Well, I'm building from a clean git repo, i.e. that's what I do:
$ git branch
* (HEAD detached at 9.1.beta1)
develop
origin
$ git reset --hard
$ git clean -fdx
$ unset _JAVA_OPTIONS
$ nice make
I tried it again, same set of scipy errors.
This is from before the errors, maybe it contains some useful info. And
yes, Matthias, #29051 sounds related.
[scipy-1.2.0] scipy-1.2.0
[scipy-1.2.0] ====================================================
[scipy-1.2.0] Setting up build directory for scipy-1.2.0
[scipy-1.2.0] Finished extraction
[scipy-1.2.0] Applying patches from ../patches...
[scipy-1.2.0] Applying
../patches/4a8a35f2c27be9f209cfc6f347e7a57a4a62e693.patch
[scipy-1.2.0] patching file scipy/io/__init__.py
[scipy-1.2.0] patching file scipy/stats/_continuous_distns.py
[scipy-1.2.0] patching file scipy/stats/_stats_mstats_common.py
[scipy-1.2.0] ****************************************************
[scipy-1.2.0] Host system:
[scipy-1.2.0] Linux ee59ece61f58 4.15.0-1036-gcp #38-Ubuntu SMP Mon Jun 24
13:49:05 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
[scipy-1.2.0] ****************************************************
[scipy-1.2.0] C compiler: gcc
[scipy-1.2.0] C compiler version:
[scipy-1.2.0] Using built-in specs.
[scipy-1.2.0] COLLECT_GCC=gcc
[scipy-1.2.0] COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/7/lto-wrapper
[scipy-1.2.0] OFFLOAD_TARGET_NAMES=nvptx-none
[scipy-1.2.0] OFFLOAD_TARGET_DEFAULT=1
[scipy-1.2.0] Target: x86_64-linux-gnu
[scipy-1.2.0] Configured with: ../src/configure -v --with-pkgversion='Ubuntu
7.4.0-1ubuntu1~18.04.1' --with-bugurl=file:///usr/
share/doc/gcc-7/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,
objc,obj-c++ --prefix=/usr --with-gcc-major-version-
only --program-suffix=-7 --program-prefix=x86_64-linux-gnu- --enable-shared
--enable-linker-build-id --libexecdir=/usr/lib --wi
thout-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls
--with-sysroot=/ --enable-clocale=gnu --enable-lib
stdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --
enable-gnu-unique-object --disable-vtable-verify --
enable-libmpx --enable-plugin --enable-default-pie --with-system-zlib --with
-target-system-zlib --enable-objc-gc=auto --enable-
multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-
multilib-list=m32,m64,mx32 --enable-multilib --with-tune=g
eneric --enable-offload-targets=nvptx-none --without-cuda-driver --enable-
checking=release --build=x86_64-linux-gnu --host=x86_
64-linux-gnu --target=x86_64-linux-gnu
[scipy-1.2.0] Thread model: posix
[scipy-1.2.0] gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1)
On Thursday, January 23, 2020 at 10:09:03 AM UTC+1, Dima Pasechnik wrote:
>
> is it a rebuild after
>
> make distclean
>
> ?
>
> Sage now is trying to use openblas and several packages, such as R and
> gsl, installed on the system
>
> On Thu, 23 Jan 2020, 09:01 Harald Schilly, <[email protected]>
> wrote:
>
>> Building it for CoCalc (ubuntu 18.04 docker container) it fails at SciPy.
>> Can't find any of the required libs. There was no change in the setup,
>> hence I wonder what's going on... I'm happy to check various env vars!
>>
>> [scipy-1.2.0] Running from scipy source directory.
