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Ortofta opened this issue May 5, 2025 · 5 comments
Open

Unable to use Docling with GraalPy #501

Ortofta opened this issue May 5, 2025 · 5 comments
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@msimacek

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@Ortofta
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Ortofta commented May 5, 2025 •
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I'm unable to get Docling 2.31.0 to work with GrallPy 24.2.1.
I know Docling is a fairly complex project, so maybe it's not feasible to try to use it on GraalPy? It gets as far as trying to install the scikit-image dependency, where it fails with an AssertionError.

This was run on a RHEL 9.5 system with Maven 3.9.9 and OpenJDK 24.

Is there anything else I can do to investigate further?

The full build log is below.

➜  graalpy ./mvnw clean install
WARNING: A restricted method in java.lang.System has been called
WARNING: java.lang.System::load has been called by org.fusesource.jansi.internal.JansiLoader in an unnamed module (file:/home/markus/.m2/wrapper/dists/apache-maven-3.9.9-bin/33b4b2b4/apache-maven-3.9.9/lib/jansi-2.4.1.jar)
WARNING: Use --enable-native-access=ALL-UNNAMED to avoid a warning for callers in this module
WARNING: Restricted methods will be blocked in a future release unless native access is enabled

WARNING: A terminally deprecated method in su
8000
n.misc.Unsafe has been called
WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.google.common.util.concurrent.AbstractFuture$UnsafeAtomicHelper (file:/home/markus/.m2/wrapper/dists/apache-maven-3.9.9-bin/33b4b2b4/apache-maven-3.9.9/lib/guava-33.2.1-jre.jar)
WARNING: Please consider reporting this to the maintainers of class com.google.common.util.concurrent.AbstractFuture$UnsafeAtomicHelper
WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
[INFO] Scanning for projects...
[INFO] 
[INFO] ------------------------< com.ortofta:graalpy >-------------------------
[INFO] Building graalpy 0.1
[INFO]   from pom.xml
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- clean:3.2.0:clean (default-clean) @ graalpy ---
[INFO] Deleting /home/markus/Documents/java/graalpy/target
[INFO] 
[INFO] --- enforcer:3.5.0:enforce (micronaut-enforce) @ graalpy ---
[INFO] Rule 0: org.apache.maven.enforcer.rules.version.RequireJavaVersion passed
[INFO] Rule 1: io.micronaut.maven.enforcer.CheckSnakeYaml passed
[INFO] 
[INFO] --- mn:4.7.2:generate-import-factory (default-generate-import-factory) @ graalpy ---
[INFO] 
[INFO] --- mn:4.7.2:generate-openapi-generic (default-generate-openapi-generic) @ graalpy ---
[INFO] 
[INFO] --- mn:4.7.2:generate-openapi-client (default-generate-openapi-client) @ graalpy ---
[INFO] 
[INFO] --- mn:4.7.2:generate-openapi-server (default-generate-openapi-server) @ graalpy ---
[INFO] 
[INFO] --- resources:3.3.1:resources (default-resources) @ graalpy ---
[INFO] Copying 2 resources from src/main/resources to target/classes
[INFO] 
[INFO] --- graalpy:24.2.1:process-graalpy-resources (default) @ graalpy ---
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/python/python-embedding-tools/24.2.1/python-embedding-tools-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/python/python-embedding-tools/24.2.1/python-embedding-tools-24.2.1.pom (1.6 kB at 4.4 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/polyglot/polyglot/24.2.1/polyglot-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/polyglot/polyglot/24.2.1/polyglot-24.2.1.pom (1.6 kB at 7.0 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/collections/24.2.1/collections-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/collections/24.2.1/collections-24.2.1.pom (1.2 kB at 9.8 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/nativeimage/24.2.1/nativeimage-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/nativeimage/24.2.1/nativeimage-24.2.1.pom (1.4 kB at 67 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/word/24.2.1/word-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/word/24.2.1/word-24.2.1.pom (1.2 kB at 60 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/python/python-launcher/24.2.1/python-launcher-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/python/python-launcher/24.2.1/python-launcher-24.2.1.pom (2.1 kB at 106 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/launcher-common/24.2.1/launcher-common-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/launcher-common/24.2.1/launcher-common-24.2.1.pom (1.9 kB at 14 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/shadowed/jline/24.2.1/jline-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/shadowed/jline/24.2.1/jline-24.2.1.pom (1.2 kB at 9.8 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/maven-downloader/24.2.1/maven-downloader-24.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/maven-downloader/24.2.1/maven-downloader-24.2.1.pom (1.4 kB at 12 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/python/python-embedding-tools/24.2.1/python-embedding-tools-24.2.1.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/python/python-embedding-tools/24.2.1/python-embedding-tools-24.2.1.jar (35 kB at 94 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/polyglot/polyglot/24.2.1/polyglot-24.2.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/collections/24.2.1/collections-24.2.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/launcher-common/24.2.1/launcher-common-24.2.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/shadowed/jline/24.2.1/jline-24.2.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/python/python-launcher/24.2.1/python-launcher-24.2.1.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/collections/24.2.1/collections-24.2.1.jar (122 kB at 419 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/maven-downloader/24.2.1/maven-downloader-24.2.1.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/python/python-launcher/24.2.1/python-launcher-24.2.1.jar (85 kB at 257 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/nativeimage/24.2.1/nativeimage-24.2.1.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/polyglot/polyglot/24.2.1/polyglot-24.2.1.jar (509 kB at 1.5 MB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/word/24.2.1/word-24.2.1.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/launcher-common/24.2.1/launcher-common-24.2.1.jar (155 kB at 441 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/maven-downloader/24.2.1/maven-downloader-24.2.1.jar (30 kB at 52 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/word/24.2.1/word-24.2.1.jar (23 kB at 39 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/sdk/nativeimage/24.2.1/nativeimage-24.2.1.jar (230 kB at 340 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/graalvm/shadowed/jline/24.2.1/jline-24.2.1.jar (1.6 MB at 685 kB/s)
