1. 症状

docker build 中に、 scipy の build に失敗する。

2. Dependencies

以下のどの docker image でも、この記事の方法で対処できていた。

Item	Version
docker image	`python:3.13.8-slim-trixie` or `python:3.12.12-slim-trixie` or `python:3.11.14-slim-trixie` or `python:3.10.19-trixie`
scipy	1.13.1

3. 解決策

記事のタイトルの通りのエラーであれば、以下の対処法で解決可能です。

Dockerfile

RUN apt -y update && apt -y upgrade
RUN apt -y install --no-install-recommends gfortran libopenblas-dev

細かいことはどうでもいいという人は、 Dockerfile に上記記述を書いてささっと解決してしまいましょう！

エラー文から原因を特定する方法を知りたい方は、「4.」以下も見てみてください。

4. 具体的な問題と対処法

以下のようなエラーログが出ている場合、この記事の対処法で対処できると思います。

エラーは何種類かありましたので、それぞれ確認してみてください。

3-1. エラー1

#0 86.18 Collecting scipy==1.13.1 (from -r requirements.txt (line 2))
#0 86.20   Downloading scipy-1.13.1.tar.gz (57.2 MB)
#0 87.02      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.2/57.2 MB 69.7 MB/s  0:00:00
#0 89.08   Installing build dependencies: started
#0 96.28   Installing build dependencies: finished with status 'done'
#0 96.29   Getting requirements to build wheel: started
#0 96.37   Getting requirements to build wheel: finished with status 'done'
#0 96.37   Installing backend dependencies: started
#0 97.55   Installing backend dependencies: finished with status 'done'
#0 97.55   Preparing metadata (pyproject.toml): started
#0 99.08   Preparing metadata (pyproject.toml): finished with status 'error'
#0 99.08   error: subprocess-exited-with-error
#0 99.08   
#0 99.08   × Preparing metadata (pyproject.toml) did not run successfully.
#0 99.08   │ exit code: 1
#0 99.08   ╰─> [53 lines of output]
#0 99.08       + meson setup /tmp/pip-install-t3cicjw2/scipy_9675f3f9e3d448c9b4bfb489c59e15be /tmp/pip-install-t3cicjw2/scipy_9675f3f9e3d448c9b4bfb489c59e15be/.mesonpy-zlcn5vht -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-t3cicjw2/scipy_9675f3f9e3d448c9b4bfb489c59e15be/.mesonpy-zlcn5vht/meson-python-native-file.ini
#0 99.08       The Meson build system
#0 99.08       Version: 1.9.1
#0 99.08       Source dir: /tmp/pip-install-t3cicjw2/scipy_9675f3f9e3d448c9b4bfb489c59e15be
#0 99.08       Build dir: /tmp/pip-install-t3cicjw2/scipy_9675f3f9e3d448c9b4bfb489c59e15be/.mesonpy-zlcn5vht
#0 99.08       Build type: native build
#0 99.08       Project name: scipy
#0 99.08       Project version: 1.13.1
#0 99.08       C compiler for the host machine: cc (gcc 14.2.0 "cc (Debian 14.2.0-19) 14.2.0")
#0 99.08       C linker for the host machine: cc ld.bfd 2.44
#0 99.08       C++ compiler for the host machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-19) 14.2.0")
#0 99.08       C++ linker for the host machine: c++ ld.bfd 2.44
#0 99.08       Cython compiler for the host machine: cython (cython 3.0.12)
#0 99.08       Host machine cpu family: aarch64
#0 99.08       Host machine cpu: aarch64
#0 99.08       Program python found: YES (/usr/local/bin/python3.13)
#0 99.08       Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1
#0 99.08       Run-time dependency python found: YES 3.13
#0 99.08       Program cython found: YES (/tmp/pip-build-env-nr672swj/overlay/bin/cython)
#0 99.08       Compiler for C supports arguments -Wno-unused-but-set-variable: YES
#0 99.08       Compiler for C supports arguments -Wno-unused-function: YES
#0 99.08       Compiler for C supports arguments -Wno-conversion: YES
