CRAN Package Submission Form <cransubmit using xmbombadil.wu.ac.at>
>>> Subject: Re: CRAN Submission xgboost 1.7.11.1
>>>
>>> Note this is relevant, as most Linux clusters will have admis who will
>>> link scientifiv software aagainst OpenBLAS for faster matriox 
>>> operations.
>>>
>>> Best,
>>> Uwe Ligges
>>>
>>> On 07.05.2025 15:48, Uwe Ligges wrote:
>>>> I think any Liniux system with R linked against the system's default
>>>> OpenBLAS installation will show this issue.
>>>> I'd try it with a standard Ubuntu or Debian with OpenBLAS installed 
>>>> and
>>>> link agasinst it.
>>>>
>>>> Best,
>>>> Uwe Ligges
>>>>
>>>>
>>>>
>>>> On 03.05.2025 08:29, jiaming yuan wrote:
>>>>> Thank you for reaching out. We can't really dive into it unless
>>>>> there's an easier way to reproduce the environment (like a container
>>>>> or using some deterministic package managers). It's very unlikely 
>>>>> that
>>>>> we can try to build that environment on our own then try to fix all
>>>>> errors and verify all fixes.
>>>>>
>>>>>
>>>>>
>>>>> ________________________________
>>>>> From: Uwe Ligges <ligges using statistik.tu-dortmund.de>
>>>>> Sent: Friday, May 2, 2025 8:00:17 PM
>>>>> To: Jiaming Yuan <jm.yuan using outlook.com>; CRAN <cran-submissions using r-
>>>>> project.org>
>>>>> Cc: CRAN Package Submission Form <cransubmit using xmbombadil.wu.ac.at>
>>>>> Subject: Re: CRAN Submission xgboost 1.7.11.1
>>>>>
>>>>> Thanks, we see you removed lots of tests. Is this really sensible and
>>>>> are you sure that users with OpenBLAS (as most Linux users and 
>>>>> cluster
>>>>> admins will use) will get correct results? Sensibly relaxing 
>>>>> numerical
>>>>> assumptions may be a better way to tweak the tests.?
>>>>>
>>>>> Best,
>>>>> Uwe Ligges
>>>>>
>>>>>
>>>>> On 01.05.2025 12:58, CRAN Package Submission Form via 
>>>>> CRAN-submissions
>>>>> wrote:
>>>>>> [This was generated from CRAN.R-project.org/submit.html]
>>>>>>
>>>>>> The following package was uploaded to CRAN:
>>>>>> ===========================================
>>>>>>
>>>>>> Package Information:
>>>>>> Package: xgboost
>>>>>> Version: 1.7.11.1
>>>>>> Title: Extreme Gradient Boosting
>>>>>> Author(s): Tianqi Chen [aut], Tong He [aut], Michael Benesty [aut],
>>>>>> Vadim
>>>>>> Khotilovich [aut], Yuan Tang [aut]
>>>>>> (<https://orcid.org/0000-0001-5243-233X>), Hyunsu Cho [aut],
>>>>>> Kailong Chen [aut], Rory Mitchell [aut], Ignacio Cano [aut],
>>>>>> Tianyi Zhou [aut], Mu Li [aut], Junyuan Xie [aut], Min Lin
>>>>>> [aut], Yifeng Geng [aut], Yutian Li [aut], Jiaming Yuan [aut,
>>>>>> cre], XGBoost contributors [cph] (base XGBoost implementation)
>>>>>> Maintainer: Jiaming Yuan <jm.yuan using outlook.com>
>>>>>> Depends: R (>= 3.3.0)
>>>>>> Suggests: knitr, rmarkdown, ggplot2 (>= 1.0.1), DiagrammeR (>= 
>>>>>> 0.9.0),
>>>>>> Ckmeans.1d.dp (>= 3.3.1), vcd (>= 1.3), cplm, e1071, caret,
>>>>>> testthat, lintr, igraph (>= 1.0.1), float, crayon, titanic
>>>>>> Description: Extreme Gradient Boosting, which is an efficient
>>>>>> implementation of the gradient boosting framework from Chen &
>>>>>> Guestrin (2016) <doi:10.1145/2939672.2939785>. This package
>>>>>> is its R interface. The package includes efficient linear
>>>>>> model solver and tree learning algorithms. The package can
>>>>>> automatically do parallel computation on a single machine
>>>>>> which could be more than 10 times faster than existing
>>>>>> gradient boosting packages. It supports various objective
>>>>>> functions, including regression, classification and ranking.
>>>>>> The package is made to be extensible, so that users are also
>>>>>> allowed to define their own objectives easily.
>>>>>> License: Apache License (== 2.0) | file LICENSE
>>>>>> Imports: Matrix (>= 1.1-0), methods, data.table (>= 1.9.6), jsonlite
>>>>>> (>= 1.0),
>>>>>>
>>>>>>
>>>>>> The maintainer confirms that he or she
>>>>>> has read and agrees to the CRAN policies.
