bootstrap -s: Configure tarball is missing the files generated from pkgs/*/*.m4

[beew]

Is there an existing issue for this?

• I have searched the existing issues for a bug report that matches the one I want to file, without success.

Did you read the documentation and troubleshoot guide?

• I have read the documentation and troubleshoot guide

Environment

- **OS**:Ubuntu 22.04
- **Sage Version**: 9.8 from source

Steps To Reproduce

After building sage successfully I tried to install the experimental package "sagemath_repl" with

sage -i sagemath_repl

it errored out with

Successfully built UNKNOWN-0.0.0.tar.gz and UNKNOWN-0.0.0-py3-none-any.whl
[sagemath_environment-9.8] -rw-rw-r-- 1 bernard bernard 69187 Mar 12 14:57 /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels/UNKNOWN-0.0.0-py3-none-any.whl
make --no-print-directory sagemath_objects-SAGE_VENV-no-deps
[sagemath_objects-9.8] * Creating venv isolated environment...
[sagemath_objects-9.8] * Installing packages in isolated environment... (setuptools >= 40.8.0, wheel)
[sagemath_objects-9.8] * Getting build dependencies for sdist...
[sagemath_objects-9.8] Traceback (most recent call last):
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
[sagemath_objects-9.8]     main()
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pyproject_hooks/_in_process/_in_process.py", line 335, in main
[sagemath_objects-9.8]     json_out['return_val'] = hook(**hook_input['kwargs'])
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pyproject_hooks/_in_process/_in_process.py", line 287, in get_requires_for_build_sdist
[sagemath_objects-9.8]     return hook(config_settings)
[sagemath_objects-9.8]   File "/tmp/build-env-1sl9wzp9/lib/python3.10/site-packages/setuptools/build_meta.py", line 341, in get_requires_for_build_sdist
[sagemath_objects-9.8]     return self._get_build_requires(config_settings, requirements=[])
[sagemath_objects-9.8]   File "/tmp/build-env-1sl9wzp9/lib/python3.10/site-packages/setuptools/build_meta.py", line 320, in _get_build_requires
[sagemath_objects-9.8]     self.run_setup()
[sagemath_objects-9.8]   File "/tmp/build-env-1sl9wzp9/lib/python3.10/site-packages/setuptools/build_meta.py", line 484, in run_setup
[sagemath_objects-9.8]     super(_BuildMetaLegacyBackend,
[sagemath_objects-9.8]   File "/tmp/build-env-1sl9wzp9/lib/python3.10/site-packages/setuptools/build_meta.py", line 335, in run_setup
[sagemath_objects-9.8]     exec(code, locals())
[sagemath_objects-9.8]   File "<string>", line 17, in <module>
[sagemath_objects-9.8] ModuleNotFoundError: No module named 'sage_setup'
[sagemath_objects-9.8] 
[sagemath_objects-9.8] ERROR Backend subprocess exited when trying to invoke get_requires_for_build_sdist
[sagemath_objects-9.8] ********************************************************************************
[sagemath_objects-9.8] Failure building sdist and wheel
[sagemath_objects-9.8] ********************************************************************************
make[2]: *** [Makefile:3346: sagemath_objects-SAGE_VENV-no-deps] Error 1
make[1]: *** [Makefile:3346: /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/var/lib/sage/installed/sagemath_objects-9.8] Error 2
make[1]: Leaving directory '/home/bernard/opt/sagemath/build/make'

real	0m19.140s
user	0m17.065s
sys	0m1.520s

Expected Behavior

package should build

Actual Behavior

it doesn't build

Additional Information

No response

[mkoeppe]

Thanks for reporting this distribution bug. A workaround is to run ./bootstrap

[beew]

Hi,

When to run ./bootstrap? I ran bootstrap and then sage -i sagemath_repl it still failed. Do you mean to rebuild sage from scratch?

[mkoeppe]

Can you post the output of running bootstrap and the installation please?

