cc-wrapper: deunify clang/gcc treatment of -isystem · Pull Request #225220 · NixOS/nixpkgs

ghost · 2023-04-07T20:59:03Z

Problem

Failures reported among packages which use gfortran:

Methodology

Add -v to NIX_CFLAGS_COMPILE
Run builds of python3Packages.scipy with and without #209870 reverted
Run nuke-refs on the resulting logs
Run wdiff -n | colordiff on the nuked logs

Diagnosis

The fix

commit 77239eb5b09e5f0c507887524557b987a5508e50
Author: Adam Joseph <[email protected]>
Date:   Fri Apr 7 21:44:28 2023 -0700

    In https://github.com/NixOS/nixpkgs/pull/209870 I tried to unify the
    treatment of clang and gcc in cc-wrapper as much as possible.
    However it appears that I went too far.

    Clang requires -isystem flags in order to be able to find gcc's
    libstdc++.  Gcc does not need these flags.  If they are added,
    gfortran will get confused:

      https://github.com/NixOS/nixpkgs/pull/209870#issuecomment-1500550903

    This commit deunifies the chunk of code that adds the -isystem
    flags, and explains why this chunk applies only to clang.

Validation

I hacked in this PR's fix to scipy (only) using wrapCCWith and scipy built correctly. Currently verifying a global rebuild with this PR, but it won't finish until after I go to sleep.

@vcunat, if the situation is urgent we can send the wrapCCWith-hacked version to staging-next. Otherwise the fix has to wait for this PR's global rebuild ☹️

ghost · 2023-04-07T22:28:46Z

Hrm, it got farther but failed (differently). Investigating.

python3.10-scipy>   FAILED: scipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p/wright.cc.o
python3.10-scipy>   g++ -Iscipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p -Iscipy/special -I../../scipy/special -I/nix/store/l8ylq3skndl7xs7zwsmdlhxwi4ik5vzy-python3.10-numpy-1.24.2/lib/python3.10/site-packages/numpy/core/include -I../../scipy/_lib/boost -Iscipy/_lib -I../../scipy/_lib -I../../scipy/_build_utils/src -I/nix/store/45v06dfypiw75jn6dwffyv4y10d3pdhy-python3-3.10.10/include/python3.10 -fvisibility=hidden -fvisibility-inlines-hidden -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O2 -fPIC -Wno-cpp -MD -MQ scipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p/wright.cc.o -MF scipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p/wright.cc.o.d -o scipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p/wright.cc.o -c ../../scipy/special/wright.cc
python3.10-scipy>   In file included from ../../scipy/special/_round.h:53,
python3.10-scipy>                    from ../../scipy/special/wright.cc:79:
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:58:11: error: ‘fenv_t’ has not been declared in ‘::’
python3.10-scipy>      58 |   using ::fenv_t;
python3.10-scipy>         |           ^~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:59:11: error: ‘fexcept_t’ has not been declared in ‘::’
python3.10-scipy>      59 |   using ::fexcept_t;
python3.10-scipy>         |           ^~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:62:11: error: ‘feclearexcept’ has not been declared in ‘::’
python3.10-scipy>      62 |   using ::feclearexcept;
python3.10-scipy>         |           ^~~~~~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:63:11: error: ‘fegetexceptflag’ has not been declared in ‘::’
python3.10-scipy>      63 |   using ::fegetexceptflag;
python3.10-scipy>         |           ^~~~~~~~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:64:11: error: ‘feraiseexcept’ has not been declared in ‘::’
python3.10-scipy>      64 |   using ::feraiseexcept;
python3.10-scipy>         |           ^~~~~~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:65:11: error: ‘fesetexceptflag’ has not been declared in ‘::’
python3.10-scipy>      65 |   using ::fesetexceptflag;
python3.10-scipy>         |           ^~~~~~~~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:66:11: error: ‘fetestexcept’ has not been declared in ‘::’
python3.10-scipy>      66 |   using ::fetestexcept;
python3.10-scipy>         |           ^~~~~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:68:11: error: ‘fegetround’ has not been declared in ‘::’
python3.10-scipy>      68 |   using ::fegetround;
python3.10-scipy>         |           ^~~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:69:11: error: ‘fesetround’ has not been declared in ‘::’
python3.10-scipy>      69 |   using ::fesetround;
python3.10-scipy>         |           ^~~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:71:11: error: ‘fegetenv’ has not been declared in ‘::’
python3.10-scipy>      71 |   using ::fegetenv;
python3.10-scipy>         |           ^~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:72:11: error: ‘feholdexcept’ has not been declared in ‘::’
python3.10-scipy>      72 |   using ::feholdexcept;
python3.10-scipy>         |           ^~~~~~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:73:11: error: ‘fesetenv’ has not been declared in ‘::’
python3.10-scipy>      73 |   using ::fesetenv;
python3.10-scipy>         |           ^~~~~~~~
python3.10-scipy>   /nix/store/8sphbc0jiba0ky3ghq7zrd4gg2ybabab-gcc-12.2.0/include/c++/12.2.0/fenv.h:74:11: error: ‘feupdateenv’ has not been declared in ‘::’
python3.10-scipy>      74 |   using ::feupdateenv;
python3.10-scipy>         |           ^~~~~~~~~~~

