Created attachment 587728 [details] emerge --info I've found this package fails to build.... x86_64-pc-linux-gnu-g++: sklearn/utils/src/MurmurHash3.cpp x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -shared -march=skylake -O2 -pipe /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/utils/murmurhash.o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/utils/src/MurmurHash3.o -L/usr/lib64 -L/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6 -lpython3.6m -o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/lib/sklearn/utils/murmurhash.cpython-36m-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -shared -march=skylake -O2 -pipe /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/utils/_logistic_sigmoid.o -L/usr/lib64 -L/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6 -lm -lpython3.6m -o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/lib/sklearn/utils/_logistic_sigmoid.cpython-36m-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -shared -march=skylake -O2 -pipe /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/utils/graph_shortest_path.o -L/usr/lib64 -L/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6 -lpython3.6m -o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/lib/sklearn/utils/graph_shortest_path.cpython-36m-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -shared -march=skylake -O2 -pipe /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/utils/seq_dataset.o -L/usr/lib64 -L/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6 -lpython3.6m -o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/lib/sklearn/utils/seq_dataset.cpython-36m-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -shared -march=skylake -O2 -pipe /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/utils/_random.o -L/usr/lib64 -L/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6 -lm -lpython3.6m -o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/lib/sklearn/utils/_random.cpython-36m-x86_64-linux-gnu.so x86_64-pc-linux-gnu-g++ -shared -Wl,-O1 -Wl,--as-needed -shared -march=skylake -O2 -pipe /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/utils/fast_dict.o -L/usr/lib64 -L/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6 -lm -lpython3.6m -o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/lib/sklearn/utils/fast_dict.cpython-36m-x86_64-linux-gnu.so x86_64-pc-linux-gnu-gcc -shared -Wl,-O1 -Wl,--as-needed -shared -march=skylake -O2 -pipe /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/utils/sparsefuncs_fast.o -L/usr/lib64 -L/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6 -lm -lpython3.6m -o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/lib/sklearn/utils/sparsefuncs_fast.cpython-36m-x86_64-linux-gnu.so Partial import of sklearn during the build process. /usr/lib64/python3.6/site-packages/numpy/distutils/system_info.py:614: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. self.calc_info() error: Command "x86_64-pc-linux-gnu-gcc -march=skylake -O2 -pipe -fPIC -DNO_ATLAS_INFO=1 -DHAVE_CBLAS -I../src/cblas -I/usr/lib64/python3.6/site-packages/numpy/core/include -Isklearn/linear_model/ -I/usr/include -I/usr/lib64/python3.6/site-packages/numpy/core/include -I/usr/include/python3.6m -c sklearn/linear_model/cd_fast.c -o /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/linear_model/cd_fast.o -MMD -MF /var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0-python3_6/temp.linux-x86_64-3.6/sklearn/linear_model/cd_fast.o.d" failed with exit status 1 * ERROR: sci-libs/scikits_learn-0.19.0-r1::gentoo failed (compile phase): * (no error message) * * Call stack: * ebuild.sh, line 125: Called src_compile * environment, line 3192: Called distutils-r1_src_compile * environment, line 1068: Called _distutils-r1_run_foreach_impl 'python_compile' * environment, line 433: Called python_foreach_impl 'distutils-r1_run_phase' 'python_compile' * environment, line 2635: Called multibuild_foreach_variant '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 1941: Called _multibuild_run '_python_multibuild_wrapper' 'distutils-r1_run_phase' 'python_compile' * environment, line 1939: Called _python_multibuild_wrapper 'distutils-r1_run_phase' 'python_compile' * environment, line 702: Called distutils-r1_run_phase 'python_compile' * environment, line 1061: Called python_compile * environment, line 2221: Called distutils-r1_python_compile 'config_fc' '--noopt' '--noarch' * environment, line 931: Called esetup.py 'build' '-j' '8' 'config_fc' '--noopt' '--noarch' * environment, line 1365: Called die * The specific snippet of code: * "${@}" || die "${die_args[@]}"; * * If you need support, post the output of `emerge --info '=sci-libs/scikits_learn-0.19.0-r1::gentoo'`, * the complete build log and the output of `emerge -pqv '=sci-libs/scikits_learn-0.19.0-r1::gentoo'`. * The complete build log is located at '/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/temp/environment'. * Working directory: '/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0' * S: '/var/tmp/portage/sci-libs/scikits_learn-0.19.0-r1/work/scikit-learn-0.19.0' However, the package is somewhat dated as 0.19.1 is from 2017, current version is 0.21.3. A request for updating exists in #675212. Further the package is slightly incorrectly named since its scikit-learn (not scikits) as detailed in #665482 There is a related old and ongoing bug for 0.19.0 at #630294 but that doesn't seem to mention that the package is dated.
Created attachment 587730 [details] build.log
Do you have the Atlas libs installed? Can you please try rebuilding it and then sci-libs/scikits_learn too?