[INFO] Virtual filesystem is deployed to default resources directory 'org.graalvm.python.vfs'. This can cause conflicts if used with other Java libraries that also deploy GraalPy virtual filesystem. Consider adding <resourceDirectory>GRAALPY-VFS/${project.groupId}/${project.artifactId}</resourceDirectory> to your pom.xml, moving any existing sources from 'org.graalvm.python.vfs/src' to 'GRAALPY-VFS/com.ortofta/graalpy', and using VirtualFileSystem$Builder#resourceDirectory.For more details, please refer to https://www.graalvm.org/latest/reference-manual/python/Embedding-Build-Tools. 
[INFO] Generating GraalPy launchers
[INFO] Creating GraalPy 24.2.0 venv
[INFO] Running: /home/markus/Documents/java/graalpy/target/graalpy.sh -m venv /home/markus/Documents/java/graalpy/target/classes/org.graalvm.python.vfs/venv --without-pip
WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
[INFO] /home/markus/Documents/java/graalpy/target/classes/org.graalvm.python.vfs/venv/bin/graalpy -I -m ensurepip
WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
Looking in links: /tmp/tmp22hhkqlb
Processing /tmp/tmp22hhkqlb/setuptools-65.5.0-py3-none-any.whl
Processing /tmp/tmp22hhkqlb/pip-23.2.1-py3-none-any.whl
Installing collected packages: setuptools, pip
  Looking for GraalPy patches for setuptools
Successfully installed pip-23.2.1 setuptools-65.5.0
[INFO] /home/markus/Documents/java/graalpy/target/classes/org.graalvm.python.vfs/venv/bin/graalpy -m pip install docling==2.31.0 requests
WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
Looking in indexes: https://pypi.org/simple, https://www.graalvm.org/python/wheels/
Collecting docling==2.31.0
  Obtaining dependency information for docling==2.31.0 from https://files.pythonhosted.org/packages/7f/62/6aaf9263770df9716f9c8b56a9b2eb186440e54d327d8ea72bb0a7b1dc31/docling-2.31.0-py3-none-any.whl.metadata
  Using cached docling-2.31.0-py3-none-any.whl.metadata (10 kB)
Collecting requests
  Obtaining dependency information for requests from https://files.pythonhosted.org/packages/f9/9b/335f9764261e915ed497fcdeb11df5dfd6f7bf257d4a6a2a686d80da4d54/requests-2.32.3-py3-none-any.whl.metadata
  Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting beautifulsoup4<5.0.0,>=4.12.3 (from docling==2.31.0)
  Obtaining dependency information for beautifulsoup4<5.0.0,>=4.12.3 from https://files.pythonhosted.org/packages/50/cd/30110dc0ffcf3b131156077b90e9f60ed75711223f306da4db08eff8403b/beautifulsoup4-4.13.4-py3-none-any.whl.metadata
  Using cached beautifulsoup4-4.13.4-py3-none-any.whl.metadata (3.8 kB)
Collecting certifi>=2024.7.4 (from docling==2.31.0)
  Obtaining dependency information for certifi>=2024.7.4 from https://files.pythonhosted.org/packages/4a/7e/3db2bd1b1f9e95f7cddca6d6e75e2f2bd9f51b1246e546d88addca0106bd/certifi-2025.4.26-py3-none-any.whl.metadata
  Using cached certifi-2025.4.26-py3-none-any.whl.metadata (2.5 kB)
Collecting docling-core[chunking]<3.0.0,>=2.26.0 (from docling==2.31.0)
  Obtaining dependency information for docling-core[chunking]<3.0.0,>=2.26.0 from https://files.pythonhosted.org/packages/4e/34/d47dd1bc50a2810ed34ce9ba28e50f1e7dcfa39f52434ec97f466618eb3c/docling_core-2.29.0-py3-none-any.whl.metadata
  Using cached docling_core-2.29.0-py3-none-any.whl.metadata (6.0 kB)
Collecting docling-ibm-models<4.0.0,>=3.4.0 (from docling==2.31.0)
  Obtaining dependency information for docling-ibm-models<4.0.0,>=3.4.0 from https://files.pythonhosted.org/packages/2c/42/c672af0db176e27fe00aa02c4f3168bc639851381fea136e0d7530378309/docling_ibm_models-3.4.2-py3-none-any.whl.metadata
  Using cached docling_ibm_models-3.4.2-py3-none-any.whl.metadata (7.4 kB)
Collecting docling-parse<5.0.0,>=4.0.0 (from docling==2.31.0)
  Using cached docling_parse-4.0.1.tar.gz (36.6 MB)
  Looking for GraalPy patches for docling_parse
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting easyocr<2.0,>=1.7 (from docling==2.31.0)
  Obtaining dependency information for easyocr<2.0,>=1.7 from https://files.pythonhosted.org/packages/bb/84/4a2cab0e6adde6a85e7ba543862e5fc0250c51f3ac721a078a55cdcff250/easyocr-1.7.2-py3-none-any.whl.metadata
  Using cached easyocr-1.7.2-py3-none-any.whl.metadata (10 kB)
Collecting filetype<2.0.0,>=1.2.0 (from docling==2.31.0)
  Obtaining dependency information for filetype<2.0.0,>=1.2.0 from https://files.pythonhosted.org/packages/18/79/1b8fa1bb3568781e84c9200f951c735f3f157429f44be0495da55894d620/filetype-1.2.0-py2.py3-none-any.whl.metadata
  Using cached filetype-1.2.0-py2.py3-none-any.whl.metadata (6.5 kB)
Collecting huggingface_hub<1,>=0.23 (from docling==2.31.0)
  Obtaining dependency information for huggingface_hub<1,>=0.23 from https://files.pythonhosted.org/packages/93/27/1fb384a841e9661faad1c31cbfa62864f59632e876df5d795234da51c395/huggingface_hub-0.30.2-py3-none-any.whl.metadata
  Using cached huggingface_hub-0.30.2-py3-none-any.whl.metadata (13 kB)
Collecting lxml<6.0.0,>=4.0.0 (from docling==2.31.0)
  Using cached lxml-5.3.0.tar.gz (3.7 MB)
auto-patching C API usages in /tmp/pip-install-adv11b5f/lxml_86be3853b72149d28ecfee3f3226c134/src/lxml/_elementpath.c
auto-patching C API usages in /tmp/pip-install-adv11b5f/lxml_86be3853b72149d28ecfee3f3226c134/src/lxml/builder.c
auto-patching C API usages in /tmp/pip-install-adv11b5f/lxml_86be3853b72149d28ecfee3f3226c134/src/lxml/etree.c
auto-patching C API usages in /tmp/pip-install-adv11b5f/lxml_86be3853b72149d28ecfee3f3226c134/src/lxml/objectify.c
auto-patching C API usages in /tmp/pip-install-adv11b5f/lxml_86be3853b72149d28ecfee3f3226c134/src/lxml/sax.c
auto-patching C API usages in /tmp/pip-install-adv11b5f/lxml_86be3853b72149d28ecfee3f3226c134/src/lxml/html/diff.c
auto-patching C API usages in /tmp/pip-install-adv11b5f/lxml_86be3853b72149d28ecfee3f3226c134/src/lxml/includes/etree_defs.h
  Looking for GraalPy patches for lxml
  Patching package lxml using lxml-5.3.0.patch
patching file pyproject.toml
patching file setupinfo.py
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: still running...
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
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Collecting marko<3.0.0,>=2.1.2 (from docling==2.31.0)
  Obtaining dependency information for marko<3.0.0,>=2.1.2 from https://files.pythonhosted.org/packages/fc/43/c82e8f528887cec56f5afa9152c921b01f98deeffaf9e1bcc3e54e90c291/marko-2.1.3-py3-none-any.whl.metadata
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Collecting openpyxl<4.0.0,>=3.1.5 (from docling==2.31.0)
  Obtaining dependency information for openpyxl<4.0.0,>=3.1.5 from https://files.pythonhosted.org/packages/c0/da/977ded879c29cbd04de313843e76868e6e13408a94ed6b987245dc7c8506/openpyxl-3.1.5-py2.py3-none-any.whl.metadata
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Collecting pandas<3.0.0,>=2.1.4 (from docling==2.31.0)