[beew]

Hi

 ./bootstrap
rm -rf config/install-sh config/compile config/config.guess config/config.sub config/missing configure build/make/Makefile-auto.in
rm -f src/doc/en/installation/*.txt
rm -rf src/doc/en/reference/spkg/*.rst
rm -f environment.yml
rm -f src/environment.yml
rm -f src/environment-dev.yml
rm -f environment-optional.yml
rm -f src/environment-optional.yml
rm -f src/Pipfile
rm -f src/pyproject.toml
rm -f src/requirements.txt
rm -f src/setup.cfg
bootstrap:: installing 'm4/sage_spkg_configures.m4'
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagelib/src/Pipfile-dist
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagelib/src/Pipfile
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagelib/src/pyproject.toml
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagelib/src/requirements.txt
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagelib/src/setup.cfg
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_categories/src/MANIFEST.in
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_categories/src/pyproject.toml
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_categories/src/requirements.txt
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_categories/src/setup.cfg
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_environment/src/pyproject.toml
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_environment/src/requirements.txt
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_environment/src/setup.cfg
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_objects/src/pyproject.toml
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_objects/src/requirements.txt
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_objects/src/setup.cfg
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_repl/src/pyproject.toml
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_repl/src/requirements.txt
./bootstrap: installing /home/bernard/opt/sagemath/build/pkgs/sagemath_repl/src/setup.cfg
./bootstrap-conda:51: generate conda environment files
src/doc/bootstrap:76: installing src/doc/en/installation/arch*.txt
src/doc/bootstrap:76: installing src/doc/en/installation/debian*.txt
src/doc/bootstrap:76: installing src/doc/en/installation/fedora*.txt
src/doc/bootstrap:76: installing src/doc/en/installation/cygwin*.txt
src/doc/bootstrap:76: installing src/doc/en/installation/homebrew*.txt
src/doc/bootstrap:76: installing src/doc/en/installation/opensuse*.txt
src/doc/bootstrap:87: installing src/doc/en/reference/spkg/*.rst
configure.ac:57: installing 'config/compile'
configure.ac:57: installing 'config/config.guess'
configure.ac:57: installing 'config/config.sub'
configure.ac:43: installing 'config/install-sh'
configure.ac:43: installing 'config/missing'

and

./sage -i sagemath_repl
make build/make/Makefile --stop
make[1]: Entering directory '/home/bernard/opt/sagemath'
make[1]: 'build/make/Makefile' is up to date.
make[1]: Leaving directory '/home/bernard/opt/sagemath'
build/bin/sage-logger \
	"cd build/make && ./install 'all-toolchain'" logs/install.log
make[1]: Entering directory '/home/bernard/opt/sagemath/build/make'
make[1]: Leaving directory '/home/bernard/opt/sagemath/build/make'
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
CLUTTER_IM_MODULE=ibus
COLORTERM=truecolor
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
DEFAULTS_PATH=/usr/share/gconf/unity.default.path