lovesegfault · 2023-04-08T07:04:03Z

@amjoseph-nixpkgs i think you want to target staging-next?

vcunat · 2023-04-08T07:05:48Z

I think I'll go for a workaround using this just for the specific breakage(s) in the current staging-next, as rebuilding linux stdenvs is quite costly.

ghost · 2023-04-08T08:00:23Z

@amjoseph-nixpkgs i think you want to target staging-next?

This causes a global rebuild; is that okay? I thought staging-next was sort of like master -- no mass-rebuilds allowed. Did I misunderstand?

Anyways it doesn't matter to me.

Also, my rebuild went way faster than I thought; I should have a rebuilt-from-scratch scipy in the next few minutes.

vcunat · 2023-04-08T08:09:23Z

I'm a bit confused that you mention scipy all the time, as that package ~~worked~~ built successfully: https://hydra.nixos.org/job/nixpkgs/staging-next/python310Packages.scipy.x86_64-linux

vcunat · 2023-04-08T08:12:13Z

(it was python3.pkgs.scikit-learn that I knew to be broken)

vcunat · 2023-04-08T11:39:08Z

No problem :-) Fortunately it still seems like simple hacks will suffice for now, so a proper solution isn't urgent and could be a mass rebuild.

ghost · 2023-04-08T17:56:52Z

✔️ This PR is ready. @vcunat @trofi please consider merging this.

It contains two commits, and both are needed. If you omit either one of them, scikit-learn will fail to build (although the failure might be different, or one of its dependencies might fail before it even starts building).

Got it! To fix scikit-learn you need both trofi's suggestion and also the change to -isystem.

Proof:

nix@moore:/git/work/fix/scikit/with-trofi-idea$ git rev-parse HEAD
de7cbf714b8562d4dddbe284a205e5d92f7b7bf7
nix@moore:/git/work/fix/scikit/with-trofi-idea$ nix-instantiate . -A python3Packages.scikit-learn
warning: you did not specify '--add-root'; the result might be removed by the garbage collector
/nix/store/j9jd3mad0624pfhn9vlmc17rvk9017a2-python3.10-scikit-learn-1.2.1.drv
nix@moore:/git/work/fix/scikit/with-trofi-idea$ nix-build . -A python3Packages.scikit-learn
/nix/store/z3fxmiam657acwl10jwkhygvvgda44ll-python3.10-scikit-learn-1.2.1

scipy fails to build if you omit cc-wrapper: deunify clang/gcc treatment of -isystem

