On OSX we don't build our own sqlite as that tends to conflict with the OSX-provided version.
On Thursday, April 2, 2015 at 4:36:03 PM UTC+2, David Einstein wrote: > > 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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