DESKTOP_SESSION=unity
DISPLAY=:0
GDM_LANG=en_CA
GDMSESSION=unity
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/e977ac0d_b615_4207_871b_459198f88285
GNOME_TERMINAL_SERVICE=:1.214
GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1
GTK2_MODULES=overlay-scrollbar
GTK3_MODULES=xapp-gtk3-module
GTK_CSD=0
GTK_IM_MODULE=ibus
GTK_MODULES=gail:atk-bridge
HOME=/home/bernard
IM_CONFIG_PHASE=1
LANG=en_CA.UTF-8
LANGUAGE=en_CA:en
LD_LIBRARY_PATH=:/home/bernard/opt/vtk/lib
LD_PRELOAD=libgtk3-nocsd.so.0
LESSCLOSE=/usr/bin/lesspipe %s %s
LESSOPEN=| /usr/bin/lesspipe %s
LOGNAME=bernard
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
MAKEFLAGS= V=1
MAKELEVEL=1
MAKE=make
MAKE_TERMERR=/dev/pts/4
MAKE_TERMOUT=/dev/pts/4
MANDATORY_PATH=/usr/share/gconf/unity.mandatory.path
MFLAGS=
MKL_THREADING_LAYER=gnu
OLDPWD=/home/bernard/opt/sagemath
PATH=/home/bernard/opt/sagemath/build/bin:/home/bernard/opt/sagemath/src/bin:/home/bernard/opt/sagemath/local/bin:/home/bernard/.local/bin:/home/bernard/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/bernard/opt/vtk/bin
PWD=/home/bernard/opt/sagemath/build/make
PYTHONPATH=/home/bernard/opt/sagemath/local
QT_ACCESSIBILITY=1
QT_IM_MODULE=ibus
SAGE_ENV_CONFIG_SOURCED=1
SAGE_LOCAL=/home/bernard/opt/sagemath/local
SAGE_LOGFILE=logs/install.log
SAGE_LOGS=/home/bernard/opt/sagemath/logs/pkgs
SAGE_NUM_THREADS=1
SAGE_NUM_THREADS_PARALLEL=8
SAGE_ORIG_PATH=/home/bernard/.local/bin:/home/bernard/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/bernard/opt/vtk/bin
SAGE_ORIG_PATH_SET=True
SAGE_PKGCONFIG=/home/bernard/opt/sagemath/local/lib/pkgconfig
SAGE_ROOT=/home/bernard/opt/sagemath
SAGE_SHARE=/home/bernard/opt/sagemath/local/share
SAGE_SRC=/home/bernard/opt/sagemath/src
SAGE_VENV=/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10
SHELL=/bin/bash
SHLVL=3
SSH_AGENT_LAUNCHER=gnome-keyring
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
SYSTEMD_EXEC_PID=2135
TERM=xterm-256color
USER=bernard
_=/usr/bin/env
VTE_VERSION=6800
XAUTHORITY=/home/bernard/.Xauthority
XDG_CONFIG_DIRS=/etc/xdg/xdg-unity:/etc/xdg
XDG_CURRENT_DESKTOP=Unity:Unity7:ubuntu
XDG_DATA_DIRS=/usr/share/unity:/usr/share/gnome:/home/bernard/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/bernard
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
XDG_SESSION_CLASS=user
XDG_SESSION_DESKTOP=unity
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SESSION_TYPE=x11
XMODIFIERS=@im=ibus
***********************************************
make[1]: Entering directory '/home/bernard/opt/sagemath/build/make'
make --no-print-directory toolchain
make[2]: Nothing to be done for 'toolchain'.
make --no-print-directory toolchain-deps
make --no-print-directory /home/bernard/opt/sagemath/local/var/lib/sage/installed/.dummy
make[3]: '/home/bernard/opt/sagemath/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /home/bernard/opt/sagemath/local/var/lib/sage/installed/.dummy
make[3]: '/home/bernard/opt/sagemath/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /home/bernard/opt/sagemath/local/var/lib/sage/installed/.dummy
make[3]: '/home/bernard/opt/sagemath/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /home/bernard/opt/sagemath/local/var/lib/sage/installed/.dummy
make[3]: '/home/bernard/opt/sagemath/local/var/lib/sage/installed/.dummy' is up to date.
make[1]: Leaving directory '/home/bernard/opt/sagemath/build/make'