Ah, I see that message above the error line now. I don't have Atlas libs currently installed, and having just tried to emerge them it refuses to compile as it detects I've "CPU throttling" enabled (unsure if this is the CPU frequency scaling in kernel options perhaps?). I'll have to give that a whirl later. It however suggests that Atlas should be a dependency of the ebuild too and perhaps adds further impetus to update ebuilds to more recent versions of scikit-learn at the same time maybe.
I had the same error recently and it seems that the Atlas-related user warning is indeed just a warning and not causing the build failure. Your build log shows the real culprit as sklearn/linear_model/cd_fast.c:17022:27: error: type of formal parameter 1 is incomplete 17022 | __pyx_v_ger(CblasRowMajor, __pyx_v_n_samples, __pyx_v_n_tasks, 1.0, (__pyx_v_X_ptr + (__pyx_v_ii * __pyx_v_n_samples)), 1, __pyx_v_wii_ptr, 1, (&(*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_R.data + __pyx_t_31 * __pyx_v_R.strides[0]) )) + __pyx_t_32)) )))), __pyx_v_n_tasks); | ^~~~~~~~~~~~~ sklearn/linear_model/cd_fast.c:17059:26: error: type of formal parameter 1 is incomplete 17059 | __pyx_v_gemv(CblasRowMajor, CblasTrans, __pyx_v_n_samples, __pyx_v_n_tasks, 1.0, (&(*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_R.data + __pyx_t_33 * __pyx_v_R.strides[0]) )) + __pyx_t_34)) )))), __pyx_v_n_tasks, (__pyx_v_X_ptr + (__pyx_v_ii * __pyx_v_n_samples)), 1, 0.0, (&(*((float *) ( /* dim=0 */ ((char *) (((float *) __pyx_v_tmp.data) + __pyx_t_35)) )))), 1); | ^~~~~~~~~~~~~ sklearn/linear_model/cd_fast.c:17059:41: error: type of formal parameter 2 is incomplete 17059 | __pyx_v_gemv(CblasRowMajor, CblasTrans, __pyx_v_n_samples, __pyx_v_n_tasks, 1.0, (&(*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_R.data + __pyx_t_33 * __pyx_v_R.strides[0]) )) + __pyx_t_34)) )))), __pyx_v_n_tasks, (__pyx_v_X_ptr + (__pyx_v_ii * __pyx_v_n_samples)), 1, 0.0, (&(*((float *) ( /* dim=0 */ ((char *) (((float *) __pyx_v_tmp.data) + __pyx_t_35)) )))), 1); | ^~~~~~~~~~ sklearn/linear_model/cd_fast.c:17126:27: error: type of formal parameter 1 is incomplete 17126 | __pyx_v_ger(CblasRowMajor, __pyx_v_n_samples, __pyx_v_n_tasks, -1.0, (__pyx_v_X_ptr + (__pyx_v_ii * __pyx_v_n_samples)), 1, (__pyx_v_W_ptr + (__pyx_v_ii * __pyx_v_n_tasks)), 1, (&(*((float *) ( /* dim=1 */ ((char *) (((float *) ( /* dim=0 */ (__pyx_v_R.data + __pyx_t_39 * __pyx_v_R.strides[0]) )) + __pyx_t_40)) )))), __pyx_v_n_tasks); which makes this bug a duplicate of bug 630294. This issue should be fixed in version 0.20. :)
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7599874114b03ecbc9592d9792e9379a3e8a760b commit 7599874114b03ecbc9592d9792e9379a3e8a760b Author: Aisha Tammy <gentoo@aisha.cc> AuthorDate: 2020-10-15 14:26:05 +0000 Commit: Benda Xu <heroxbd@gentoo.org> CommitDate: 2020-11-09 14:01:44 +0000 sci-libs/scikits_learn: version bump to 0.23.2 drop dependency on sci-libs/scikits drop old versions. Closes: https://bugs.gentoo.org/692662 Closes: https://bugs.gentoo.org/626796 Closes: https://bugs.gentoo.org/614558 Closes: https://bugs.gentoo.org/469924 Reported-by: Zoltan Puskas, Roman Yurchak, Крыськов Денис Reported-by: Roman Yurchak, Neil, Tomáš Mózes, Thomas Kemmer Package-Manager: Portage-3.0.8, Repoman-3.0.1 Signed-off-by: Aisha Tammy <gentoo@aisha.cc> Signed-off-by: Benda Xu <heroxbd@gentoo.org> sci-libs/scikits_learn/Manifest | 4 +- .../files/scikits_learn-0.18.1-system-cblas.patch | 32 ------ .../files/scikits_learn-0.20.2-fix-cdfast.patch | 42 -------- .../scikits_learn/scikits_learn-0.19.0-r1.ebuild | 107 -------------------- sci-libs/scikits_learn/scikits_learn-0.20.2.ebuild | 109 --------------------- sci-libs/scikits_learn/scikits_learn-0.20.4.ebuild | 109 --------------------- ...p1.ebuild => scikits_learn-0.22.2_p1-r1.ebuild} | 8 +- sci-libs/scikits_learn/scikits_learn-0.23.2.ebuild | 70 +++++++++++++ 8 files changed, 72 insertions(+), 409 deletions(-)
