ERROR: pip's dependency resolver does not currently take into account all the packages that are installed

[konosubakonoakua]

• PYNQ version : 3.1.2
• Board name : Pynq-Z1
• Pull request type : bug fix
• Pull request number:
• Description:
  Here's the build log on ubuntu 22.04 with vivado & petalinux 2024.1 toolchains.

+ python3 -m pip install --upgrade git+https://github.com/Xilinx/PYNQ-Utils.git
Collecting git+https://github.com/Xilinx/PYNQ-Utils.git
  Cloning https://github.com/Xilinx/PYNQ-Utils.git to /tmp/pip-req-build-d4m0twdw
  Running command git clone --filter=blob:none --quiet https://github.com/Xilinx/PYNQ-Utils.git /tmp/pip-req-build-d4m0twdw
  Resolved https://github.com/Xilinx/PYNQ-Utils.git to commit abb0b4dd3052dae68c878603a44fb7ff7e1f9b80
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: python-magic>=0.4.25 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pynqutils==0.1.2) (0.4.27)
Requirement already satisfied: numpy<2.0 in /usr/lib/python3/dist-packages (from pynqutils==0.1.2) (1.21.5)
Requirement already satisfied: pynqmetadata>=0.0.1 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pynqutils==0.1.2) (0.1.9)
Requirement already satisfied: tqdm in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pynqutils==0.1.2) (4.64.0)
Requirement already satisfied: cffi in /usr/lib/python3/dist-packages (from pynqutils==0.1.2) (1.15.0)
Requirement already satisfied: setuptools<=80 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pynqutils==0.1.2) (59.6.0)
Requirement already satisfied: ipython in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pynqmetadata>=0.0.1->pynqutils==0.1.2) (8.4.0)
Requirement already satisfied: jsonschema>=3.2.0 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pynqmetadata>=0.0.1->pynqutils==0.1.2) (4.9.0)
Requirement already satisfied: pydantic==1.9.1 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pynqmetadata>=0.0.1->pynqutils==0.1.2) (1.9.1)
Requirement already satisfied: typing-extensions>=3.7.4.3 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pydantic==1.9.1->pynqmetadata>=0.0.1->pynqutils==0.1.2) (4.3.0)
Requirement already satisfied: attrs>=17.4.0 in /usr/lib/python3/dist-packages (from jsonschema>=3.2.0->pynqmetadata>=0.0.1->pynqutils==0.1.2) (21.2.0)
Requirement already satisfied: pyrsistent!=0.17.0,!=0.17.1,!=0.17.2,>=0.14.0 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from jsonschema>=3.2.0->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.18.1)
Requirement already satisfied: pygments>=2.4.0 in /usr/lib/python3/dist-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (2.11.2)
Requirement already satisfied: prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (3.0.30)
Requirement already satisfied: pexpect>4.3 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (4.8.0)
Requirement already satisfied: backcall in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.2.0)
Requirement already satisfied: decorator in /usr/lib/python3/dist-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (4.4.2)
Requirement already satisfied: pickleshare in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.7.5)
Requirement already satisfied: stack-data in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.3.0)
Requirement already satisfied: traitlets>=5 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (5.3.0)
Requirement already satisfied: jedi>=0.16 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.18.1)
Requirement already satisfied: matplotlib-inline in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.1.3)
Requirement already satisfied: parso<0.9.0,>=0.8.0 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from jedi>=0.16->ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.8.3)
Requirement already satisfied: ptyprocess>=0.5 in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from pexpect>4.3->ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.7.0)
Requirement already satisfied: wcwidth in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0->ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.2.5)
Requirement already satisfied: asttokens in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from stack-data->ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (2.0.5)
Requirement already satisfied: executing in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from stack-data->ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.9.1)
Requirement already satisfied: pure-eval in /usr/local/share/pynq-venv/lib/python3.10/site-packages (from stack-data->ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (0.2.2)
Requirement already satisfied: six in /usr/lib/python3/dist-packages (from asttokens->stack-data->ipython->pynqmetadata>=0.0.1->pynqutils==0.1.2) (1.16.0)
Building wheels for collected packages: pynqutils
  Building wheel for pynqutils (pyproject.toml) ... done
  Created wheel for pynqutils: filename=pynqutils-0.1.2-py3-none-any.whl size=30458 sha256=3bbda1c42d23098c8d6b7acccd7be0b4e37d2d8a9e25735d1a85b49804f31ebc
  Stored in directory: /tmp/pip-ephem-wheel-cache-j87c264h/wheels/d3/6e/7f/ac713ae44465a8201e103f0e640944095a042e5fc3ea787938
Successfully built pynqutils
Installing collected packages: pynqutils
  Attempting uninstall: pynqutils
    Found existing installation: pynqutils 0.1.1
    Uninstalling pynqutils-0.1.1:
      Successfully uninstalled pynqutils-0.1.1
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
pynq 3.1.0 requires grpcio==1.64.0, which is not installed.
pynq 3.1.0 requires grpcio-tools==1.64.0, which is not installed.
Successfully installed pynqutils-0.1.2
WARNING: You are using pip version 22.0.2; however, version 25.3 is available.
You should consider upgrading via the '/usr/local/share/pynq-venv/bin/python3 -m pip install --upgrade pip' command.

BTW, there's an error when generating final image:

WARNING: bootloader config not specified, using defaults

INFO: The new image(s) can be found here:
  /home/pynq/Documents/PYNQ/sdbuild/build/Pynq-Z1/petalinux_project/build/wic/wic-tmp/image-202511070955-mmcblk0.direct

The following build artifacts were used to create the image(s):
  ROOTFS_DIR:                   /home/pynq/Documents/PYNQ/sdbuild/build/Pynq-Z1/petalinux_project/build/wic/rootfs
  BOOTIMG_DIR:                  /home/pynq/Documents/PYNQ/sdbuild/build/jammy.Pynq-Z1
  KERNEL_DIR:                   /home/pynq/Documents/PYNQ/sdbuild/build/jammy.Pynq-Z1
  NATIVE_SYSROOT:               /home/pynq/Documents/PYNQ/sdbuild/build/Pynq-Z1/petalinux_project/build/tmp/work/cortexa9t2hf-neon-xilinx-linux-gnueabi/wic-tools/1.0-r0/recipe-sysroot-native

INFO: The image(s) were created using OE kickstart file:
  /home/pynq/Documents/PYNQ/sdbuild/boot/image.wks
[ERROR] list index out of range
make: [Makefile:433: /home/pynq/Documents/PYNQ/sdbuild/output/Pynq-Z1-3.1.2.img] Error 1 (ignored)
mv /home/pynq/Documents/PYNQ/sdbuild/build/Pynq-Z1/petalinux_project/build/wic/wic-tmp/image-*.direct /home/pynq/Documents/PYNQ/sdbuild/output/Pynq-Z1-3.1.2.img
mkdir -p /home/pynq/Documents/PYNQ/sdbuild/output/dist
mkdir -p /home/pynq/Documents/PYNQ/sdbuild/output/dist/arm
cp -rf /home/pynq/Documents/PYNQ/sdbuild/prebuilt/pynq_sdist.tar.gz /home/pynq/Documents/PYNQ/sdbuild/output/dist/arm

[konosubakonoakua]

Here's the entire log file:

pynq.log

[jogomojo]

Hi @konosubakonoakua

For your PIP question: can you try running pip3 install --upgrade --upgrade-strategy only-if-needed pynq as sudo. If that doesn't work try PIP's --no-build-isolation argument.

For your image generation question: this error is a known issue with Petalinux and can be safely ignored. The image still builds correctly.