real	0m0.249s
user	0m0.249s
sys	0m0.000s
Sage build/upgrade complete!

make build/make/Makefile --stop
make[1]: Entering directory '/home/bernard/opt/sagemath'
make[1]: 'build/make/Makefile' is up to date.
make[1]: Leaving directory '/home/bernard/opt/sagemath'
build/bin/sage-logger \
	"cd build/make && ./install 'sagemath_repl'" logs/install.log
make[1]: Entering directory '/home/bernard/opt/sagemath/build/make'
make[1]: Leaving directory '/home/bernard/opt/sagemath/build/make'
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
CLUTTER_IM_MODULE=ibus
COLORTERM=truecolor
DBUS_SESSION_BUS_ADDRESS=unix:path=/run/user/1000/bus
DEFAULTS_PATH=/usr/share/gconf/unity.default.path
DESKTOP_SESSION=unity
DISPLAY=:0
GDM_LANG=en_CA
GDMSESSION=unity
GNOME_DESKTOP_SESSION_ID=this-is-deprecated
GNOME_TERMINAL_SCREEN=/org/gnome/Terminal/screen/e977ac0d_b615_4207_871b_459198f88285
GNOME_TERMINAL_SERVICE=:1.214
GPG_AGENT_INFO=/run/user/1000/gnupg/S.gpg-agent:0:1
GTK2_MODULES=overlay-scrollbar
GTK3_MODULES=xapp-gtk3-module
GTK_CSD=0
GTK_IM_MODULE=ibus
GTK_MODULES=gail:atk-bridge
HOME=/home/bernard
IM_CONFIG_PHASE=1
LANG=en_CA.UTF-8
LANGUAGE=en_CA:en
LD_LIBRARY_PATH=:/home/bernard/opt/vtk/lib
LD_PRELOAD=libgtk3-nocsd.so.0
LESSCLOSE=/usr/bin/lesspipe %s %s
LESSOPEN=| /usr/bin/lesspipe %s
LOGNAME=bernard
LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=00:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.zst=01;31:*.tzst=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.wim=01;31:*.swm=01;31:*.dwm=01;31:*.esd=01;31:*.jpg=01;35:*.jpeg=01;35:*.mjpg=01;35:*.mjpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.webp=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=00;36:*.au=00;36:*.flac=00;36:*.m4a=00;36:*.mid=00;36:*.midi=00;36:*.mka=00;36:*.mp3=00;36:*.mpc=00;36:*.ogg=00;36:*.ra=00;36:*.wav=00;36:*.oga=00;36:*.opus=00;36:*.spx=00;36:*.xspf=00;36:
MAKEFLAGS= -- SAGE_SPKG=sage-spkg\  V=1
MAKELEVEL=1
MAKE=make
MAKEOVERRIDES=${-*-command-variables-*-}
MAKE_TERMERR=/dev/pts/4
MAKE_TERMOUT=/dev/pts/4
MANDATORY_PATH=/usr/share/gconf/unity.mandatory.path
MFLAGS=
MKL_THREADING_LAYER=gnu
OLDPWD=/home/bernard/opt/sagemath
PATH=/home/bernard/opt/sagemath/build/bin:/home/bernard/opt/sagemath/src/bin:/home/bernard/opt/sagemath/local/bin:/home/bernard/.local/bin:/home/bernard/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/bernard/opt/vtk/bin
PWD=/home/bernard/opt/sagemath/build/make
PYTHONPATH=/home/bernard/opt/sagemath/local
QT_ACCESSIBILITY=1
QT_IM_MODULE=ibus
SAGE_ENV_CONFIG_SOURCED=1
SAGE_LOCAL=/home/bernard/opt/sagemath/local
SAGE_LOGFILE=logs/install.log
SAGE_LOGS=/home/bernard/opt/sagemath/logs/pkgs
SAGE_NUM_THREADS=1
SAGE_NUM_THREADS_PARALLEL=8
SAGE_ORIG_PATH=/home/bernard/.local/bin:/home/bernard/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/bernard/opt/vtk/bin
SAGE_ORIG_PATH_SET=True
SAGE_PKGCONFIG=/home/bernard/opt/sagemath/local/lib/pkgconfig
SAGE_ROOT=/home/bernard/opt/sagemath
SAGE_SHARE=/home/bernard/opt/sagemath/local/share
SAGE_SPKG=sage-spkg 
SAGE_SRC=/home/bernard/opt/sagemath/src
SAGE_VENV=/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10
SHELL=/bin/bash
SHLVL=3
SSH_AGENT_LAUNCHER=gnome-keyring
SSH_AUTH_SOCK=/run/user/1000/keyring/ssh
SYSTEMD_EXEC_PID=2135
TERM=xterm-256color
USER=bernard
_=/usr/bin/env
VTE_VERSION=6800
XAUTHORITY=/home/bernard/.Xauthority
XDG_CONFIG_DIRS=/etc/xdg/xdg-unity:/etc/xdg
XDG_CURRENT_DESKTOP=Unity:Unity7:ubuntu
XDG_DATA_DIRS=/usr/share/unity:/usr/share/gnome:/home/bernard/.local/share/flatpak/exports/share:/var/lib/flatpak/exports/share:/usr/local/share:/usr/share
XDG_GREETER_DATA_DIR=/var/lib/lightdm-data/bernard
XDG_RUNTIME_DIR=/run/user/1000
XDG_SEAT_PATH=/org/freedesktop/DisplayManager/Seat0
XDG_SESSION_CLASS=user
XDG_SESSION_DESKTOP=unity
XDG_SESSION_PATH=/org/freedesktop/DisplayManager/Session0
XDG_SESSION_TYPE=x11
XMODIFIERS=@im=ibus
***********************************************
make[1]: Entering directory '/home/bernard/opt/sagemath/build/make'
make --no-print-directory python_build-no-deps
sage-logger -p 'sage --pip install -r "/home/bernard/opt/sagemath/build/pkgs/python_build/requirements.txt"' '/home/bernard/opt/sagemath/logs/pkgs/python_build.log'
[python_build] Requirement already satisfied: build in /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages (from -r /home/bernard/opt/sagemath/build/pkgs/python_build/requirements.txt (line 1)) (0.10.0)
[python_build] Requirement already satisfied: pyproject_hooks in /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages (from build->-r /home/bernard/opt/sagemath/build/pkgs/python_build/requirements.txt (line 1)) (1.0.0)