  Using cached pandas-2.2.3.tar.gz (4.4 MB)
auto-patching C API usages in /tmp/pip-install-adv11b5f/pandas_9a117e2ac48a4214a0424298877c86a1/pandas/_libs/include/pandas/vendored/klib/khash_python.h
  Looking for GraalPy patches for pandas
  Patching package pandas using pandas-2.2.3.patch
patching file pandas/_libs/include/pandas/vendored/klib/khash_python.h
patching file pyproject.toml
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
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  Preparing metadata (pyproject.toml): started
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Collecting pillow<12.0.0,>=10.0.0 (from docling==2.31.0)
  Using cached pillow-11.2.1.tar.gz (47.0 MB)
auto-patching C API usages in /tmp/pip-install-adv11b5f/pillow_7b9e3969babc470397b0cae981e6ffb9/src/thirdparty/pythoncapi_compat.h
  Looking for GraalPy patches for pillow
  Installing build dependencies: started
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  Getting requirements to build wheel: started
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  Preparing metadata (pyproject.toml): started
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Collecting pluggy<2.0.0,>=1.0.0 (from docling==2.31.0)
  Obtaining dependency information for pluggy<2.0.0,>=1.0.0 from https://files.pythonhosted.org/packages/88/5f/e351af9a41f866ac3f1fac4ca0613908d9a41741cfcf2228f4ad853b697d/pluggy-1.5.0-py3-none-any.whl.metadata
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Collecting pydantic<3.0.0,>=2.0.0 (from docling==2.31.0)
  Obtaining dependency information for pydantic<3.0.0,>=2.0.0 from https://files.pythonhosted.org/packages/62/51/72c18c55cf2f46ff4f91ebcc8f75aa30f7305f3d726be3f4ebffb4ae972b/pydantic-2.10.3-py3-none-any.whl.metadata
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Collecting pydantic-settings<3.0.0,>=2.3.0 (from docling==2.31.0)
  Obtaining dependency information for pydantic-settings<3.0.0,>=2.3.0 from https://files.pythonhosted.org/packages/b6/5f/d6d641b490fd3ec2c4c13b4244d68deea3a1b970a97be64f34fb5504ff72/pydantic_settings-2.9.1-py3-none-any.whl.metadata
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Collecting pylatexenc<3.0,>=2.10 (from docling==2.31.0)
  Using cached pylatexenc-2.10.tar.gz (162 kB)
  Looking for GraalPy patches for pylatexenc
  Installing build dependencies: started
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Collecting pypdfium2<5.0.0,>=4.30.0 (from docling==2.31.0)
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  Looking for GraalPy patches for scipy
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Collecting tqdm<5.0.0,>=4.65.0 (from docling==2.31.0)
  Obtaining dependency information for tqdm<5.0.0,>=4.65.0 from https://files.pythonhosted.org/packages/d0/30/dc54f88dd4a2b5dc8a0279bdd7270e735851848b762aeb1c1184ed1f6b14/tqdm-4.67.1-py3-none-any.whl.metadata
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  Obtaining dependency information for typer<0.16.0,>=0.12.5 from https://files.pythonhosted.org/packages/48/20/9d953de6f4367163d23ec823200eb3ecb0050a2609691e512c8b95827a9b/typer-0.15.3-py3-none-any.whl.metadata
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  Obtaining dependency information for soupsieve>1.2 from https://files.pythonhosted.org/packages/e7/9c/0e6afc12c269578be5c0c1c9f4b49a8d32770a080260c333ac04cc1c832d/soupsieve-2.7-py3-none-any.whl.metadata
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Collecting latex2mathml<4.0.0,>=3.77.0 (from docling-core[chunking]<3.0.0,>=2.26.0->docling==2.31.0)
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auto-patching C API usages in /tmp/pip-install-adv11b5f/opencv-python-headless_3d4205bbab804a509f58946aba6443d6/opencv/modules/python/src2/pycompat.hpp
  Looking for GraalPy patches for opencv-python-headless
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Collecting torch<3.0.0,>=2.2.2 (from docling-ibm-models<4.0.0,>=3.4.0->docling==2.31.0)
  Using cached torch-2.4.1-graalpy311-graalpy242_311_native-linux_x86_64.whl
Collecting torchvision<1,>=0 (from docling-ibm-models<4.0.0,>=3.4.0->docling==2.31.0)
  Using cached https://github.com/pytorch/vision/archive/refs/tags/v0.19.1.tar.gz
  Looking for GraalPy patches for torchvision
  Patching package torchvision using torchvision-1.19.1.patch
patching file setup.py
patching file version.txt
  Installing build dependencies: started
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Collecting scikit-image (from easyocr<2.0,>=1.7->docling==2.31.0)
  Using cached scikit_image-0.25.2.tar.gz (22.7 MB)
  Looking for GraalPy patches for scikit_image
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  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [184 lines of output]
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      + meson setup /tmp/pip-install-adv11b5f/scikit-image_b77de0aca3d840609c44c42b66766ad7 /tmp/pip-install-adv11b5f/scikit-image_b77de0aca3d840609c44c42b66766ad7/.mesonpy-cjrxe539 -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-adv11b5f/scikit-image_b77de0aca3d840609c44c42b66766ad7/.mesonpy-cjrxe539/meson-python-native-file.ini
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to 
8000
the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      The Meson build system
      Version: 1.8.0
      Source dir: /tmp/pip-install-adv11b5f/scikit-image_b77de0aca3d840609c44c42b66766ad7
      Build dir: /tmp/pip-install-adv11b5f/scikit-image_b77de0aca3d840609c44c42b66766ad7/.mesonpy-cjrxe539
      Build type: native build
      Project name: scikit-image
      Project version: 0.25.2
      C compiler for the host machine: cc (gcc 11.5.0 "cc (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)")
      C linker for the host machine: cc ld.bfd 2.35.2-54
      C++ compiler for the host machine: c++ (gcc 11.5.0 "c++ (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)")
      C++ linker for the host machine: c++ ld.bfd 2.35.2-54
      Cython compiler for the host machine: cython (cython 3.0.11)
      Host machine cpu family: x86_64
      Host machine cpu: x86_64
      Compiler for C supports arguments -Wno-unused-function: YES
      Library m found: YES
      Checking if "-Wl,--version-script" links: YES
      Program cython found: YES (/tmp/pip-build-env-60havzky/overlay/bin/cython)
      Program pythran found: YES (/tmp/pip-build-env-60havzky/overlay/bin/pythran)
      Program cp found: YES (/usr/bin/cp)
      Program python found: YES (/home/markus/Documents/java/graalpy/target/classes/org.graalvm.python.vfs/venv/bin/graalpy)
      Run-time dependency python found: YES 3.11
      Program _build_utils/cythoner.py found: YES (/tmp/pip-install-adv11b5f/scikit-image_b77de0aca3d840609c44c42b66766ad7/skimage/_build_utils/cythoner.py)
      Compiler for C++ supports arguments -Wno-cpp: YES
      Build targets in project: 57
      