#0 99.08       Compiler for C supports arguments -Wno-misleading-indentation: YES
#0 99.08       Library m found: YES
#0 99.08       
#0 99.08       ../meson.build:78:0: ERROR: Unknown compiler(s): [['gfortran'], ['flang-new'], ['flang'], ['nvfortran'], ['pgfortran'], ['ifort'], ['ifx'], ['g95']]
#0 99.08       The following exception(s) were encountered:
#0 99.08       Running `gfortran --help` gave "[Errno 2] No such file or directory: 'gfortran'"
#0 99.08       Running `gfortran --version` gave "[Errno 2] No such file or directory: 'gfortran'"
#0 99.08       Running `gfortran -V` gave "[Errno 2] No such file or directory: 'gfortran'"
#0 99.08       Running `flang-new --help` gave "[Errno 2] No such file or directory: 'flang-new'"
#0 99.08       Running `flang-new --version` gave "[Errno 2] No such file or directory: 'flang-new'"
#0 99.08       Running `flang-new -V` gave "[Errno 2] No such file or directory: 'flang-new'"
#0 99.08       Running `flang --help` gave "[Errno 2] No such file or directory: 'flang'"
#0 99.08       Running `flang --version` gave "[Errno 2] No such file or directory: 'flang'"
#0 99.08       Running `flang -V` gave "[Errno 2] No such file or directory: 'flang'"
#0 99.08       Running `nvfortran --help` gave "[Errno 2] No such file or directory: 'nvfortran'"
#0 99.08       Running `nvfortran --version` gave "[Errno 2] No such file or directory: 'nvfortran'"
#0 99.08       Running `nvfortran -V` gave "[Errno 2] No such file or directory: 'nvfortran'"
#0 99.08       Running `pgfortran --help` gave "[Errno 2] No such file or directory: 'pgfortran'"
#0 99.08       Running `pgfortran --version` gave "[Errno 2] No such file or directory: 'pgfortran'"
#0 99.08       Running `pgfortran -V` gave "[Errno 2] No such file or directory: 'pgfortran'"
#0 99.08       Running `ifort --help` gave "[Errno 2] No such file or directory: 'ifort'"
#0 99.08       Running `ifort --version` gave "[Errno 2] No such file or directory: 'ifort'"
#0 99.08       Running `ifort -V` gave "[Errno 2] No such file or directory: 'ifort'"
#0 99.08       Running `ifx --help` gave "[Errno 2] No such file or directory: 'ifx'"
#0 99.08       Running `ifx --version` gave "[Errno 2] No such file or directory: 'ifx'"
#0 99.08       Running `ifx -V` gave "[Errno 2] No such file or directory: 'ifx'"
#0 99.08       Running `g95 --help` gave "[Errno 2] No such file or directory: 'g95'"
#0 99.08       Running `g95 --version` gave "[Errno 2] No such file or directory: 'g95'"
#0 99.08       Running `g95 -V` gave "[Errno 2] No such file or directory: 'g95'"
#0 99.08       
#0 99.08       A full log can be found at /tmp/pip-install-t3cicjw2/scipy_9675f3f9e3d448c9b4bfb489c59e15be/.mesonpy-zlcn5vht/meson-logs/meson-log.txt
#0 99.08       [end of output]
#0 99.08   
#0 99.08   note: This error originates from a subprocess, and is likely not a problem with pip.
#0 99.09 error: metadata-generation-failed
#0 99.09 
#0 99.09 × Encountered error while generating package metadata.
#0 99.09 ╰─> See above for output.
#0 99.09 
#0 99.09 note: This is an issue with the package mentioned above, not pip.
#0 99.09 hint: See above for details.
------
failed to solve: executor failed running [/bin/sh -c pip install -r requirements.txt]: exit code: 1

