GNU bug report logs - #53363
[PATCH] gnu: xgboost: Update to 1.5.2.

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Vinicius Monego <monego <at> posteo.net>
To: guix-patches <at> gnu.org
Cc: Vinicius Monego <monego <at> posteo.net>
Subject: [PATCH] gnu: xgboost: Update to 1.5.2.
Date: Wed, 19 Jan 2022 13:43:56 +0000

* gnu/packages/machine-learning.scm (xgboost, python-xgboost): Update to
1.5.2.
(python-xgboost): Enable previously failing test.
* gnu/packages/patches/xgboost-use-system-dmlc-core.patch: Update patch.
---
 gnu/packages/machine-learning.scm             |  8 ++-
 .../xgboost-use-system-dmlc-core.patch        | 53 ++++++++++---------
 2 files changed, 30 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/machine-learning.scm b/gnu/packages/machine-learning.scm
index e5dbba21dd..318c7a0c17 100644
--- a/gnu/packages/machine-learning.scm
+++ b/gnu/packages/machine-learning.scm
@@ -15,7 +15,7 @@
 ;;; Copyright © 2019 Brett Gilio <brettg <at> gnu.org>
 ;;; Copyright © 2020 Konrad Hinsen <konrad.hinsen <at> fastmail.net>
 ;;; Copyright © 2020 Edouard Klein <edk <at> beaver-labs.com>
-;;; Copyright © 2020, 2021 Vinicius Monego <monego <at> posteo.net>
+;;; Copyright © 2020, 2021, 2022 Vinicius Monego <monego <at> posteo.net>
 ;;; Copyright © 2020, 2021 Maxim Cournoyer <maxim.cournoyer <at> gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -2497,7 +2497,7 @@ learning libraries.")
 (define-public xgboost
   (package
     (name "xgboost")
-    (version "1.4.2")
+    (version "1.5.2")
     (source
      (origin
        (method git-fetch)
@@ -2507,7 +2507,7 @@ learning libraries.")
        (file-name (git-file-name name version))
        (patches (search-patches "xgboost-use-system-dmlc-core.patch"))
        (sha256
-        (base32 "00liz816ahk9zj3jv3m2fqwlf6xxfbgvpmpl72iklx32vl192w5d"))))
+        (base32 "0qx04y7cz8z7qv6bk9q7d7ba9b7xzj53l83l2x9ykdwhzacc3dn0"))))
     (build-system cmake-build-system)
     (arguments
      `(#:configure-flags (list "-DGOOGLE_TEST=ON")))
@@ -2580,8 +2580,6 @@ in a fast and accurate way.")
                         " and not test_cv_no_shuffle"
                         " and not test_cv"
                         " and not test_training"
-                        ;; FIXME: May pass in the next version.
-                        " and not test_pandas"
                         ;; "'['./runexp.sh']' returned non-zero exit status 1"
                         " and not test_cli_binary_classification"))))))))
     (native-inputs
diff --git a/gnu/packages/patches/xgboost-use-system-dmlc-core.patch b/gnu/packages/patches/xgboost-use-system-dmlc-core.patch
index c654694fec..6b2a1651a5 100644
--- a/gnu/packages/patches/xgboost-use-system-dmlc-core.patch
+++ b/gnu/packages/patches/xgboost-use-system-dmlc-core.patch
@@ -1,34 +1,35 @@
-From 34167cc105e47589b86b6f62da76e0ab744002dd Mon Sep 17 00:00:00 2001
-From: Vinicius Monego <monego <at> posteo.net>
-Date: Tue, 11 May 2021 19:35:30 -0300
-Subject: [PATCH] Use dmlc-core from Guix.
-
----
-This patch is a subset of the following Debian patch: https://sources.debian.org/src/xgboost/1.2.1-1/debian/patches/cmake.patch/
-
-Rabit is now developed as part of xgboost, so we don't build it separately.
-
- CMakeLists.txt | 8 +++-----
- 1 file changed, 3 insertions(+), 5 deletions(-)
-
-diff --git a/CMakeLists.txt b/CMakeLists.txt
-index 6cc19fbd..3b42bc17 100644
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -150,11 +150,9 @@ endif (USE_OPENMP)
+# This patch was imported from Debian: https://sources.debian.org/src/xgboost/1.5.1-1/debian/patches/cmake-dmlc-core.patch/
 