      scikit-image 0.25.2
      
        User defined options
          Native files: /tmp/pip-install-adv11b5f/scikit-image_b77de0aca3d840609c44c42b66766ad7/.mesonpy-cjrxe539/meson-python-native-file.ini
          b_ndebug    : if-release
          b_vscrt     : md
          buildtype   : release
      
      Found ninja-1.11.1.git.kitware.jobserver-1 at /tmp/pip-build-env-60havzky/normal/bin/ninja
      + /tmp/pip-build-env-60havzky/normal/bin/ninja
      [1/165] Generating skimage/feature/_brief_pythran with a custom command
      FAILED: skimage/feature/brief_cy.cpp
      /tmp/pip-build-env-60havzky/overlay/bin/pythran -E ../skimage/feature/brief_pythran.py -o skimage/feature/brief_cy.cpp
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      Traceback (most recent call last):
        File "/tmp/pip-build-env-60havzky/overlay/bin/pythran", line 8, in <module>
          sys.exit(run())
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/run.py", line 190, in run
          pythran.compile_pythranfile(args.input_file,
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/__init__.py", line 127, in __getattr__
          import pythran.toolchain
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/toolchain.py", line 6, in <module>
          from pythran.backend import Cxx, Python
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/backend.py", line 7, in <module>
          from pythran.analyses import LocalNodeDeclarations, GlobalDeclarations, Scope
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/analyses/__init__.py", line 12, in <module>
          from .aliases import Aliases, StrictAliases, InterproceduralAliases
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/analyses/aliases.py", line 6, in <module>
          from pythran.tables import functions, methods, MODULES
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/tables.py", line 4666, in <module>
          save_arguments((), MODULES)
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/tables.py", line 4600, in save_arguments
          save_arguments(module_name + (elem,), signature)
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/tables.py", line 4620, in save_arguments
          assert signature.args.args, "{} require an explicit description".format(elem)
      AssertionError: BaseException require an explicit description
      [2/165] Generating skimage/feature/_hessian_det_appx_pythran with a custom command
      FAILED: skimage/feature/_hessian_det_appx.cpp
      /tmp/pip-build-env-60havzky/overlay/bin/pythran -E ../skimage/feature/_hessian_det_appx_pythran.py -o skimage/feature/_hessian_det_appx.cpp
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      Traceback (most recent call last):
        File "/tmp/pip-build-env-60havzky/overlay/bin/pythran", line 8, in <module>
          sys.exit(run())
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/run.py", line 190, in run
          pythran.compile_pythranfile(args.input_file,
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/__init__.py", line 127, in __getattr__
          import pythran.toolchain
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/toolchain.py", line 6, in <module>
          from pythran.backend import Cxx, Python
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/backend.py", line 7, in <module>
          from pythran.analyses import LocalNodeDeclarations, GlobalDeclarations, Scope
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/analyses/__init__.py", line 12, in <module>
          from .aliases import Aliases, StrictAliases, InterproceduralAliases
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/analyses/aliases.py", line 6, in <module>
          from pythran.tables import functions, methods, MODULES
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/tables.py", line 4666, in <module>
          save_arguments((), MODULES)
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/tables.py", line 4600, in save_arguments
          save_arguments(module_name + (elem,), signature)
        File "/tmp/pip-build-env-60havzky/overlay/lib/python3.11/site-packages/pythran/tables.py", line 4620, in save_arguments
          assert signature.args.args, "{} require an explicit description".format(elem)
      AssertionError: BaseException require an explicit description
      [3/165] Generating 'skimage/_shared/fast_exp.graalpy242-311-native-x86_64-linux.so.p/fast_exp.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [4/165] Generating 'skimage/_shared/geometry.graalpy242-311-native-x86_64-linux.so.p/geometry.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [5/165] Generating 'skimage/feature/censure_cy.graalpy242-311-native-x86_64-linux.so.p/censure_cy.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [6/165] Generating 'skimage/feature/_hoghistogram.graalpy242-311-native-x86_64-linux.so.p/_hoghistogram.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [7/165] Generating 'skimage/_shared/transform.graalpy242-311-native-x86_64-linux.so.p/transform.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [8/165] Generating 'skimage/filters/_multiotsu.graalpy242-311-native-x86_64-linux.so.p/_multiotsu.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [9/165] Generating 'skimage/draw/_draw.graalpy242-311-native-x86_64-linux.so.p/_draw.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [10/165] Generating 'skimage/feature/_sift.graalpy242-311-native-x86_64-linux.so.p/_sift.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [11/165] Generating 'skimage/feature/corner_cy.graalpy242-311-native-x86_64-linux.so.p/corner_cy.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [12/165] Generating 'skimage/feature/_canny_cy.graalpy242-311-native-x86_64-linux.so.p/_canny_cy.