[python_build] Requirement already satisfied: tomli>=1.1.0 in /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages (from build->-r /home/bernard/opt/sagemath/build/pkgs/python_build/requirements.txt (line 1)) (2.0.1)
[python_build] Requirement already satisfied: packaging>=19.0 in /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages (from build->-r /home/bernard/opt/sagemath/build/pkgs/python_build/requirements.txt (line 1)) (21.3)
[python_build] Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages (from packaging>=19.0->build->-r /home/bernard/opt/sagemath/build/pkgs/python_build/requirements.txt (line 1)) (3.0.9)
make --no-print-directory sagemath_objects-SAGE_VENV-no-deps
[sagemath_objects-9.8] * Creating venv isolated environment...
[sagemath_objects-9.8] * Installing packages in isolated environment... (cysignals >=1.10.2, cython >=0.29.21, <1.0, gmpy2 >=2.1.0, sage-setup ~= 9.8, sagemath-environment ~= 9.8, setuptools >=49.6.0, wheel >=0.36.2)
[sagemath_objects-9.8] Looking in links: file:///home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels
[sagemath_objects-9.8] Processing /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels/cysignals-1.11.2-cp310-cp310-linux_x86_64.whl
[sagemath_objects-9.8] Processing /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels/wheel-0.38.4-py3-none-any.whl
[sagemath_objects-9.8] Processing /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/var/lib/sage/wheels/gmpy2-2.1.2-cp310-cp310-linux_x86_64.whl
[sagemath_objects-9.8] ERROR: Could not find a version that satisfies the requirement sage-setup~=9.8 (from versions: none)
[sagemath_objects-9.8] ERROR: No matching distribution found for sage-setup~=9.8
[sagemath_objects-9.8] 
[sagemath_objects-9.8] Traceback (most recent call last):
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/build/__main__.py", line 375, in main
[sagemath_objects-9.8]     built = build_call(
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/build/__main__.py", line 235, in build_package_via_sdist
[sagemath_objects-9.8]     sdist = _build(isolation, builder, outdir, 'sdist', config_settings, skip_dependency_check)
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/build/__main__.py", line 145, in _build
[sagemath_objects-9.8]     return _build_in_isolated_env(builder, outdir, distribution, config_settings)
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/build/__main__.py", line 113, in _build_in_isolated_env
[sagemath_objects-9.8]     env.install(builder.build_system_requires)
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/build/env.py", line 214, in install
[sagemath_objects-9.8]     _subprocess(cmd)
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/build/env.py", line 79, in _subprocess
[sagemath_objects-9.8]     raise e
[sagemath_objects-9.8]   File "/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/build/env.py", line 76, in _subprocess
[sagemath_objects-9.8]     subprocess.run(cmd, check=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
[sagemath_objects-9.8]   File "/usr/lib/python3.10/subprocess.py", line 524, in run
[sagemath_objects-9.8]     raise CalledProcessError(retcode, process.args,
[sagemath_objects-9.8] subprocess.CalledProcessError: Command '['/tmp/build-env-c9jj2ory/bin/python', '-Im', 'pip', 'install', '--use-pep517', '--no-warn-script-location', '-r', '/tmp/build-reqs-wcn9r22y.txt']' returned non-zero exit status 1.
[sagemath_objects-9.8] 
[sagemath_objects-9.8] ERROR Command '['/tmp/build-env-c9jj2ory/bin/python', '-Im', 'pip', 'install', '--use-pep517', '--no-warn-script-location', '-r', '/tmp/build-reqs-wcn9r22y.txt']' returned non-zero exit status 1.
[sagemath_objects-9.8] *******************************************************************************************************************************************************************************************************************
[sagemath_objects-9.8] Failure building sdist and wheel
[sagemath_objects-9.8] *******************************************************************************************************************************************************************************************************************
make[2]: *** [Makefile:3347: sagemath_objects-SAGE_VENV-no-deps] Error 1
make[1]: *** [Makefile:3347: /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/var/lib/sage/installed/sagemath_objects-9.8] Error 2
make[1]: Leaving directory '/home/bernard/opt/sagemath/build/make'