+Index: xgboost/CMakeLists.txt
+===================================================================
+--- xgboost.orig/CMakeLists.txt
++++ xgboost/CMakeLists.txt
+@@ -164,7 +164,9 @@ endif (USE_NCCL)
+ 
  # dmlc-core
  msvc_use_static_runtime()
 -add_subdirectory(${xgboost_SOURCE_DIR}/dmlc-core)
--set_target_properties(dmlc PROPERTIES
--  CXX_STANDARD 14
--  CXX_STANDARD_REQUIRED ON
--  POSITION_INDEPENDENT_CODE ON)
 +add_library(dmlc SHARED IMPORTED)
 +find_library(DMLC_LIBRARY dmlc)
 +set_property(TARGET dmlc PROPERTY IMPORTED_LOCATION "${DMLC_LIBRARY}")
+ 
  if (MSVC)
-   target_compile_options(dmlc PRIVATE
-                          -D_CRT_SECURE_NO_WARNINGS -D_CRT_SECURE_NO_DEPRECATE)
---
-2.31.1
+   if (TARGET dmlc_unit_tests)
+@@ -222,7 +224,7 @@ set_target_properties(runxgboost PROPERT
+ #-- End CLI for xgboost
+ 
+ # Common setup for all targets
+-foreach(target xgboost objxgboost dmlc runxgboost)
++foreach(target xgboost objxgboost runxgboost)
+   xgboost_target_properties(${target})
+   xgboost_target_link_libraries(${target})
+   xgboost_target_defs(${target})
+@@ -273,7 +275,7 @@ install(DIRECTORY ${xgboost_SOURCE_DIR}/
+ #
+ # https://github.com/dmlc/xgboost/issues/6085
+ if (BUILD_STATIC_LIB)
+-  set(INSTALL_TARGETS xgboost runxgboost objxgboost dmlc)
++  set(INSTALL_TARGETS xgboost runxgboost objxgboost)
+ else (BUILD_STATIC_LIB)
+   set(INSTALL_TARGETS xgboost runxgboost)
+ endif (BUILD_STATIC_LIB)

base-commit: 36f4745dc10e5d0e8b2a62cd2c8439629debae4f
-- 
2.30.2

Message #8 received at 53363 <at> debbugs.gnu.org (full text, mbox):

From: Ludovic Courtès <ludo <at> gnu.org>
To: Vinicius Monego <monego <at> posteo.net>
Cc: 53363 <at> debbugs.gnu.org
Subject: Re: bug#53363: [PATCH] gnu: xgboost: Update to 1.5.2.
Date: Mon, 24 Jan 2022 10:36:51 +0100

Hi Vinicius,

Vinicius Monego <monego <at> posteo.net> skribis:

> * gnu/packages/machine-learning.scm (xgboost, python-xgboost): Update to
> 1.5.2.
> (python-xgboost): Enable previously failing test.
> * gnu/packages/patches/xgboost-use-system-dmlc-core.patch: Update patch.

LGTM, but I cannot apply it:

--8<---------------cut here---------------start------------->8---
$ git am --show-current-patch=diff|patch -p1
patching file gnu/packages/machine-learning.scm
Hunk #2 succeeded at 2490 (offset -7 lines).
Hunk #3 succeeded at 2500 (offset -7 lines).
Hunk #4 succeeded at 2573 (offset -7 lines).
patching file gnu/packages/patches/xgboost-use-system-dmlc-core.patch
patch: **** malformed patch at line 93: -2.31.1
--8<---------------cut here---------------end--------------->8---

It’s the second time today I fail to apply a patch-containing patch.
Does that ring a bell?

Thanks,
Ludo’.

Message #13 received at 53363-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: 53363-done <at> debbugs.gnu.org
Subject: [PATCH] gnu: xgboost: Update to 1.5.2.
Date: Mon, 24 Jan 2022 12:34:47 +0100

Hi,

I applied the patch and pushed it to the “master” branch with commit
c30fa177f3717094e72c01ebba330b638a5e6e65.

Thanks!

-- 
Ricardo

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