Ask Your Question

Revision history [back]

click to hide/show revision 1
initial version

Install for sage 9.2 & 9.3 'hangs' on build of rpy2

Hi, I have had some trouble installing Sage 9.2 & 9.3 on my Linux Ubuntu system.

I couldn't find any other references to this build problem.

In April, I tried installing 9.2, and and it hung on rpy2 twice, but the 3rd time it worked OK.

I installed 9.3 in this month, and it hung twice. I decided to comment out or remove the rpy2 entries in the "configure" file, and the build was OK.

My Ubuntu system does not use "snap", otherwise generally normal.

[tzlocal-2.1] /media/kevin/KCY_Samsung_T5/Sage/sage-9.3/var/tmp/sage/build/tzlocal-2.1 [tzlocal-2.1] Finished installing tzlocal-2.1 make --no-print-directory rpy2-no-deps sage-logger -p 'SAGE_CHECK=no sage-spkg rpy2-3.3.6' '/media/kevin/KCY_Samsung_T5/Sage/sage-9.3/logs/pkgs/rpy2-3.3.6.log' [rpy2-3.3.6] Using cached file /media/kevin/KCY_Samsung_T5/Sage/sage-9.3/upstream/rpy2-3.3.6.tar.gz [rpy2-3.3.6] rpy2-3.3.6 [rpy2-3.3.6] ==================================================== [rpy2-3.3.6] Setting up build directory for rpy2-3.3.6 [rpy2-3.3.6] Finished extraction [rpy2-3.3.6] Applying patches from ../patches... [rpy2-3.3.6] Applying ../patches/716.patch [rpy2-3.3.6] patching file setup.py [rpy2-3.3.6] Applying ../patches/setup-no-pytest.patch [rpy2-3.3.6] patching file setup.py [rpy2-3.3.6] Hunk #1 succeeded at 177 (offset 35 lines). [rpy2-3.3.6] **************** [rpy2-3.3.6] Host system: [rpy2-3.3.6] Linux KCYDell 5.8.0-63-generic #71-Ubuntu SMP Tue Jul 13 15:59:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux [rpy2-3.3.6] **************** [rpy2-3.3.6] C compiler: gcc [rpy2-3.3.6] C compiler version: [rpy2-3.3.6] Using built-in specs. [rpy2-3.3.6] COLLECT_GCC=gcc [rpy2-3.3.6] COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper [rpy2-3.3.6] OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa [rpy2-3.3.6] OFFLOAD_TARGET_DEFAULT=1 [rpy2-3.3.6] Target: x86_64-linux-gnu [rpy2-3.3.6] Configured with: ../src/configure -v --with-pkgversion='Ubuntu 10.3.0-1ubuntu1~20.10' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --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=generic --enable-offload-targets=nvptx-none=/build/gcc-10-poYruo/gcc-10-10.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-poYruo/gcc-10-10.3.0/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex [rpy2-3.3.6] Thread model: posix [rpy2-3.3.6] Supported LTO compression algorithms: zlib zstd [rpy2-3.3.6] gcc version 10.3.0 (Ubuntu 10.3.0-1ubuntu1~20.10) [rpy2-3.3.6] **************** [rpy2-3.3.6] Package 'rpy2' is currently not installed [rpy2-3.3.6] No legacy uninstaller found for 'rpy2'; nothing to do [rpy2-3.3.6] Installing rpy2-3.3.6 make[3]: * [Makefile:2486: /media/kevin/KCY_Samsung_T5/Sage/sage-9.3/var/lib/sage/installed/rpy2-3.3.6] Killed make[2]: * [Makefile:2160: all-start] Error 2 make[2]: Leaving directory '/media/kevin/KCY_Samsung_T5/Sage/sage-9.3/build/make'

real 352m44.110s user 267m11.446s sys 11m34.531s


Error building Sage.

The following package(s) may have failed to build (not necessarily during this run of 'make all-start'):

It is safe to delete any log files and build directories, but they contain information that is helpful for debugging build problems. WARNING: If you now run 'make' again, the build directory of the same version of the package will, by default, be deleted. Set the environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

make[1]: * [Makefile:39: all-start] Error 1 make[1]: Leaving directory '/media/kevin/KCY_Samsung_T5/Sage/sage-9.3' make: * [Makefile:13: all] Error 2 kevin@KCYDell:/media/kevin/KCY_Samsung_T5/Sage/sage-9.3$

Install for sage 9.2 & 9.3 'hangs' on build of rpy2

Hi, I have had some trouble installing Sage 9.2 & 9.3 on my Linux Ubuntu system.

I couldn't find any other references to this build problem.

In April, I tried installing 9.2, and and it hung on rpy2 twice, but the 3rd time it worked OK.

I installed 9.3 in this month, and it hung twice. I decided to comment out or remove the rpy2 entries in the "configure" file, and the build was OK.