real	0m6.440s
user	0m5.949s
sys	0m0.467s
***************************************************************
Error building Sage.

[mkoeppe]

Thanks. That's a different error now. This can be fixed by typing make wheels

[beew]

So I did make wheels and after running for more than an hour it failed

 error: Command "gcc -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -g -O2 -fPIC -I/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/cysignals -I/home/bernard/opt/sagemath/pkgs/sagemath-standard -I/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/numpy/core/include -I/usr/include/python3.10 -Ibuild/cythonized -I/home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/include -I/usr/include/python3.10 -c build/cythonized/sage/graphs/bliss.cpp -o build/temp.linux-x86_64-cpython-310/build/cythonized/sage/graphs/bliss.o -fno-strict-aliasing -DCYTHON_CLINE_IN_TRACEBACK=1" failed with exit status 1
[sagelib-9.8]   Exception ignored in: <function Pool.__del__ at 0x7fa3653f7760>
[sagelib-9.8]   Traceback (most recent call last):
[sagelib-9.8]     File "/usr/lib/python3.10/multiprocessing/pool.py", line 271, in __del__
[sagelib-9.8]       self._change_notifier.put(None)
[sagelib-9.8]     File "/usr/lib/python3.10/multiprocessing/queues.py", line 377, in put
[sagelib-9.8]       self._writer.send_bytes(obj)
[sagelib-9.8]     File "/usr/lib/python3.10/multiprocessing/connection.py", line 200, in send_bytes
[sagelib-9.8]       self._send_bytes(m[offset:offset + size])
[sagelib-9.8]     File "/usr/lib/python3.10/multiprocessing/connection.py", line 411, in _send_bytes
[sagelib-9.8]       self._send(header + buf)
[sagelib-9.8]     File "/usr/lib/python3.10/multiprocessing/connection.py", line 368, in _send
[sagelib-9.8]       n = write(self._handle, buf)
[sagelib-9.8]   OSError: [Errno 9] Bad file descriptor
[sagelib-9.8]   error: subprocess-exited-with-error
[sagelib-9.8]   
[sagelib-9.8]   × Building wheel for sagemath-standard (pyproject.toml) did not run successfully.
[sagelib-9.8]   │ exit code: 1
[sagelib-9.8]   ╰─> See above for output.
[sagelib-9.8]   
[sagelib-9.8]   note: This error originates from a subprocess, and is likely not a problem with pip.
[sagelib-9.8]   full command: /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/bin/python3 /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpol30l2cn
[sagelib-9.8]   cwd: /home/bernard/opt/sagemath/pkgs/sagemath-standard
[sagelib-9.8]   Building wheel for sagemath-standard (pyproject.toml): finished with status 'error'
[sagelib-9.8]   ERROR: Failed building wheel for sagemath-standard
[sagelib-9.8] Failed to build sagemath-standard
[sagelib-9.8] ERROR: Failed to build one or more wheels
[sagelib-9.8] ********************************************************************************
[sagelib-9.8] Error building a wheel for
[sagelib-9.8] ********************************************************************************
[sagelib-9.8] 
[sagelib-9.8] real	0m14.030s
[sagelib-9.8] user	0m12.083s
[sagelib-9.8] sys	0m1.839s
make[3]: *** [Makefile:3347: sagelib-SAGE_VENV-no-deps] Error 1
make[2]: *** [Makefile:3347: /home/bernard/opt/sagemath/local/var/lib/sage/venv-python3.10/var/lib/sage/installed/sagelib-9.8] Error 2
make[2]: Leaving directory '/home/bernard/opt/sagemath/build/make'

real	0m14.688s
user	0m12.697s
sys	0m1.874s
***************************************************************
Error building Sage.

So now sagelib doesn't build, does it mean my copy of sage is broken now and that I have to rebuild the whole thing?

[mkoeppe]

"OSError: [Errno 9] Bad file descriptor" looks like a sporadic error from multiprocessing. Try "make build" again

[beew]

Hi, so I ran make build and it was successfully completed and sage -i sagemath_repl works!

so does it mean make wheels was not really needed?

I am a bit confused about what happened

1. ./bootsrap

2. make wheels, it failed

3. make build, it works
   (make wheels again failed, then make build again, this time I use -j8 and it finishes a lot faster)

4. sage -i sagemath_repl finally works.

so 2) is not really needed since it always failed.

Thanks for the help.

[mkoeppe]

Building sagemath_repl needs a wheel of the package sage_setup.
Normally, we build sage_setup in legacy editable mode (setup.py develop), so no wheel is created.
See https://github.com/sagemath/sage/wiki/Sage-9.8-Release-Tour#wheels-for-venvs-configure---enable-wheels for more details.

When you ran make wheels, it created this (and other) wheels. Although it failed to complete because of the (likely) sporadic error, the necessary wheel was already made.
You can see these wheels in venv/var/libs/sage/wheels/.

[beew]

Hi, Thanks for the explanation.