>>>>>>
>>>>>> =================================================
>>>>>>
>>>>>> Original content of DESCRIPTION file:
>>>>>>
>>>>>> Package: xgboost
>>>>>> Type: Package
>>>>>> Title: Extreme Gradient Boosting
>>>>>> Version: 1.7.11.1
>>>>>> Date: 2025-05-01
>>>>>> Authors using R: c(
>>>>>> person("Tianqi", "Chen", role = c("aut"),
>>>>>> email = "tianqi.tchen using gmail.com"),
>>>>>> person("Tong", "He", role = c("aut"),
>>>>>> email = "hetong007 using gmail.com"),
>>>>>> person("Michael", "Benesty", role = c("aut"),
>>>>>> email = "michael using benesty.fr"),
>>>>>> person("Vadim", "Khotilovich", role = c("aut"),
>>>>>> email = "khotilovich using gmail.com"),
>>>>>> person("Yuan", "Tang", role = c("aut"),
>>>>>> email = "terrytangyuan using gmail.com",
>>>>>> comment = c(ORCID = "0000-0001-5243-233X")),
>>>>>> person("Hyunsu", "Cho", role = c("aut"),
>>>>>> email = "chohyu01 using cs.washington.edu"),
>>>>>> person("Kailong", "Chen", role = c("aut")),
>>>>>> person("Rory", "Mitchell", role = c("aut")),
>>>>>> person("Ignacio", "Cano", role = c("aut")),
>>>>>> person("Tianyi", "Zhou", role = c("aut")),
>>>>>> person("Mu", "Li", role = c("aut")),
>>>>>> person("Junyuan", "Xie", role = c("aut")),
>>>>>> person("Min", "Lin", role = c("aut")),
>>>>>> person("Yifeng", "Geng", role = c("aut")),
>>>>>> person("Yutian", "Li", role = c("aut")),
>>>>>> person("Jiaming", "Yuan", role = c("aut", "cre"),
>>>>>> email = "jm.yuan using outlook.com"),
>>>>>> person("XGBoost contributors", role = c("cph"),
>>>>>> comment = "base XGBoost implementation")
>>>>>> )
>>>>>> Maintainer: Jiaming Yuan <jm.yuan using outlook.com>
>>>>>> Description: Extreme Gradient Boosting, which is an efficient
>>>>>> implementation
>>>>>> of the gradient boosting framework from Chen & Guestrin (2016)
>>>>>> <doi:10.1145/2939672.2939785>.
>>>>>> This package is its R interface. The package includes efficient 
>>>>>> linear
>>>>>> model solver and tree learning algorithms. The package can 
>>>>>> automatically
>>>>>> do parallel computation on a single machine which could be more 
>>>>>> than 10
>>>>>> times faster than existing gradient boosting packages. It supports
>>>>>> various objective functions, including regression, classification 
>>>>>> and
>>>>>> ranking.
>>>>>> The package is made to be extensible, so that users are also allowed
>>>>>> to define
>>>>>> their own objectives easily.
>>>>>> License: Apache License (== 2.0) | file LICENSE
>>>>>> URL: https://github.com/dmlc/xgboost
>>>>>> BugReports: https://github.com/dmlc/xgboost/issues
>>>>>> NeedsCompilation: yes
>>>>>> VignetteBuilder: knitr
>>>>>> Suggests: knitr, rmarkdown, ggplot2 (>= 1.0.1), DiagrammeR (>= 
>>>>>> 0.9.0),
>>>>>> Ckmeans.1d.dp (>= 3.3.1), vcd (>= 1.3), cplm, e1071, caret,
>>>>>> testthat, lintr, igraph (>= 1.0.1), float, crayon, titanic
>>>>>> Depends: R (>= 3.3.0)
>>>>>> Imports: Matrix (>= 1.1-0), methods, data.table (>= 1.9.6), jsonlite
>>>>>> (>= 1.0),
>>>>>> RoxygenNote: 7.3.2
>>>>>> Encoding: UTF-8
>>>>>> SystemRequirements: GNU make, C++17
>>>>>> Packaged: 2025-05-01 10:56:14 UTC; jiamingy
>>>>>> Author: Tianqi Chen [aut],
>>>>>> Tong He [aut],
>>>>>> Michael Benesty [aut],
>>>>>> Vadim Khotilovich [aut],
>>>>>> Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>),
>>>>>> Hyunsu Cho [aut],
>>>>>> Kailong Chen [aut],
>>>>>> Rory Mitchell [aut],
>>>>>> Ignacio Cano [aut],
>>>>>> Tianyi Zhou [aut],
>>>>>> Mu Li [aut],
>>>>>> Junyuan Xie [aut],
>>>>>> Min Lin [aut],
>>>>>> Yifeng Geng [aut],
>>>>>> Yutian Li [aut],
>>>>>> Jiaming Yuan [aut, cre],
>>>>>> XGBoost contributors [cph] (base XGBoost implementation)
>>>>>>
>>>>>
>>>>>
>>>>>
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>>>>>
>>>>
>>>
>>>
>>>
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>