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [13/165] Generating 'skimage/filters/rank/bilateral_cy.graalpy242-311-native-x86_64-linux.so.p/bilateral_cy.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [14/165] Generating 'skimage/feature/_haar.graalpy242-311-native-x86_64-linux.so.p/_haar.cpp'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [15/165] Generating 'skimage/_shared/interpolation.graalpy242-311-native-x86_64-linux.so.p/interpolation.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [16/165] Generating 'skimage/feature/orb_cy.graalpy242-311-native-x86_64-linux.so.p/orb_cy.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [17/165] Generating 'skimage/feature/_texture.graalpy242-311-native-x86_64-linux.so.p/_texture.c'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      [18/165] Generating 'skimage/feature/_cascade.graalpy242-311-native-x86_64-linux.so.p/_cascade.cpp'
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.0/truffle-api-24.2.0.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      ninja: build stopped: subcommand failed.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  50:34 min
[INFO] Finished at: 2025-05-05T18:50:41+02:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.graalvm.python:graalpy-maven-plugin:24.2.1:process-graalpy-resources (default) on project graalpy: Execution default of goal org.graalvm.python:graalpy-maven-plugin:24.2.1:process-graalpy-resources failed: Running command: '/home/markus/Documents/java/graalpy/target/classes/org.graalvm.python.vfs/venv/bin/graalpy -m pip install docling==2.31.0 requests' ended with code 1.See the error output above. -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException
➜  graalpy
@msimacek msimacek self-assigned this May 6, 2025
graalvmbot pushed a commit that referenced this issue May 7, 2025
@msimacek
Add patch for pythran 0.16+
38ef0e0 
Related #501
graalvmbot pushed a commit that referenced this issue May 16, 2025
@msimacek
Add patch for pythran 0.16+
b50b6bc 
Related #501
@msimacek
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I've added a patch that fixes the scikit-image dependency and backported it to our patch branch. You should be able to restart the build and the patch should be picked up automatically.

@Ortofta
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Ortofta commented May 19, 2025

Thank you.

I'm running into a different issue now - that seems to occur earlier than the previous error. I assume this worked before - do you have any idea about why this has started failing?

...
Collecting scipy<2.0.0,>=1.6.0 (from docling==2.31.0)
  Using cached scipy-1.13.1.tar.gz (57.2 MB)
  Looking for GraalPy patches for scipy
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Installing backend dependencies: started
  Installing backend dependencies: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'error'
  error: subprocess-exited-with-error
  
  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [39 lines of output]
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.1/truffle-api-24.2.1.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      + meson setup /tmp/pip-install-bx_d9eie/scipy_471afc2f06344171915d7fa4ee98c3de /tmp/pip-install-bx_d9eie/scipy_471afc2f06344171915d7fa4ee98c3de/.mesonpy-szh6owxq -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-bx_d9eie/scipy_471afc2f06344171915d7fa4ee98c3de/.mesonpy-szh6owxq/meson-python-native-file.ini
      WARNING: A terminally deprecated method in sun.misc.Unsafe has been called
      WARNING: sun.misc.Unsafe::objectFieldOffset has been called by com.oracle.truffle.api.dsl.InlineSupport$UnsafeField (file:/home/markus/.m2/repository/org/graalvm/truffle/truffle-api/24.2.1/truffle-api-24.2.1.jar)
      WARNING: Please consider reporting this to the maintainers of class com.oracle.truffle.api.dsl.InlineSupport$UnsafeField
      WARNING: sun.misc.Unsafe::objectFieldOffset will be removed in a future release
      The Meson build system
      Version: 1.8.0
      Source dir: /tmp/pip-install-bx_d9eie/scipy_471afc2f06344171915d7fa4ee98c3de
      Build dir: /tmp/pip-install-bx_d9eie/scipy_471afc2f06344171915d7fa4ee98c3de/.mesonpy-szh6owxq
      Build type: native build
      Project name: scipy
      Project version: 1.13.1
      C compiler for the host machine: cc (gcc 11.5.0 "cc (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)")
      C linker for the host machine: cc ld.bfd 2.35.2-63
      C++ compiler for the host machine: c++ (gcc 11.5.0 "c++ (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)")
      C++ linker for the host machine: c++ ld.bfd 2.35.2-63
      Cython compiler for the host machine: cython (cython 3.0.12)
      Host machine cpu family: x86_64
      Host machine cpu: x86_64
      Program python found: YES (/home/markus/Documents/java/graalpy/target/classes/org.graalvm.python.vfs/venv/bin/graalpy)
      Run-time dependency python found: YES 3.11
      Program cython found: YES (/tmp/pip-build-env-f20qo05i/overlay/bin/cython)
      Compiler for C supports arguments -Wno-unused-but-set-variable: YES
      Compiler for C supports arguments -Wno-unused-function: YES
      Compiler for C supports arguments -Wno-conversion: YES
      Compiler for C supports arguments -Wno-misleading-indentation: YES
      Library m found: YES
      Fortran compiler for the host machine: gfortran (gcc 11.5.0 "GNU Fortran (GCC) 11.5.0 20240719 (Red Hat 11.5.0-5)")
      Fortran linker for the host machine: gfortran ld.bfd 2.35.2-63
      Compiler for Fortran supports arguments -Wno-conversion: YES
      Checking if "-Wl,--version-script" links: YES
      
      ../meson.build:138:12: ERROR: Command `/tmp/pip-build-env-f20qo05i/overlay/bin/pythran --version` failed with status 1.
      
