I'm beginning to understand what is wrong. A couple of years ago I must have overwritten the default python 2.7 with something newer (I have vague recollections of needing it to get scipy working). A stupid thing to do, and I should know better.
Now _sqlite3 is in /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-dynload/ as opposed to /System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/ and so is not being loaded. (the other modules that are missing in my build also seem to appear in lib-dynload) adding the lib-dynload directory to sys.path in the sage copy of python does not work, it complains about missing symbols, a not entirely unexpected result. I see that sage builds its own sqlite. Is there some way of getting the sage python to use that ? On Tuesday, March 31, 2015 at 5:18:31 PM UTC-4, John H Palmieri wrote: > > > > On Tuesday, March 31, 2015 at 1:03:08 PM UTC-7, David Einstein wrote: >> >> When building python it does complain about not finding _sqlite3 along >> with >> >> _bsddb _sqlite3 _ssl >> bsddb185 dbm dl >> gdbm imageop linuxaudiodev >> nis ossaudiodev spwd >> sunaudiodev >> >> > For what it's worth, on my OS X machine, it only complains about > > _bsddb dl gdbm > imageop linuxaudiodev ossaudiodev > spwd sunaudiodev > > > -- John > > > > >> Could this be because I have the anaconda python distribution shadowing >> the base python distribution? This is presumably a bad idea. >> >> If I run python from the command line it does find _sqlite3 though. >> >> I'll try removing anaconda from my path and see what happens. >> >> Thanks for the help. >> >> On Tuesday, March 31, 2015 at 2:50:38 PM UTC-4, John H Palmieri wrote: >>> >>> >>> >>> On Tuesday, March 31, 2015 at 11:31:42 AM UTC-7, David Einstein wrote: >>>> >>>> The sqlite package seems to have installed correctly. Log attached. >>>> >>> >>> On OS X, Sage's sqlite package just creates a link to the pre-existing >>> file /usr/bin/sqlite3. The error mentioned "_sqlite3", which is a Python >>> module and it is supposed to be installed as part of Sage's Python package. >>> There might have been an error message in the Python log file about >>> building _sqlite3. >>> >>> >>>> I am guilty of having a homebrew sqlite (It was quarantined in the >>>> Cellar) I have removed it and will try to recompile from scratch. >>>> >>>> >>>> Found local metadata for sqlite-3.8.4.3 >>>> Attempting to download package sqlite-3.8.4.3 >>>> >>> Trying to download >>>> http://www.sagemath.org/packages/upstream/sqlite/sqlite-3.8.4.3.tar.bz2 >>>> % Total % Received % Xferd Average Speed Time Time Time >>>> Current >>>> Dload Upload Total Spent Left >>>> Speed >>>> >>>> 0 0 0 0 0 0 0 0 --:--:-- --:--:-- >>>> --:--:-- 0 >>>> 1 1433k 1 23376 0 0 37081 0 0:00:39 --:--:-- >>>> 0:00:39 37045 >>>> 35 1433k 35 506k 0 0 324k 0 0:00:04 0:00:01 >>>> 0:00:03 324k >>>> 100 1433k 100 1433k 0 0 616k 0 0:00:02 0:00:02 >>>> --:--:-- 616k >>>> Checksum: d721fb8c43d91321b58f020a06351d15b321b2a3 vs >>>> d721fb8c43d91321b58f020a06351d15b321b2a3 >>>> sqlite-3.8.4.3 >>>> ==================================================== >>>> Setting up build directory for sqlite-3.8.4.3 >>>> Finished set up >>>> **************************************************** >>>> Host system: >>>> Darwin Davids-MacBook-Pro-2.local 13.4.0 Darwin Kernel Version 13.4.0: >>>> Wed Dec 17 19:05:52 PST 2014; root:xnu-2422.115.10~1/RELEASE_X86_64 x86_64 >>>> **************************************************** >>>> C compiler: gcc >>>> C compiler version: >>>> Using built-in specs. >>>> COLLECT_GCC=gcc >>>> >>>> COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/4.8.2_1/libexec/gcc/x86_64-apple-darwin13.2.0/4.8.2/lto-wrapper >>>> Target: x86_64-apple-darwin13.2.0 >>>> Configured with: ../configure --build=x86_64-apple-darwin13.2.0 >>>> --prefix=/usr/local/Cellar/gcc/4.8.2_1 >>>> --enable-languages=c,c++,objc,obj-c++,fortran >>>> --with-gmp=/usr/local/opt/gmp >>>> --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc >>>> --with-cloog=/usr/local/opt/cloog --with-isl=/usr/local/opt/isl >>>> --with-system-zlib --enable-version-specific-runtime-libs >>>> --enable-libstdcxx-time=yes --enable-stage1-checking >>>> --enable-checking=release --enable-lto --disable-werror --enable-plugin >>>> --disable-nls --enable-multilib >>>> --with-native-system-header-dir=/usr/include >>>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk >>>> Thread model: posix >>>> gcc version 4.8.2 (GCC) >>>> **************************************************** >>>> >>>> real 0m0.010s >>>> user 0m0.006s >>>> sys 0m0.006s >>>> Successfully installed sqlite-3.8.4.3 >>>> Deleting temporary build directory >>>> >>>> /Users/davideinstein/projects/sage-git/local/var/tmp/sage/build/sqlite-3.8.4.3 >>>> Finished installing sqlite-3.8.4.3.spkg >>>> >>>> On Tuesday, March 31, 2015 at 2:08:42 PM UTC-4, Volker Braun wrote: >>>>> >>>>> Whats in your sqlite and python compile log (in $SAGE_ROOT/logs/pkgs)? >>>>> >>>>> Do you have another conflicting sqlite install in /usr/local, e.g. >>>>> homebrew and friends? >>>>> >>>>> >>>>> >>>>> On Tuesday, March 31, 2015 at 7:51:58 PM UTC+2, David Einstein wrote: >>>>>> >>>>>> When attempting to compile sage from source on my laptop it dies >>>>>> attempting to compile conway polynomials >>>>>> I've attached the log file. >>>>>> This appears connected to ticket #15433, but AFAICT that code has >>>>>> been merged into master. >>>>>> >>>>>> >>>>>> Found local metadata for conway_polynomials-0.4.p0 >>>>>> Attempting to download package conway_polynomials-0.4.p0 >>>>>> >>> Trying to download >>>>>> http://www.sagemath.org/packages/upstream/conway_polynomials/conway_polynomials-0.4.tar.bz2 >>>>>> [...........................] >>>>>> Checksum: 25b7abe5c935d20c3ebcde943308652c412d14dc vs >>>>>> 25b7abe5c935d20c3ebcde943308652c412d14dc >>>>>> conway_polynomials-0.4.p0 >>>>>> ==================================================== >>>>>> Setting up build directory for conway_polynomials-0.4.p0 >>>>>> Finished set up >>>>>> **************************************************** >>>>>> Host system: >>>>>> Darwin Davids-MacBook-Pro-2.local 13.4.0 Darwin Kernel Version >>>>>> 13.4.0: Wed Dec 17 19:05:52 PST 2014; >>>>>> root:xnu-2422.115.10~1/RELEASE_X86_64 >>>>>> x86_64 >>>>>> **************************************************** >>>>>> C compiler: gcc >>>>>> C compiler version: >>>>>> Using built-in specs. >>>>>> COLLECT_GCC=gcc >>>>>> >>>>>> COLLECT_LTO_WRAPPER=/usr/local/Cellar/gcc/4.8.2_1/libexec/gcc/x86_64-apple-darwin13.2.0/4.8.2/lto-wrapper >>>>>> Target: x86_64-apple-darwin13.2.0 >>>>>> Configured with: ../configure --build=x86_64-apple-darwin13.2.0 >>>>>> --prefix=/usr/local/Cellar/gcc/4.8.2_1 >>>>>> --enable-languages=c,c++,objc,obj-c++,fortran >>>>>> --with-gmp=/usr/local/opt/gmp >>>>>> --with-mpfr=/usr/local/opt/mpfr --with-mpc=/usr/local/opt/libmpc >>>>>> --with-cloog=/usr/local/opt/cloog --with-isl=/usr/local/opt/isl >>>>>> --with-system-zlib --enable-version-specific-runtime-libs >>>>>> --enable-libstdcxx-time=yes --enable-stage1-checking >>>>>> --enable-checking=release --enable-lto --disable-werror --enable-plugin >>>>>> --disable-nls --enable-multilib >>>>>> --with-native-system-header-dir=/usr/include >>>>>> --with-sysroot=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk >>>>>> Thread model: posix >>>>>> gcc version 4.8.2 (GCC) >>>>>> **************************************************** >>>>>> Traceback (most recent call last): >>>>>> File "./spkg-install", line 4, in <module> >>>>>> from sage.all import save >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python2.7/site-packages/sage/all.py", >>>>>> >>>>>> line 110, in <module> >>>>>> from sage.modular.all import * >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python2.7/site-packages/sage/modular/all.py", >>>>>> >>>>>> line 9, in <module> >>>>>> from abvar.all import * >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python2.7/site-packages/sage/modular/abvar/__init__.py", >>>>>> >>>>>> line 1, in <module> >>>>>> import all >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python2.7/site-packages/sage/modular/abvar/all.py", >>>>>> >>>>>> line 7, in <module> >>>>>> from constructor import J0, J1, JH, AbelianVariety >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python2.7/site-packages/sage/modular/abvar/constructor.py", >>>>>> >>>>>> line 21, in <module> >>>>>> from abvar_newform import ModularAbelianVariety_newform >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python2.7/site-packages/sage/modular/abvar/abvar_newform.py", >>>>>> >>>>>> line 18, in <module> >>>>>> from sage.databases.cremona import cremona_letter_code >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python2.7/site-packages/sage/databases/cremona.py", >>>>>> >>>>>> line 54, in <module> >>>>>> from sql_db import SQLDatabase, verify_column >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python2.7/site-packages/sage/databases/sql_db.py", >>>>>> >>>>>> line 80, in <module> >>>>>> import sqlite3 as sqlite >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python/sqlite3/__init__.py", >>>>>> >>>>>> line 24, in <module> >>>>>> from dbapi2 import * >>>>>> File >>>>>> "/Users/davideinstein/projects/sage-git/local/lib/python/sqlite3/dbapi2.py", >>>>>> >>>>>> line 28, in <module> >>>>>> from _sqlite3 import * >>>>>> ImportError: No module named _sqlite3 >>>>>> >>>>>> real 0m14.950s >>>>>> user 0m1.160s >>>>>> sys 0m0.874s >>>>>> >>>>>> ************************************************************************ >>>>>> Error installing package conway_polynomials-0.4.p0 >>>>>> >>>>>> ************************************************************************ >>>>>> Please email sage-devel (http://groups.google.com/group/sage-devel) >>>>>> explaining the problem and including the relevant part of the log file >>>>>> >>>>>> /Users/davideinstein/projects/sage-git/logs/pkgs/conway_polynomials-0.4.p0.log >>>>>> Describe your computer, operating system, etc. >>>>>> If you want to try to fix the problem yourself, *don't* just cd to >>>>>> /Users/davideinstein/projects/sage-git/local/var/tmp/sage/build/conway_polynomials-0.4.p0 >>>>>> >>>>>> and type 'make' or whatever is appropriate. >>>>>> Instead, the following commands setup all environment variables >>>>>> correctly and load a subshell for you to debug the error: >>>>>> (cd >>>>>> '/Users/davideinstein/projects/sage-git/local/var/tmp/sage/build/conway_polynomials-0.4.p0' >>>>>> >>>>>> && '/Users/davideinstein/projects/sage-git/sage' --sh) >>>>>> When you are done debugging, you can type "exit" to leave the >>>>>> subshell. >>>>>> >>>>>> ************************************************************************ >>>>>> >>>>>> -- You received this message because you are subscribed to the Google Groups "sage-devel" group. 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