nix@moore:/git/work/fix/scikit/with-trofi-idea$ git log | head -n 8 commit 9d5d1f7cb3aa329b2029b0cdf97334b26b4118e9 Author: Adam Joseph Date: Sat Apr 8 10:54:19 2023 -0700 Revert "cc-wrapper: deunify clang/gcc treatment of -isystem" This reverts commit de7cbf714b8562d4dddbe284a205e5d92f7b7bf7. nix@moore:/git/work/fix/scikit/with-trofi-idea$ nix build -f . -L python3Packages.scikit-learn ... python3.10-scipy> g++ -Iscipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p -Iscipy/special -I../../scipy/special -I/nix/store/15ln23q9jqphzp2py537819y5p4hs4rl-python3.10-numpy-1.24.2/lib/python3.10/site-packages/numpy/core/include -I../../scipy/_lib/boost -Iscipy/_lib -I../../scipy/_lib -I../../scipy/_build_utils/src -I/nix/store/aaqc8qslczqpjbyl9l3djrcaylm0kxlk-python3-3.10.11/include/python3.10 -fvisibility=hidden -fvisibility-inlines-hidden -fdiagnostics-color=always -D_FILE_OFFSET_BITS=64 -Wall -Winvalid-pch -std=c++14 -O2 -fPIC -Wno-cpp -MD -MQ scipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p/wright.cc.o -MF scipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p/wright.cc.o.d -o scipy/special/_ufuncs_cxx.cpython-310-x86_64-linux-gnu.so.p/wright.cc.o -c ../../scipy/special/wright.cc python3.10-scipy> In file included from ../../scipy/special/_round.h:53, python3.10-scipy> from ../../scipy/special/wright.cc:79: python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:58:11: error: ‘fenv_t’ has not been declared in ‘::’ python3.10-scipy> 58 | using ::fenv_t; python3.10-scipy> | ^~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:59:11: error: ‘fexcept_t’ has not been declared in ‘::’ python3.10-scipy> 59 | using ::fexcept_t; python3.10-scipy> | ^~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:62:11: error: ‘feclearexcept’ has not been declared in ‘::’ python3.10-scipy> 62 | using ::feclearexcept; python3.10-scipy> | ^~~~~~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:63:11: error: ‘fegetexceptflag’ has not been declared in ‘::’ python3.10-scipy> 63 | using ::fegetexceptflag; python3.10-scipy> | ^~~~~~~~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:64:11: error: ‘feraiseexcept’ has not been declared in ‘::’ python3.10-scipy> 64 | using ::feraiseexcept; python3.10-scipy> | ^~~~~~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:65:11: error: ‘fesetexceptflag’ has not been declared in ‘::’ python3.10-scipy> 65 | using ::fesetexceptflag; python3.10-scipy> | ^~~~~~~~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:66:11: error: ‘fetestexcept’ has not been declared in ‘::’ python3.10-scipy> 66 | using ::fetestexcept; python3.10-scipy> | ^~~~~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:68:11: error: ‘fegetround’ has not been declared in ‘::’ python3.10-scipy> 68 | using ::fegetround; python3.10-scipy> | ^~~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:69:11: error: ‘fesetround’ has not been declared in ‘::’ python3.10-scipy> 69 | using ::fesetround; python3.10-scipy> | ^~~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:71:11: error: ‘fegetenv’ has not been declared in ‘::’ python3.10-scipy> 71 | using ::fegetenv; python3.10-scipy> | ^~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:72:11: error: ‘feholdexcept’ has not been declared in ‘::’ python3.10-scipy> 72 | using ::feholdexcept; python3.10-scipy> | ^~~~~~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:73:11: error: ‘fesetenv’ has not been declared in ‘::’ python3.10-scipy> 73 | using ::fesetenv; python3.10-scipy> | ^~~~~~~~ python3.10-scipy> /nix/store/g69llwf0yh385r5gr545zckkfz7g0fq0-gcc-12.2.0/include/c++/12.2.0/fenv.h:74:11: error: ‘feupdateenv’ has not been declared in ‘::’ python3.10-scipy> 74 | using ::feupdateenv; python3.10-scipy> | ^~~~~~~~~~~ ... python3.10-scipy> ninja: build stopped: subcommand failed. python3.10-scipy> INFO: autodetecting backend as ninja python3.10-scipy> INFO: calculating backend command to run: /nix/store/z13jdpnmh5qb7w2k3hb86d7nnrvz322c-ninja-1.11.1/bin/ninja python3.10-scipy> + meson setup --prefix=/nix/store/aaqc8qslczqpjbyl9l3djrcaylm0kxlk-python3-3.10.11 /build/scipy-1.10.1 /build/scipy-1.10.1/.mesonpy-1dniauw0/build --native-file=/build/scipy-1.10.1/.mesonpy-native-file.ini -Ddebug=false -Doptimization=2 python3.10-scipy> + meson compile python3.10-scipy> error: subprocess-exited-with-error python3.10-scipy> × Preparing metadata (pyproject.toml) did not run successfully. python3.10-scipy> │ exit code: 1 python3.10-scipy> ╰─> See above for output. python3.10-scipy> note: This error originates from a subprocess, and is likely not a problem with pip. python3.10-scipy> full command: /nix/store/aaqc8qslczqpjbyl9l3djrcaylm0kxlk-python3-3.10.11/bin/python3.10 /nix/store/9mc17h3wsdrb2gfflr6a0475dx7vy6mz-python3.10-pip-23.0.1/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /build/tmp_lylr9n5 python3.10-scipy> cwd: /build/scipy-1.10.1 python3.10-scipy> Preparing metadata (pyproject.toml) ... error python3.10-scipy> error: metadata-generation-failed python3.10-scipy> × Encountered error while generating package metadata. python3.10-scipy> ╰─> See above for output. python3.10-scipy> note: This is an issue with the package mentioned above, not pip. python3.10-scipy> hint: See above for details. error: build of '/nix/store/djx1wxzwdy7hn2r50i5rrrdwlw0maqyp-python3.10-scipy-1.10.1.drv' on 'ssh://[email protected]' failed: builder for '/nix/store/djx1wxzwdy7hn2r50i5rrrdwlw0maqyp-python3.10-scipy-1.10.1.drv' failed with exit code 1 error: builder for '/nix/store/djx1wxzwdy7hn2r50i5rrrdwlw0maqyp-python3.10-scipy-1.10.1.drv' failed with exit code 1; last 10 log lines: > full command: /nix/store/aaqc8qslczqpjbyl9l3djrcaylm0kxlk-python3-3.10.11/bin/python3.10 /nix/store/9mc17h3wsdrb2gfflr6a0475dx7vy6mz-python3.10-pip-23.0.1/lib/python3.10/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py prepare_metadata_for_build_wheel /build/tmp_lylr9n5 > cwd: /build/scipy-1.10.1 > Preparing metadata (pyproject.toml) ... error > 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. For full logs, run 'nix log /nix/store/djx1wxzwdy7hn2r50i5rrrdwlw0maqyp-python3.10-scipy-1.10.1.drv'. error: 1 dependencies of derivation '/nix/store/zwc76q4cjq1jd1pzsbyvz63la57dlf14-python3.10-scikit-learn-1.2.1.drv' failed to build