      A full log can be found at /tmp/pip-install-bx_d9eie/scipy_471afc2f06344171915d7fa4ee98c3de/.mesonpy-szh6owxq/meson-logs/meson-log.txt
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  17:11 min
[INFO] Finished at: 2025-05-19T21:22:33+02:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.graalvm.python:graalpy-maven-plugin:24.2.1:process-graalpy-resources (default) on project graalpy: Execution default of goal org.graalvm.python:graalpy-maven-plugin:24.2.1:process-graalpy-resources failed: Running command: '/home/markus/Documents/java/graalpy/target/classes/org.graalvm.python.vfs/venv/bin/graalpy -m pip install docling==2.31.0 pythran==0.17.0 requests' ended with code 1.See the error output above. -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginExecutionException
➜  graalpy

@msimacek
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It seems that it's because numpy was updated and older pythran pulled in by older scipy doesn't work with it. I'll need to remove the pinning of the older scipy version. Can you try to force a newer scipy version? pip install scipy==1.15.3 docling==2.31.0

@Ortofta
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Ortofta commented May 20, 2025 •
edited
Loading

Thanks for the advice - I tried setting scipy to 1.15.3, but unfortunately I ran into some other issue with that:

Build targets in project: 195

 scipy 1.15.3
      
        Subprojects
          highs       : YES
      
        User defined options
          Native files: /tmp/pip-install-3dyu93s4/scipy_577eccdc972a4756944501d0ab7aa1ef/.mesonpy-59ppso_q/meson-python-native-file.ini
          b_ndebug    : if-release
          b_vscrt     : md
          buildtype   : release
      
