hpages
commented
4 years ago It failed to install for me. Showing only the truncated output of R CMD INSTALL basilisk:
First 55 lines:
* installing to library ‘/home/hpages/R/R-3.6.r76454/library’
* installing *source* package ‘basilisk’ ...
** using non-staged installation via StagedInstall field
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
downloading Python 3.7.0...
--2019-10-08 18:00:11-- https://www.python.org/ftp/python/3.7.0/Python-3.7.0.tgz
Resolving www.python.org (www.python.org)... 151.101.52.223, 2a04:4e42:d::223
Connecting to www.python.org (www.python.org)|151.101.52.223|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 22745726 (22M) [application/octet-stream]
Saving to: 'Python-3.7.0.tgz'
Python-3.7.0.tgz 100%[===================>] 21.69M 3.46MB/s in 6.4s
2019-10-08 18:00:17 (3.41 MB/s) - 'Python-3.7.0.tgz' saved [22745726/22745726]
building Python...
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for python3.7... no
checking for python3... python3
checking for --enable-universalsdk... no
checking for --with-universal-archs... no
checking MACHDEP... checking for --without-gcc... no
checking for --with-icc... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for a sed that does not truncate output... /bin/sed
checking for --with-cxx-main=<compiler>... no
checking for g++... no
configure:
By default, distutils will build C++ extension modules with "g++".
If this is not intended, then set CXX on the configure command line.
checking for the platform triplet based on compiler characteristics... x86_64-linux-gnu
checking for -Wl,--no-as-needed... yes
checking for egrep... /bin/grep -E
...Last 65 lines:
...
rm -f /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin/idle3
(cd /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin; ln -s idle3.7 idle3)
rm -f /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin/pydoc3
(cd /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin; ln -s pydoc3.7 pydoc3)
rm -f /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin/2to3
(cd /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin; ln -s 2to3-3.7 2to3)
rm -f /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin/pyvenv
(cd /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin; ln -s pyvenv-3.7 pyvenv)
if test "x" != "x" ; then \
rm -f /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin/python3-32; \
(cd /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/bin; ln -s python3.7-32 python3-32) \
fi
rm -f /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/share/man/man1/python3.1
(cd /home/hpages/R/R-3.6.r76454/library/basilisk/inst/python/share/man/man1; ln -s python3.7.1 python3.1)
if test "xupgrade" != "xno" ; then \
case upgrade in \
upgrade) ensurepip="--upgrade" ;; \
install|*) ensurepip="" ;; \
esac; \
LD_LIBRARY_PATH=/home/hpages/github/LTLA/basilisk/src/Python-3.7.0:/home/hpages/R/R-3.6.r76454/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server:/home/hpages/R/R-3.6.r76454/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server ./python -E -m ensurepip \
$ensurepip --root=/ ; \
fi
Traceback (most recent call last):
File "/home/hpages/github/LTLA/basilisk/src/Python-3.7.0/Lib/runpy.py", line 193, in _run_module_as_main
"__main__", mod_spec)
File "/home/hpages/github/LTLA/basilisk/src/Python-3.7.0/Lib/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/hpages/github/LTLA/basilisk/src/Python-3.7.0/Lib/ensurepip/__main__.py", line 5, in <module>
sys.exit(ensurepip._main())
File "/home/hpages/github/LTLA/basilisk/src/Python-3.7.0/Lib/ensurepip/__init__.py", line 204, in _main
default_pip=args.default_pip,
File "/home/hpages/github/LTLA/basilisk/src/Python-3.7.0/Lib/ensurepip/__init__.py", line 117, in _bootstrap
return _run_pip(args + [p[0] for p in _PROJECTS], additional_paths)
File "/home/hpages/github/LTLA/basilisk/src/Python-3.7.0/Lib/ensurepip/__init__.py", line 27, in _run_pip
import pip._internal
File "/tmp/tmpfmgyofri/pip-10.0.1-py2.py3-none-any.whl/pip/_internal/__init__.py", line 42, in <module>
File "/tmp/tmpfmgyofri/pip-10.0.1-py2.py3-none-any.whl/pip/_internal/cmdoptions.py", line 16, in <module>
File "/tmp/tmpfmgyofri/pip-10.0.1-py2.py3-none-any.whl/pip/_internal/index.py", line 25, in <module>
File "/tmp/tmpfmgyofri/pip-10.0.1-py2.py3-none-any.whl/pip/_internal/download.py", line 39, in <module>
File "/tmp/tmpfmgyofri/pip-10.0.1-py2.py3-none-any.whl/pip/_internal/utils/glibc.py", line 3, in <module>
File "/home/hpages/github/LTLA/basilisk/src/Python-3.7.0/Lib/ctypes/__init__.py", line 7, in <module>
from _ctypes import Union, Structure, Array
ModuleNotFoundError: No module named '_ctypes'
Makefile:1122: recipe for target 'install' failed
make[1]: *** [install] Error 1
make[1]: Leaving directory '/home/hpages/github/LTLA/basilisk/src/Python-3.7.0'
Makevars:6: recipe for target 'copying' failed
make: *** [copying] Error 2
ERROR: compilation failed for package ‘basilisk’
* removing ‘/home/hpages/R/R-3.6.r76454/library/basilisk’
LTLA
grimbough
vjcitn
Tagging @hpages and @grimbough.
The idea is to package up a self-contained instance of Python for distribution via the R package management system. This aims to control the version of both Python and all of its modules for a given Bioconductor release, thus allowing BioC packages to reliably deploy with Python code.
The current version of this package works well enough on Unix, provided libffi is available. The tricky bit is what to do with the pre-built binaries for macs and windows. The Python executable can either be linked to a shared library or a static library, and while the latter is more obviously portable, the former is necessary for reticulate to work at all. And we really want reticulate to work here, otherwise no one's going to get on board with this solution.
So, this means that we need to distribute the compiled shared library along with the executable, which is not great. However, R already faces (and solves) this challenge when it distributes pre-built binaries of any package with native code, as these also contain shared libraries. Casual inspection of those libraries indicate that they have hard-coded paths like:
So in principle, we could just piggy-back off that by hard-coding similar paths into the Python shared library (which would also be dumped somewhere in the basilisk installation directory, so it wouldn't be any different from what we see above).
I also had some difficulties linking to OpenSSL on my mac, but I don't know whether that would be a more general problem or just something to do with my system. Looking at the openssl
configurefile suggests that some fiddling is required there.