>>
>> [scipy-1.2.0] lapack_opt_info:
>> [scipy-1.2.0] lapack_mkl_info:
>>
>> [scipy-1.2.0] Disabled lapack_mkl_info: (MKLROOT is None)
>> [scipy-1.2.0] Disabled lapack_mkl_info: (MKLROOT is None)
>>
>> [scipy-1.2.0] customize UnixCCompiler
>> [scipy-1.2.0] libraries mkl_rt not found in []
>>
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] openblas_lapack_info:
>> [scipy-1.2.0] customize UnixCCompiler
>> [scipy-1.2.0] Disabled openblas_lapack_info: (OPENBLAS is None)
>> [scipy-1.2.0] customize UnixCCompiler
>> [scipy-1.2.0] libraries openblas not found in []
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] openblas_clapack_info:
>> [scipy-1.2.0] customize UnixCCompiler
>> [scipy-1.2.0] Disabled openblas_clapack_info: (OPENBLAS is None)
>> [scipy-1.2.0] customize UnixCCompiler
>> [scipy-1.2.0] libraries openblas,lapack not found in []
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] atlas_3_10_threads_info:
>> [scipy-1.2.0] Disabled atlas_3_10_threads_info: (PTATLAS is None)
>> [scipy-1.2.0] <class
>> 'numpy.distutils.system_info.atlas_3_10_threads_info'>
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] atlas_3_10_info:
>> [scipy-1.2.0] Disabled atlas_3_10_info: (ATLAS is None)
>> [scipy-1.2.0] <class 'numpy.distutils.system_info.atlas_3_10_info'>
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] atlas_threads_info:
>> [scipy-1.2.0] Disabled atlas_threads_info: (PTATLAS is None)
>> [scipy-1.2.0] <class 'numpy.distutils.system_info.atlas_threads_info'
>> >
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] atlas_info:
>> [scipy-1.2.0] Disabled atlas_info: (ATLAS is None)
>> [scipy-1.2.0] <class 'numpy.distutils.system_info.atlas_info'>
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] accelerate_info:
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] /ext/sage/sage-dev/local/lib/python3.7/site-packages/
>> numpy/distutils/system_info.py:636: UserWarning:
>> [scipy-1.2.0] Atlas (http://math-atlas.sourceforge.net/)
>> libraries not found.
>> [scipy-1.2.0] Directories to search for the libraries can be
>> specified in the
>> [scipy-1.2.0] numpy/distutils/site.cfg file (section [atlas]) or
>> by setting
>> [scipy-1.2.0] the ATLAS environment variable.
>> [scipy-1.2.0] self.calc_info()
>> [scipy-1.2.0] lapack_info:
>> [scipy-1.2.0] customize UnixCCompiler
>> [scipy-1.2.0] libraries openblas not found in [
>> '/ext/sage/sage-dev/local/lib']
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] /ext/sage/sage-dev/local/lib/python3.7/site-packages/
>> numpy/distutils/system_info.py:636: UserWarning:
>> [scipy-1.2.0] Lapack (http://www.netlib.org/lapack/) libraries
>> not found.
>> [scipy-1.2.0] Directories to search for the libraries can be
>> specified in the
>> [scipy-1.2.0] numpy/distutils/site.cfg file (section [lapack]) or
>> by setting
>> [scipy-1.2.0] the LAPACK environment variable.
>> [scipy-1.2.0] self.calc_info()
>> [scipy-1.2.0] lapack_src_info:
>> [scipy-1.2.0] NOT AVAILABLE
>> [scipy-1.2.0]
>> [scipy-1.2.0] /ext/sage/sage-dev/local/lib/python3.7/site-packages/
>> numpy/distutils/system_info.py:636: UserWarning:
>> [scipy-1.2.0] Lapack (http://www.netlib.org/lapack/) sources not
>> found.
>> [scipy-1.2.0] Directories to search for the sources can be
>> specified in the
>> [scipy-1.2.0] numpy/distutils/site.cfg file (section [lapack_src
>> ]) or by setting
>> [scipy-1.2.0] the LAPACK_SRC environment variable.
>> [scipy-1.2.0] self.calc_info()
>> [scipy-1.2.0] NOT AVAILABLE
>>
>>
>>
>> --
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>>
>> <https://groups.google.com/d/msgid/sage-release/3cffdf1a-ae49-4621-8697-2c15dff11f46%40googlegroups.com?utm_medium=email&utm_source=footer>
>> .
>>
>
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