      Found ninja-1.11.1.git.kitware.jobserver-1 at /tmp/pip-build-env-8fvt6aih/normal/bin/ninja
      + /tmp/pip-build-env-8fvt6aih/normal/bin/ninja
      [1/1490] Compiling C object scipy/_lib/_fpumode.graalpy242-311-native-x86_64-linux.so.p/_fpumode.c.o
      [2/1490] Compiling C object scipy/libdummy_g77_abi_wrappers.a.p/_build_utils_src_wrap_dummy_g77_abi.c.o
      [3/1490] Linking target scipy/_lib/_fpumode.graalpy242-311-native-x86_64-linux.so
      [4/1490] Linking static target scipy/libdummy_g77_abi_wrappers.a
      [5/1490] Compiling C object scipy/_lib/_test_ccallback.graalpy242-311-native-x86_64-linux.so.p/src__test_ccallback.c.o
      [6/1490] Linking target scipy/_lib/_test_ccallback.graalpy242-311-native-x86_64-linux.so
      [7/1490] Compiling C++ object scipy/_lib/_uarray/_uarray.graalpy242-311-native-x86_64-linux.so.p/vectorcall.cxx.o
      [8/1490] Compiling C object scipy/lib_fortranobject.a.p/eb2f5de13bf05c239f2cf069537172d13c4be000_site-packages_numpy_f2py_src_fortranobject.c.o
      [9/1490] Linking static target scipy/lib_fortranobject.a
      [10/1490] Compiling C++ object scipy/_lib/_uarray/_uarray.graalpy242-311-native-x86_64-linux.so.p/_uarray_dispatch.cxx.o
      [11/1490] Linking target scipy/_lib/_uarray/_uarray.graalpy242-311-native-x86_64-linux.so
      [12/1490] Copying file scipy/special/_agm.pxd
      [13/1490] Copying file scipy/special/_cdflib_wrappers.pxd
      [14/1490] Copying file scipy/_lib/messagestream.pxd
      [15/1490] Copying file scipy/special/_cunity.pxd
      [16/1490] Copying file scipy/_lib/_ccallback_c.pxd
      [17/1490] Copying file scipy/special/_boxcox.pxd
      [18/1490] Copying file scipy/_lib/ccallback.pxd
      [19/1490] Copying file scipy/special/_ellipk.pxd
      [20/1490] Copying file scipy/_lib/__init__.py
      [21/1490] Copying file scipy/special/_complexstuff.pxd
      [22/1490] Compiling C object scipy/special/libsf_error_state.so.p/sf_error_state.c.o
      [23/1490] Copying file scipy/special/_ellip_harm_2.pxd
      [24/1490] Copying file scipy/special/_ellip_harm.pxd
      [25/1490] Linking target scipy/special/libsf_error_state.so
      [26/1490] Copying file scipy/special/__init__.py
      [27/1490] Copying file scipy/special/_hyp0f1.pxd
      [28/1490] Compiling C++ object scipy/special/_special_ufuncs.graalpy242-311-native-x86_64-linux.so.p/_special_ufuncs_docs.cpp.o
      [29/1490] Copying file scipy/__init__.py
      [30/1490] Copying file scipy/special/_convex_analysis.pxd
      [31/1490] Copying file scipy/special/_factorial.pxd
      [32/1490] Compiling C++ object scipy/special/_special_ufuncs.graalpy242-311-native-x86_64-linux.so.p/sf_error.cc.o
      [33/1490] Compiling C object scipy/special/libcdflib.a.p/cdflib.c.o
      [34/1490] Linking static target scipy/special/libcdflib.a
      [35/1490] Compiling C++ object scipy/special/_gufuncs.graalpy242-311-native-x86_64-linux.so.p/_gufuncs_docs.cpp.o
      [36/1490] Copying file scipy/special/_hypergeometric.pxd
      [37/1490] Compiling C++ object scipy/special/_gufuncs.graalpy242-311-native-x86_64-linux.so.p/sf_error.cc.o
      [38/1490] Copying file scipy/special/_legacy.pxd
      [39/1490] Copying file scipy/special/_xlogy.pxd
      [40/1490] Copying file scipy/special/_sici.pxd
      [41/1490] Compiling C object scipy/special/_ufuncs.graalpy242-311-native-x86_64-linux.so.p/_cosine.c.o
      [42/1490] Copying file scipy/special/_ufuncs_extra_code_common.pxi
      [43/1490] Copying file scipy/special/_ndtri_exp.pxd
      [44/1490] Copying file scipy/special/orthogonal_eval.pxd
      [45/1490] Copying file scipy/special/_ufuncs_extra_code.pxi
      [46/1490] Generating symbol file scipy/special/libsf_error_state.so.p/libsf_error_state.so.symbols
      [47/1490] Compiling C++ object scipy/special/_ufuncs_cxx.graalpy242-311-native-x86_64-linux.so.p/_faddeeva.cxx.o
      [48/1490] Compiling C++ object scipy/special/_ufuncs_cxx.graalpy242-311-native-x86_64-linux.so.p/_wright.cxx.o
      [49/1490] Copying file scipy/special/sf_error.pxd
      [50/1490] Compiling C++ object scipy/special/_ufuncs.graalpy242-311-native-x86_64-linux.so.p/sf_error.cc.o
      [51/1490] Copying file scipy/special/_spence.pxd
      [52/1490] Compiling C++ object scipy/special/_ufuncs.graalpy242-311-native-x86_64-linux.so.p/dd_real_wrappers.cpp.o
      [53/1490] Compiling C object scipy/special/cython_special.graalpy242-311-native-x86_64-linux.so.p/_cosine.c.o
      [54/1490] Compiling C++ object scipy/special/_ufuncs_cxx.graalpy242-311-native-x86_64-linux.so.p/sf_error.cc.o
      [55/1490] Compiling C++ object scipy/special/_ellip_harm_2.graalpy242-311-native-x86_64-linux.so.p/sf_error.cc.o
      [56/1490] Compiling C++ object scipy/special/_ufuncs_cxx.graalpy242-311-native-x86_64-linux.so.p/Faddeeva.cc.o
      [57/1490] Compiling C++ object scipy/special/_ufuncs_cxx.graalpy242-311-native-x86_64-linux.so.p/wright.cc.o
      [58/1490] Compiling C++ object scipy/special/cython_special.graalpy242-311-native-x86_64-linux.so.p/sf_error.cc.o
      [59/1490] Compiling C++ object scipy/special/cython_special.graalpy242-311-native-x86_64-linux.so.p/dd_real_wrappers.cpp.o
      [60/1490] Compiling C++ object scipy/special/_test_internal.graalpy242-311-native-x86_64-linux.so.p/dd_real_wrappers.cpp.o
      [61/1490] Generating scipy/special/cython_special with a custom command
      [62/1490] Compiling C++ object scipy/special/_ufuncs_cxx.graalpy242-311-native-x86_64-linux.so.p/ellint_carlson_wrap.cxx.o
      [63/1490] Copying file scipy/special/cython_special.pxd
      [64/1490] Copying file scipy/special/__init__.pxd
      [65/1490] Compiling C++ object scipy/special/_gufuncs.graalpy242-311-native-x86_64-linux.so.p/_gufuncs.cpp.o
      [66/1490] Linking target scipy/special/_gufuncs.graalpy242-311-native-x86_64-linux.so
      [67/1490] Generating 'scipy/_lib/_test_deprecation_call.graalpy242-311-native-x86_64-linux.so.p/_test_deprecation_call.c'
      [68/1490] Compiling C object scipy/_lib/_test_deprecation_call.graalpy242-311-native-x86_64-linux.so.p/meson-generated__test_deprecation_call.c.o
      [69/1490] Linking target scipy/_lib/_test_deprecation_call.graalpy242-311-native-x86_64-linux.so
      [70/1490] Copying file scipy/linalg/__init__.py
      [71/1490] Generating 'scipy/_lib/_test_deprecation_def.graalpy242-311-native-x86_64-linux.so.p/_test_deprecation_def.c'
      [72/1490] Compiling C++ object scipy/special/_ufuncs.graalpy242-311-native-x86_64-linux.so.p/xsf_wrappers.cpp.o
      [73/1490] Compiling C object scipy/_lib/_test_deprecation_def.graalpy242-311-native-x86_64-linux.so.p/meson-generated__test_deprecation_def.c.o
      [74/1490] Linking target scipy/_lib/_test_deprecation_def.graalpy242-311-native-x86_64-linux.so
