Installing from Cygwin: make cannot find setuptools, deletes /usr/bin/env.exe

[Jonas Bertels]

After reinstalling Cygwin and Sage 3 times, I consistently get the following issue:
(I'm following : https://github.com/sagemath/sage/tree/master Readme)

Jonas@LAPTOP-GV22BQAP ~/sage/sage-9.6
$ make

make build/make/Makefile --stop
make[1]: Entering directory '/home/jonascyg/sage/sage-9.6'
make[1]: 'build/make/Makefile' is up to date.
make[1]: Leaving directory '/home/jonascyg/sage/sage-9.6'
build/bin/sage-logger \
        "cd build/make && ./install 'base-toolchain'" logs/install.log
make[1]: Entering directory '/home/jonascyg/sage/sage-9.6/build/make'
make[1]: Leaving directory '/home/jonascyg/sage/sage-9.6/build/make'
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
!::=::\
ALLUSERSPROFILE=C:\ProgramData


...


***********************************************
make[2]: Entering directory '/home/jonascyg/sage/sage-9.6/build/make'
make --no-print-directory /home/jonascyg/sage/sage-9.6/local/var/lib/sage/installed/.dummy
make[3]: '/home/jonascyg/sage/sage-9.6/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /home/jonascyg/sage/sage-9.6/local/var/lib/sage/installed/.dummy
make[3]: '/home/jonascyg/sage/sage-9.6/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /home/jonascyg/sage/sage-9.6/local/var/lib/sage/installed/.dummy
make[3]: '/home/jonascyg/sage/sage-9.6/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory /home/jonascyg/sage/sage-9.6/local/var/lib/sage/installed/.dummy
make[3]: '/home/jonascyg/sage/sage-9.6/local/var/lib/sage/installed/.dummy' is up to date.
make --no-print-directory all-sage-docs all-sage
/usr/bin/python3 /home/jonascyg/sage/sage-9.6/build/bin/sage-venv "/home/jonascyg/sage/sage-9.6/local/var/lib/sage/venv-python3.9"
make --no-print-directory setuptools-SAGE_VENV-no-deps
[setuptools-59.8.0] Using cached file /home/jonascyg/sage/sage-9.6/upstream/setuptools-59.8.0.tar.gz
[setuptools-59.8.0] setuptools-59.8.0
[setuptools-59.8.0] ====================================================
[setuptools-59.8.0] Setting up build directory for setuptools-59.8.0
[setuptools-59.8.0] Finished extraction
[setuptools-59.8.0] No patch files found in ../patches
[setuptools-59.8.0] ****************************************************
[setuptools-59.8.0] Host system:
[setuptools-59.8.0] CYGWIN_NT-10.0-19044 LAPTOP-GV22BQAP 3.3.5-341.x86_64 2022-05-13 12:27 UTC x86_64 Cygwin
[setuptools-59.8.0] ****************************************************
[setuptools-59.8.0] C compiler: gcc
[setuptools-59.8.0] C compiler version:
[setuptools-59.8.0] Using built-in specs.
[setuptools-59.8.0] COLLECT_GCC=gcc
[setuptools-59.8.0] COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-cygwin/11/lto-wrapper.exe
[setuptools-59.8.0] Target: x86_64-pc-cygwin
[setuptools-59.8.0] Configured with: /mnt/share/cygpkgs/gcc/gcc.x86_64/src/gcc-11.3.0/configure --srcdir=/mnt/share/cygpkgs/gcc/gcc.x86_64/src/gcc-11.3.0 --prefix=/usr --exec-prefix=/usr --localstatedir=/var --sysconfdir=/etc --docdir=/usr/share/doc/gcc --htmldir=/usr/share/doc/gcc/html -C --build=x86_64-pc-cygwin --host=x86_64-pc-cygwin --target=x86_64-pc-cygwin --without-libiconv-prefix --without-libintl-prefix --libexecdir=/usr/lib --with-gcc-major-version-only --enable-shared --enable-shared-libgcc --enable-static --enable-version-specific-runtime-libs --enable-bootstrap --enable-__cxa_atexit --with-dwarf2 --with-tune=generic --enable-languages=c,c++,fortran,lto,objc,obj-c++,jit --enable-graphite --enable-threads=posix --enable-libatomic --enable-libgomp --enable-libquadmath --enable-libquadmath-support --disable-libssp --enable-libada --disable-symvers --with-gnu-ld --with-gnu-as --with-cloog-include=/usr/include/cloog-isl --without-libiconv-prefix --without-libintl-prefix --with-system-zlib --enable-linker-build-id --with-default-libstdcxx-abi=gcc4-compatible --enable-libstdcxx-filesystem-ts
[setuptools-59.8.0] Thread model: posix
[setuptools-59.8.0] Supported LTO compression algorithms: zlib zstd
[setuptools-59.8.0] gcc version 11.3.0 (GCC)
[setuptools-59.8.0] ****************************************************
[setuptools-59.8.0] Package 'setuptools' is currently not installed
[setuptools-59.8.0] No legacy uninstaller found for 'setuptools'; nothing to do
make[1]: Leaving directory '/home/jonascyg/sage/sage-9.6'



Additionally, the make process seems to mess with cygwin, and deletes /usr/bin/env.exe, so that when I run make again:

Jonas@LAPTOP-GV22BQAP ~/sage/sage-9.6
$ make
make build/make/Makefile --stop
make[1]: Entering directory '/home/jonascyg/sage/sage-9.6'
make[1]: 'build/make/Makefile' is up to date.
make[1]: Leaving directory '/home/jonascyg/sage/sage-9.6'
build/bin/sage-logger \
        "cd build/make && ./install 'base-toolchain'" logs/install.log
/bin/sh: build/bin/sage-logger: /usr/bin/env: bad interpreter: No such file or directory
make: *** [Makefile:39: base-toolchain] Error 126

(Text in bold was added by me)

[Jonas Bertels]

In attachment the config.log