ダラダラとエラー文が吐かれますが、重要なのはここです。

../meson.build:78:0: ERROR: Unknown compiler(s): [['gfortran'], ['flang-new'], ['flang'], ['nvfortran'], ['pgfortran'], ['ifort'], ['ifx'], ['g95']]

上記の8つのパッケージが足りないようです。
まずは gfortran から用意してあげましょう。

以下の記述を Dockerfile に入れることで、 gfortran を Docker イメージに入れてあげることができます。pip install よりも先にこの gfortran がインストールされるようにしましょう。

Dockerfile

RUN apt -y update && apt -y upgrade
RUN apt -y install --no-install-recommends gfortran

これにより、 gfortran がないことによる問題は解決します。

Error 2

gfortran を入れた後の環境では、以下のようなエラーになりました。

#0 86.10 Collecting scipy==1.13.1 (from -r requirements.txt (line 2))
#0 86.13   Downloading scipy-1.13.1.tar.gz (57.2 MB)
#0 87.02      ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 57.2/57.2 MB 64.5 MB/s  0:00:00
#0 89.18   Installing build dependencies: started
#0 95.95   Installing build dependencies: finished with status 'done'
#0 95.95   Getting requirements to build wheel: started
#0 96.04   Getting requirements to build wheel: finished with status 'done'
#0 96.04   Installing backend dependencies: started
#0 96.93   Installing backend dependencies: finished with status 'done'
#0 96.93   Preparing metadata (pyproject.toml): started
#0 99.91   Preparing metadata (pyproject.toml): finished with status 'error'
#0 99.91   error: subprocess-exited-with-error
#0 99.91   
#0 99.91   × Preparing metadata (pyproject.toml) did not run successfully.
#0 99.91   │ exit code: 1
#0 99.91   ╰─> [43 lines of output]
#0 99.91       + meson setup /tmp/pip-install-e_m5ewqq/scipy_6f6b226425e04f04a094014770ad5f10 /tmp/pip-install-e_m5ewqq/scipy_6f6b226425e04f04a094014770ad5f10/.mesonpy-ypeafcek -Dbuildtype=release -Db_ndebug=if-release -Db_vscrt=md --native-file=/tmp/pip-install-e_m5ewqq/scipy_6f6b226425e04f04a094014770ad5f10/.mesonpy-ypeafcek/meson-python-native-file.ini
#0 99.91       The Meson build system
#0 99.91       Version: 1.9.1
#0 99.91       Source dir: /tmp/pip-install-e_m5ewqq/scipy_6f6b226425e04f04a094014770ad5f10
#0 99.91       Build dir: /tmp/pip-install-e_m5ewqq/scipy_6f6b226425e04f04a094014770ad5f10/.mesonpy-ypeafcek
#0 99.91       Build type: native build
#0 99.91       Project name: scipy
#0 99.91       Project version: 1.13.1
#0 99.91       C compiler for the host machine: cc (gcc 14.2.0 "cc (Debian 14.2.0-19) 14.2.0")
#0 99.91       C linker for the host machine: cc ld.bfd 2.44
#0 99.91       C++ compiler for the host machine: c++ (gcc 14.2.0 "c++ (Debian 14.2.0-19) 14.2.0")
#0 99.91       C++ linker for the host machine: c++ ld.bfd 2.44
#0 99.91       Cython compiler for the host machine: cython (cython 3.0.12)
#0 99.91       Host machine cpu family: aarch64
#0 99.91       Host machine cpu: aarch64
#0 99.91       Program python found: YES (/usr/local/bin/python3.13)
#0 99.91       Found pkg-config: YES (/usr/bin/pkg-config) 1.8.1
#0 99.91       Run-time dependency python found: YES 3.13
#0 99.91       Program cython found: YES (/tmp/pip-build-env-ouvhtmfu/overlay/bin/cython)
#0 99.91       Compiler for C supports arguments -Wno-unused-but-set-variable: YES
#0 99.91       Compiler for C supports arguments -Wno-unused-function: YES
#0 99.91       Compiler for C supports arguments -Wno-conversion: YES
#0 99.91       Compiler for C supports arguments -Wno-misleading-indentation: YES
#0 99.91       Library m found: YES
#0 99.91       Fortran compiler for the host machine: gfortran (gcc 14.2.0 "GNU Fortran (Debian 14.2.0-19) 14.2.0")
#0 99.91       Fortran linker for the host machine: gfortran ld.bfd 2.44
#0 99.91       Compiler for Fortran supports arguments -Wno-conversion: YES
#0 99.91       Checking if "-Wl,--version-script" links: YES
#0 99.91       Program pythran found: YES 0.15.0 0.15.0 (/tmp/pip-build-env-ouvhtmfu/overlay/bin/pythran)
#0 99.91       Found CMake: /usr/bin/cmake (3.31.6)
#0 99.91       Run-time dependency xsimd found: NO (tried pkgconfig and cmake)
#0 99.91       Run-time dependency threads found: YES
#0 99.91       Library npymath found: YES
#0 99.91       Library npyrandom found: YES
#0 99.91       pybind11-config found: YES (/tmp/pip-build-env-ouvhtmfu/overlay/bin/pybind11-config) 2.12.1
#0 99.91       Run-time dependency pybind11 found: YES 2.12.1
#0 99.91       Run-time dependency scipy-openblas found: NO (tried pkgconfig)
#0 99.91       Run-time dependency openblas found: NO (tried pkgconfig and cmake)
#0 99.91       Run-time dependency openblas found: NO (tried pkgconfig and cmake)
#0 99.91       
#0 99.91       ../scipy/meson.build:163:9: ERROR: Dependency "OpenBLAS" not found, tried pkgconfig and cmake
#0 99.91       
#0 99.91       A full log can be found at /tmp/pip-install-e_m5ewqq/scipy_6f6b226425e04f04a094014770ad5f10/.mesonpy-ypeafcek/meson-logs/meson-log.txt
#0 99.91       [end of output]
#0 99.91   
#0 99.91   note: This error originates from a subprocess, and is likely not a problem with pip.
#0 99.92 error: metadata-generation-failed
#0 99.92 
#0 99.92 × Encountered error while generating package metadata.
#0 99.92 ╰─> See above for output.
#0 99.92 
#0 99.92 note: This is an issue with the package mentioned above, not pip.
#0 99.92 hint: See above for details.
------
failed to solve: executor failed running [/bin/sh -c pip install -r requirements.txt]: exit code: 1

今度は重要なのはここです。

../scipy/meson.build:163:9: ERROR: Dependency "OpenBLAS" not found, tried pkgconfig and cmake

不足パッケージが OpenBLAS だけになりましたね。

openblas は以下のようにインストール可能でした。

Dockerfile

RUN apt -y update && apt -y upgrade
RUN apt -y install --no-install-recommends gfortran libopenblas-dev

このようにしてあげれば、scipy が無事インストールされます( *¯ ꒳¯*)✨

5. 参考

linux の Docker じゃなくて、 MacOS 上で作業している場合は、以下の記事の方法で解決できる模様。本当に解決できてるのかどうかはわからないけど、 thumb up のアイコンが押されている。