      [75/1490] Generating scipy/special/_data_gsl with a custom command
      [76/1490] Generating scipy/special/_data_local with a custom command
      [77/1490] Compiling C++ object scipy/special/cython_special.graalpy242-311-native-x86_64-linux.so.p/xsf_wrappers.cpp.o
      [78/1490] Copying file scipy/linalg/_cythonized_array_utils.pxd
      [79/1490] Generating scipy/special/_data_boost with a custom command
      [80/1490] Copying file scipy/linalg/__init__.pxd
      [81/1490] Compiling C object scipy/linalg/_matfuncs_expm.graalpy242-311-native-x86_64-linux.so.p/_matfuncs_expm.c.o
      [82/1490] Generating 'scipy/_lib/_ccallback_c.graalpy242-311-native-x86_64-linux.so.p/_ccallback_c.c'
      [83/1490] Compiling C++ object scipy/special/_special_ufuncs.graalpy242-311-native-x86_64-linux.so.p/_special_ufuncs.cpp.o
      [84/1490] Linking target scipy/special/_special_ufuncs.graalpy242-311-native-x86_64-linux.so
      [85/1490] Linking target scipy/linalg/_matfuncs_expm.graalpy242-311-native-x86_64-linux.so
      [86/1490] Compiling C object scipy/_lib/_ccallback_c.graalpy242-311-native-x86_64-linux.so.p/meson-generated__ccallback_c.c.o
      [87/1490] Linking target scipy/_lib/_ccallback_c.graalpy242-311-native-x86_64-linux.so
      [88/1490] Generating scipy/linalg/_decomp_update with a custom command
      [89/1490] Generating scipy/linalg/cython_linalg with a custom command
      [90/1490] Generating 'scipy/special/_comb.graalpy242-311-native-x86_64-linux.so.p/_comb.c'
      [91/1490] Generating scipy/sparse/_csparsetools_pyx with a custom command
      [92/1490] Generating 'scipy/_lib/messagestream.graalpy242-311-native-x86_64-linux.so.p/messagestream.c'
      [93/1490] Compiling C object scipy/special/_comb.graalpy242-311-native-x86_64-linux.so.p/meson-generated__comb.c.o
      [94/1490] Linking target scipy/special/_comb.graalpy242-311-native-x86_64-linux.so
      [95/1490] Compiling C object scipy/_lib/messagestream.graalpy242-311-native-x86_64-linux.so.p/meson-generated_messagestream.c.o
      [96/1490] Linking target scipy/_lib/messagestream.graalpy242-311-native-x86_64-linux.so
      [97/1490] Generating scipy/sparse/sparsetools/_sparsetools_headers with a custom command
      [98/1490] Generating 'scipy/special/_specfun.graalpy242-311-native-x86_64-linux.so.p/_specfun.cpp'
      [99/1490] Generating 'scipy/linalg/_linalg_pythran.graalpy242-311-native-x86_64-linux.so.p/_linalg_pythran.cpp'
      FAILED: scipy/linalg/_linalg_pythran.graalpy242-311-native-x86_64-linux.so.p/_linalg_pythran.cpp
      /tmp/pip-build-env-8fvt6aih/overlay/bin/pythran -E ../scipy/linalg/_linalg_pythran.py -o scipy/linalg/_linalg_pythran.graalpy242-311-native-x86_64-linux.so.p/_linalg_pythran.cpp
      Traceback (most recent call last):
        File "/tmp/pip-build-env-8fvt6aih/overlay/bin/pythran", line 8, in <module>
          sys.exit(run())
        File "/tmp/pip-build-env-8fvt6aih/overlay/lib/python3.11/site-packages/pythran/run.py", line 190, in run
          pythran.compile_pythranfile(args.input_file,
        File "/tmp/pip-build-env-8fvt6aih/overlay/lib/python3.11/site-packages/pythran/__init__.py", line 127, in __getattr__
          import pythran.toolchain
        File "/tmp/pip-build-env-8fvt6aih/overlay/lib/python3.11/site-packages/pythran/toolchain.py", line 6, in <module>
          from pythran.backend import Cxx, Python
        File "/tmp/pip-build-env-8fvt6aih/overlay/lib/python3.11/site-packages/pythran/backend.py", line 7, in <module>
          from pythran.analyses import LocalNodeDeclarations, GlobalDeclarations, Scope
        File "/tmp/pip-build-env-8fvt6aih/overlay/lib/python3.11/site-packages/pythran/analyses/__init__.py", line 12, in <module>
          from .aliases import Aliases, StrictAliases, InterproceduralAliases
        File "/tmp/pip-build-env-8fvt6aih/overlay/lib/python3.11/site-packages/pythran/analyses/aliases.py", line 6, in <module>
          from pythran.tables import functions, methods, MODULES
        File "/tmp/pip-build-env-8fvt6aih/overlay/lib/python3.11/site-packages/pythran/tables.py", line 4570, in <module>
          if not hasattr(numpy, method):
        File "/tmp/pip-build-env-8fvt6aih/overlay/lib/python3.11/site-packages/numpy/
83ED
__init__.py", line 400, in __getattr__
          raise AttributeError(
      TypeError: AttributeError takes no keyword arguments
      [100/1490] Copying file scipy/sparse/csgraph/parameters.pxi
      [101/1490] Scanning target lib__spropack for modules
      [102/1490] Compiling C++ object scipy/special/_specfun.graalpy242-311-native-x86_64-linux.so.p/meson-generated__specfun.cpp.o
      [103/1490] Generating 'scipy/special/_ufuncs_cxx.graalpy242-311-native-x86_64-linux.so.p/_ufuncs_cxx.cpp'
      [104/1490] Generating 'scipy/special/_test_internal.graalpy242-311-native-x86_64-linux.so.p/_test_internal.c'
      [105/1490] Generating 'scipy/special/_ellip_harm_2.graalpy242-311-native-x86_64-linux.so.p/_ellip_harm_2.c'
      [106/1490] Generating 'scipy/linalg/_matfuncs_sqrtm_triu.graalpy242-311-native-x86_64-linux.so.p/_matfuncs_sqrtm_triu.c'
      [107/1490] Generating 'scipy/linalg/_solve_toeplitz.graalpy242-311-native-x86_64-linux.so.p/_solve_toeplitz.c'
      [108/1490] Generating scipy/linalg/fblas_module with a custom command
      [109/1490] Generating 'scipy/linalg/cython_blas.graalpy242-311-native-x86_64-linux.so.p/cython_blas.c'
      [110/1490] Generating 'scipy/linalg/_decomp_lu_cython.graalpy242-311-native-x86_64-linux.so.p/_decomp_lu_cython.c'
      [111/1490] Generating 'scipy/linalg/_decomp_interpolative.graalpy242-311-native-x86_64-linux.so.p/_decomp_interpolative.c'
      [112/1490] Generating 'scipy/linalg/_decomp_update.graalpy242-311-native-x86_64-linux.so.p/_decomp_update.c'
      [113/1490] Generating 'scipy/special/_ufuncs.graalpy242-311-native-x86_64-linux.so.p/_ufuncs.c'
      [114/1490] Generating 'scipy/special/cython_special.graalpy242-311-native-x86_64-linux.so.p/cython_special.c'
      [115/1490] Generating 'scipy/linalg/cython_lapack.graalpy242-311-native-x86_64-linux.so.p/cython_lapack.c'
      [116/1490] Generating scipy/linalg/flapack_module with a custom command
      ninja: build stopped: subcommand failed.
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  10:24 min
[INFO] Finished at: 2025-05-20T17:48:45+02:00
[INFO] ------------------------------------------------------------------------

@msimacek
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Right, sorry, that bug is fixed on master, but not in the release. I'll try to add a workaround to the patch branch, gimme a few days

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