scikit-learn fails to build if you omit gcc: never disableBootstrap for gfortran

nix@moore:/git/work/fix/scikit/with-trofi-idea$ git reset --hard de7cbf714b8562d4dddbe284a205e5d92f7b7bf7
HEAD is now at de7cbf714b85 cc-wrapper: deunify clang/gcc treatment of -isystem
nix@moore:/git/work/fix/scikit/with-trofi-idea$ git revert HEAD^
[with-trofi-idea 797d9b6aaad1] Revert "gcc: never disableBootstrap for gfortran"
 1 file changed, 1 insertion(+), 4 deletions(-)
nix@moore:/git/work/fix/scikit/with-trofi-idea$ nix-build . -A python3Packages.scikit-learn
...
       > gcc -shared -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.2.13/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.5.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.4.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.4.4/lib -L/nix/store/2scdlrgd8sqmm1sgsg9b7sjnwlmr9s1p-libxcrypt-4.4.33/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.23/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.41.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.2p1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.0.8/lib -L/nix/store/1whrncscgc90j7dh08wcyvygjgzcjkgm-tzdata-2023c/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-zlib-1.2.13/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-bzip2-1.0.8/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-expat-2.5.0/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-xz-5.4.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-libffi-3.4.4/lib -L/nix/store/2scdlrgd8sqmm1sgsg9b7sjnwlmr9s1p-libxcrypt-4.4.33/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-gdbm-1.23/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-sqlite-3.41.2/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-readline-8.2p1/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-ncurses-6.4/lib -L/nix/store/eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee-openssl-3.0.8/lib -L/nix/store/1whrncscgc90j7dh08wcyvygjgzcjkgm-tzdata-2023c/lib build/temp.linux-x86_64-cpython-310/sklearn/_loss/_loss.o -L/nix/store/xasxsk7n57j3mx50vz848gd04i95kj4v-python3-3.10.11/lib -Lbuild/temp.linux-x86_64-cpython-310 -lm -llibsvm-skl -lliblinear-skl -o build/lib.linux-x86_64-cpython-310/sklearn/_loss/_loss.cpython-310-x86_64-linux-gnu.so -fopenmp
       > error: command '/nix/store/02nzdnalvzi8mf6p2l8svl6swy9bp5by-gfortran-wrapper-12.2.0/bin/gcc' failed with exit code 1
       > /nix/store/fqvpf04307g05fibxjg287z5cga3pcd9-stdenv-linux/setup: line 1594: pop_var_context: head of shell_variables not a function context
       For full logs, run 'nix log /nix/store/0khrvashssrr1rr7z0cyx8b77xjiyy7a-python3.10-scikit-learn-1.2.1.drv'.

trofi

LGTM, to state the obvious it's a full linux rebuild:

$ ./maintainers/scripts/rebuild-amount.sh HEAD^
Estimating rebuild amount by counting changed Hydra jobs (parallel=unset).
      1 pkgs-lib-tests
      2 x86_64-darwin
  57773 x86_64-linux

ghost · 2023-04-08T19:19:03Z

LGTM, to state the obvious it's a full linux rebuild:

Yes indeed.

The low-rebuilds version in #225273 has been updated; I'm just waiting to make sure it works before undraftifying it. If it works, I think the best plan is to merge that one to staging-next, and then in the next full-rebuild cycle revert #225273 and merge this. Edit: @vcunat intends to put this into the next full-rebuild cycle, so the low-rebuilds version is not needed.

ghost · 2023-04-08T19:39:11Z

I have cherry-picked 4b9280f8fd008b7bd22aeff50ede5195dcf355fb and then reverted it so we won't forget to do so.

Once staging-next merges to staging github will drop the cherry-picked commit, and then when this merges it will revert 4b9280f8fd008b7bd22aeff50ede5195dcf355fb.

This is a low-rebuild version of PR #225273 /cc the proper and hopefully complete fix in PR #225220

Artturin · 2023-04-10T18:21:42Z

Needs rebase

vcunat · 2023-04-10T18:25:30Z

Well yes, it needs a revert of e269122.

