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

asked 2021-08-21 03:24:44 +0100

kyouren gravatar image

updated 2021-08-21 11:42:33 +0100

slelievre gravatar image

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
[rpy2-3.3.6] Applying ../patches/setup-no-pytest.patch
[rpy2-3.3.6] patching file
[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] 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
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Welcome to Ask Sage! Thank you for this report!

slelievre gravatar imageslelievre ( 2021-08-21 11:40:56 +0100 )edit

2 Answers

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answered 2021-09-06 10:38:05 +0100

kyouren gravatar image

I may have found the cause of the problems.

I saved the /tmp files from the build.

File pip-req-build-d0lh1wr4/rpy2.egg-info/requires.txt has content:

cffi>=1.10.0 jinja2 pytest pytz tzlocal

whereas pip-req-build-d0lh1wr4/ has:

if __name__ == '__main__': pack_dir = {PACKAGE_NAME: os.path.join(package_prefix, 'rpy2')}

requires = ['jinja2', 'pytz', 'tzlocal']

So, pytest is missing.

Could anyone confirm this possible error, please?

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Note the line Applying ../patches/setup-no-pytest.patch in the log file: this patch removes pytest as a dependency in rpy2's So I don't know why it's in the file you quoted. On the other hand, you could try sage -i pytest to install that package and see if that helps with rpy2.

John Palmieri gravatar imageJohn Palmieri ( 2021-09-07 20:26:03 +0100 )edit

answered 2021-08-21 11:40:23 +0100

slelievre gravatar image

If you're not planning to use R at all, you can disable it in the build with a configure option:

$ make configure
$ ./configure --disable-r
$ make -s V=0  # or just `make` if you prefer verbose
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Thank you, I will use the disable configure option.

I'll have a go at working out why it the build hangs, as well.

kyouren gravatar imagekyouren ( 2021-08-22 00:01:32 +0100 )edit

I hope you work that out and it can be fixed.

slelievre gravatar imageslelievre ( 2021-08-22 01:08:47 +0100 )edit

I installed 9.4 yesterday, with rpy2 hanging.

I didn't modify the configure, however I was "successful" using export MAKE="make -j4". I think this helped by leaving the rpy2 build running, but successfully running everything else.

The build seemed to have finished, with the last message:

[dochtml] Build finished. The built documents can be found in /media/kevin/KCY_Samsung_T5/Sage/sage-9.4/local/share/doc/sage/html/en/thematic_tutorials

I checked my "System Monitor", and there was about a dozen rpy2 tasks hanging, so I killed them. Sage and Jupyter worked OK.

I think the problem is rpy2 "requires" pytest, which doesn't seem compatible with Sage.

I'll keep looking.

kyouren gravatar imagekyouren ( 2021-09-04 19:15:43 +0100 )edit

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Asked: 2021-08-21 03:24:44 +0100

Seen: 148 times

Last updated: Sep 06 '21