My Ubuntu system does not use "snap", otherwise generally normal.

[tzlocal-2.1] /media/kevin/KCY_Samsung_T5/Sage/sage-9.3/var/tmp/sage/build/tzlocal-2.1
[tzlocal-2.1] Finished installing tzlocal-2.1
make --no-print-directory rpy2-no-deps
sage-logger -p 'SAGE_CHECK=no sage-spkg   rpy2-3.3.6' '/media/kevin/KCY_Samsung_T5/Sage/sage-9.3/logs/pkgs/rpy2-3.3.6.log'
[rpy2-3.3.6] Using cached file /media/kevin/KCY_Samsung_T5/Sage/sage-9.3/upstream/rpy2-3.3.6.tar.gz
[rpy2-3.3.6] rpy2-3.3.6
[rpy2-3.3.6] ====================================================
[rpy2-3.3.6] Setting up build directory for rpy2-3.3.6
[rpy2-3.3.6] Finished extraction
[rpy2-3.3.6] Applying patches from ../patches...
[rpy2-3.3.6] Applying ../patches/716.patch
[rpy2-3.3.6] patching file setup.py
[rpy2-3.3.6] Applying ../patches/setup-no-pytest.patch
[rpy2-3.3.6] patching file setup.py
[rpy2-3.3.6] Hunk #1 succeeded at 177 (offset 35 lines).
[rpy2-3.3.6] **************** ****************************************************
[rpy2-3.3.6] Host system:
[rpy2-3.3.6] Linux KCYDell 5.8.0-63-generic #71-Ubuntu SMP Tue Jul 13 15:59:12 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
[rpy2-3.3.6] **************** ****************************************************
[rpy2-3.3.6] C compiler: gcc
[rpy2-3.3.6] C compiler version:
[rpy2-3.3.6] Using built-in specs.
[rpy2-3.3.6] COLLECT_GCC=gcc
[rpy2-3.3.6] COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/10/lto-wrapper
[rpy2-3.3.6] OFFLOAD_TARGET_NAMES=nvptx-none:amdgcn-amdhsa:hsa
[rpy2-3.3.6] OFFLOAD_TARGET_DEFAULT=1
[rpy2-3.3.6] Target: x86_64-linux-gnu
[rpy2-3.3.6] Configured with: ../src/configure -v --with-pkgversion='Ubuntu 10.3.0-1ubuntu1~20.10' --with-bugurl=file:///usr/share/doc/gcc-10/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,m2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-10 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --enable-libphobos-checking=release --with-target-system-zlib=auto --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=generic --enable-offload-targets=nvptx-none=/build/gcc-10-poYruo/gcc-10-10.3.0/debian/tmp-nvptx/usr,amdgcn-amdhsa=/build/gcc-10-poYruo/gcc-10-10.3.0/debian/tmp-gcn/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex
[rpy2-3.3.6] Thread model: posix
[rpy2-3.3.6] Supported LTO compression algorithms: zlib zstd
[rpy2-3.3.6] gcc version 10.3.0 (Ubuntu 10.3.0-1ubuntu1~20.10) 
[rpy2-3.3.6] **************** ****************************************************
[rpy2-3.3.6] Package 'rpy2' is currently not installed
[rpy2-3.3.6] No legacy uninstaller found for 'rpy2'; nothing to do
[rpy2-3.3.6] Installing rpy2-3.3.6
make[3]: * *** [Makefile:2486: /media/kevin/KCY_Samsung_T5/Sage/sage-9.3/var/lib/sage/installed/rpy2-3.3.6] Killed
make[2]: * *** [Makefile:2160: all-start] Error 2
make[2]: Leaving directory '/media/kevin/KCY_Samsung_T5/Sage/sage-9.3/build/make'

'/media/kevin/KCY_Samsung_T5/Sage/sage-9.3/build/make' real 352m44.110s user 267m11.446s sys 11m34.531s


11m34.531s *************************************************************** Error building Sage.

Sage. The following package(s) may have failed to build (not necessarily during this run of 'make all-start'):

all-start'): It is safe to delete any log files and build directories, but they contain information that is helpful for debugging build problems. WARNING: If you now run 'make' again, the build directory of the same version of the package will, by default, be deleted. Set the environment variable SAGE_KEEP_BUILT_SPKGS=yes to prevent this.

this. make[1]: * *** [Makefile:39: all-start] Error 1 make[1]: Leaving directory '/media/kevin/KCY_Samsung_T5/Sage/sage-9.3' make: * *** [Makefile:13: all] Error 2 kevin@KCYDell:/media/kevin/KCY_Samsung_T5/Sage/sage-9.3$

kevin@KCYDell:/media/kevin/KCY_Samsung_T5/Sage/sage-9.3$