Artturin · 2023-04-10T18:40:31Z

Well yes, it needs a revert of e269122.

i did

git rebase --onto staging HEAD~4 --interactive

then added exec git revert e269122 at the top, exited, then got the following

$ git rebase --onto staging HEAD~4 --interactive
Executing: git revert e269122
Auto-merging pkgs/top-level/all-packages.nix
[detached HEAD a8c95cf146b] Revert "julia{18,19,}: fix build by a temporary hack"
 3 files changed, 4 insertions(+), 22 deletions(-)
The previous cherry-pick is now empty, possibly due to conflict resolution.
If you wish to commit it anyway, use:

    git commit --allow-empty

Otherwise, please use 'git rebase --skip'
interactive rebase in progress; onto da9d5848454
Last commands done (2 commands done):
   exec git revert e269122
   pick e64a751c475 python3Packages.scikit-learn: hack-fix missing libstdc++
Next commands to do (3 remaining commands):
   pick 3d904285202 Revert "python3Packages.scikit-learn: hack-fix missing libstdc++"
   pick 68ed28c77d6 gcc: never disableBootstrap for gfortran
  (use "git rebase --edit-todo" to view and edit)
You are currently rebasing branch 'pr/gfortran/do-not-disable-bootstrap' on 'da9d5848454'.
  (all conflicts fixed: run "git rebase --continue")

then ran git rebase --continue

and i think it worked

$ git log staging...HEAD
commit 613e199c0d05457114dab4a2925032dae27a1578 (HEAD -> pr/gfortran/do-not-disable-bootstrap)
Author: Adam Joseph <[email protected]>
Date:   Fri Apr 7 21:44:28 2023 -0700

    cc-wrapper: deunify clang/gcc treatment of -isystem

    In https://github.com/NixOS/nixpkgs/pull/209870 I tried to unify the
    treatment of clang and gcc in cc-wrapper as much as possible.
    However it appears that I went too far.

    Clang requires -isystem flags in order to be able to find gcc's
    libstdc++.  Gcc does not need these flags.  If they are added,
    gfortran will get confused:

      https://github.com/NixOS/nixpkgs/pull/209870#issuecomment-1500550903

    This commit deunifies the chunk of code that adds the -isystem
    flags, and explains why this chunk applies only to clang.

commit ba3792975a42f75a54c27a1c8bb9c2f57decf270
Author: Adam Joseph <[email protected]>
Date:   Fri Apr 7 13:50:35 2023 -0700

    gcc: never disableBootstrap for gfortran

    As suggested by @trofi here:

      https://github.com/NixOS/nixpkgs/pull/209870#issuecomment-1500635687

    This should fix failures among packages which use gfortran:

      https://github.com/NixOS/nixpkgs/pull/209870#issuecomment-1500550903
      https://hydra.nixos.org/build/215195834

commit a83e1a0d194fb88931ba037c74e97e75c1014c93
Author: Adam Joseph <[email protected]>
Date:   Sat Apr 8 12:30:33 2023 -0700

    Revert "python3Packages.scikit-learn: hack-fix missing libstdc++"

    This reverts commit 46f29d4bd6305a9f7c743d3f9022a8d5f6d3cb12.

commit a8c95cf146bc927b73904778d88863ee9a420e50
Author: Artturin <[email protected]>
Date:   Mon Apr 10 21:37:31 2023 +0300

    Revert "julia{18,19,}: fix build by a temporary hack"

    This reverts commit e2691227cdc424c643511d40fd6234acdf77372e.

Again, temporary until PR #225220

ghost · 2023-04-11T17:07:37Z

git rebase --onto staging HEAD~4 --interactive

BTW thanks for telling me about this trick earlier. I figured out how to do it without manually counting commits (I often rebase 100+-long branches):

git-rebase-from-to() {
  echo "rebasing from $1 to $2"
  git rebase --onto $2 $(git merge-base $1 HEAD) HEAD
}

and then you can do things like

$ git-rebase-from-to origin/master origin/staging
rebasing from origin/master to origin/staging
...

This reverts commit 398b54b.

This reverts commit e269122.

This reverts commit 46f29d4.

@trofi

As suggested by @trofi here: #209870 (comment) This should fix failures among packages which use gfortran: #209870 (comment) https://hydra.nixos.org/build/215195834

In #209870 I tried to unify the treatment of clang and gcc in cc-wrapper as much as possible. However it appears that I went too far. Clang requires -isystem flags in order to be able to find gcc's libstdc++. Gcc does not need these flags. If they are added, gfortran will get confused: #209870 (comment) This commit deunifies the chunk of code that adds the -isystem flags, and explains why this chunk applies only to clang.

Artturin · 2023-04-11T17:22:14Z

added another revert

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ghost marked this pull request as ready for review April 7, 2023 21:24

ghost requested a review from matthewbauer as a code owner April 7, 2023 21:24

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ghost marked this pull request as draft April 8, 2023 00:22

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ghost changed the base branch from staging-next to staging April 8, 2023 04:53

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ghost changed the title ~~gcc: never disableBootstrap for gfortran~~ cc-wrapper: deunify clang/gcc treatment of -isystem Apr 8, 2023

ghost marked this pull request as ready for review April 8, 2023 05:29

ghost requested a review from Ericson2314 as a code owner April 8, 2023 05:29

ghost mentioned this pull request Apr 8, 2023

stdenv: Nix-driven bootstrap of gcc #209870

Merged

4 tasks

ghost requested review from trofi and vcunat April 8, 2023 05:30

ofborg bot added 10.rebuild-linux-stdenv This PR causes stdenv to rebuild on Linux and must target a staging branch. and removed 10.rebuild-darwin: 1 This PR causes 1 package to rebuild on Darwin. labels Apr 8, 2023

trofi approved these changes Apr 8, 2023

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ghost mentioned this pull request Apr 8, 2023

cc-wrapper: gross hack for staging-next to fix scipy **revert this when merging staging-next to staging** #225273

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ghost marked this pull request as draft April 8, 2023 10:19

ghost marked this pull request as ready for review April 8, 2023 17:56

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trofi approved these changes Apr 8, 2023

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vcunat added a commit that referenced this pull request Apr 10, 2023

julia{18,19,}: fix build by a temporary hack

e269122

This is a low-rebuild version of PR #225273 /cc the proper and hopefully complete fix in PR #225220

github-actions bot added the 6.topic: python Python is a high-level, general-purpose programming language. label Apr 10, 2023

ofborg bot added the 8.has: clean-up This PR removes packages or removes other cruft label Apr 10, 2023

vcunat added a commit that referenced this pull request Apr 11, 2023

python310Packages.kaldi-active-grammar: fixup build

398b54b

Again, temporary until PR #225220

Artturin and others added 5 commits April 11, 2023 20:19

Revert "python310Packages.kaldi-active-grammar: fixup build"

fd004f1

This reverts commit 398b54b.

Revert "julia{18,19,}: fix build by a temporary hack"

b1d4dfd

This reverts commit e269122.

Revert "python3Packages.scikit-learn: hack-fix missing libstdc++"

88fc226

This reverts commit 46f29d4.

gcc: never disableBootstrap for gfortran

f06ab17

As suggested by @trofi here: #209870 (comment) This should fix failures among packages which use gfortran: #209870 (comment) https://hydra.nixos.org/build/215195834

This was referenced Apr 11, 2023

#209870 broke llvmPackages_rocm.clang #225780

Closed

#209870 broke llvmPackages_13.compiler-rt-libc #225779

Closed

Artturin merged commit a2da3d6 into NixOS:staging Apr 11, 2023

ghost mentioned this pull request Apr 12, 2023

cc-wrapper: deunify clang/gcc handling of -B flag #225846

Merged

This was referenced Apr 17, 2023

WIP staging->master: Update flake.lock Nix-QChem/NixOS-QChem#278

Merged

Build failure: python310Packages.openmm #226895

Closed

ghost deleted the pr/gfortran/do-not-disable-bootstrap branch January 23, 2024 06:48

Artturin mentioned this pull request Jan 29, 2024

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