You didn't set SAGE_FAT_BINARY=yes I guess since in that case we configure R --without-ICU
I take it you have Ubuntu's version of ATLAS installed on snapperkob and not on muizenberg? On Friday, November 21, 2014 8:21:28 AM UTC, pipedream wrote: > > Hi Volker, > > I repeated on snapperkob, not via buildbot just as my own user: > > real 125m41.153s > user 208m24.169s > sys 20m6.421s > *************************************************************** > Error building Sage. > > The following package(s) may have failed to build: > > package: r-3.1.1.p0 > log file: /home/jan/sage-6.4/logs/pkgs/r-3.1.1.p0.log > build directory: /home/jan/sage-6.4/local/var/tmp/sage/build/r-3.1.1.p0 > > The build directory may contain configuration files and other potentially > helpful information. WARNING: if you now run 'make' again, the build > directory will, by default, be deleted. Set the environment variable > SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this. > > make: *** [build] Error 1 > 2 jan@snapperkob:~/sage-6.4$ > > I can try investigate what is different on muizenberg and snapperkob or my > user on muizenberg & snapperkob. > > They are both Dell Optiplex, 64 bit, entirely up to date Ubuntu 14.04.1, > though: > > snapperkob is a text-only server install > muizenberg is a GUI full desktop install > > There is little difference underneath in ubuntu though. It is the same > kernel. (the package linux-server depends on linux-generic which is also on > the desktop, and depends on the actual kernel) > > They both have the Intel E8400 CPU. They both have 8G RAM. > > Comparing the logs for the two R builds, I found these differences in the > configure parts, due to different packages available on the system: > > muizenberg (built successfully) > > R is now configured for x86_64-unknown-linux-gnu > > Source directory: . > Installation directory: /srv/sysadm/sage/sage-6.4/local > > C compiler: gcc -std=gnu99 -g -O2 > Fortran 77 compiler: gfortran -g -O2 > > C++ compiler: g++ > C++ 11 compiler: g++ -std=c++11 > Fortran 90/95 compiler: gfortran -g -O2 > Obj-C compiler: > > Interfaces supported: > External libraries: readline, ICU, lzma > Additional capabilities: PNG, JPEG, TIFF, NLS, cairo > Options enabled: shared R library, shared BLAS, R profiling > > Recommended packages: yes > > > And snapperkob (failed): > > R is now configured for x86_64-unknown-linux-gnu > > Source directory: . > Installation directory: /home/jan/sage-6.4/local > > C compiler: gcc -std=gnu99 -g -O2 > Fortran 77 compiler: gfortran -g -O2 > > C++ compiler: g++ > C++ 11 compiler: g++ -std=c++11 > Fortran 90/95 compiler: gfortran -g -O2 > Obj-C compiler: > > Interfaces supported: X11, tcltk > External libraries: readline, BLAS(ATLAS), LAPACK(generic), ICU > Additional capabilities: PNG, JPEG, NLS, cairo > Options enabled: shared R library, R profiling > > Recommended packages: yes > > > Can you think what I can change on snapperkob to test? BLAS or LAPACK > perhaps? > > Regards, > Jan > > > > > > > On 20 November 2014 20:35, Jan Groenewald <[email protected] <javascript:>> > wrote: > >> Different machine: >> >> 0 root@muizenberg:/srv/sysadm/sage#dpkg -S >> /usr/lib/x86_64-linux-gnu/libgomp.so.* >> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1 >> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >> 0 root@muizenberg:/srv/sysadm/sage#dpkg -l libgomp1 >> Desired=Unknown/Install/Remove/Purge/Hold >> | >> Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend >> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) >> ||/ Name Version >> Architecture Description >> >> +++-=======================================-========================-========================-=================================================================================== >> ii libgomp1:amd64 4.8.2-19ubuntu1 >> amd64 GCC OpenMP (GOMP) support library >> 0 root@muizenberg:/srv/sysadm/sage# >> >> Same version: >> >> 0 jan@snapperkob:~/src$dpkg -S /usr/lib/x86_64-linux-gnu/libgomp.so.* >> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1 >> libgomp1:amd64: /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0 >> 0 jan@snapperkob:~/src$dpkg -l libgomp1 >> Desired=Unknown/Install/Remove/Purge/Hold >> | >> Status=Not/Inst/Conf-files/Unpacked/halF-conf/Half-inst/trig-aWait/Trig-pend >> |/ Err?=(none)/Reinst-required (Status,Err: uppercase=bad) >> ||/ Name Version >> Architecture Description >> >> +++-=======================================-========================-========================-=================================================================================== >> ii libgomp1:amd64 4.8.2-19ubuntu1 >> amd64 GCC OpenMP (GOMP) support library >> 0 jan@snapperkob:~/src$ >> >> Regards, >> Jan >> >> >> >> On 20 November 2014 18:32, Volker Braun <[email protected] <javascript:> >> > wrote: >> >>> Is this on "snapperkob" or on a different machine? Do you >>> have /usr/lib/x86_64-linux-gnu/libgomp.so.* and if yes, which version? >>> >>> >>> >>> On Thursday, November 20, 2014 12:02:18 PM UTC, pipedream wrote: >>>> >>>> Hi >>>> >>>> I rebuilt sage from a cleanly unpacked source tree on Ubuntu 14.04, and >>>> it still did not fail on R >>>> >>>> >>>> export SAGE_INSTALL_GCC=yes >>>> make >>>> ... >>>> Successfully installed r-3.1.1.p0 >>>> >>>> I'd like to assist running any tests to get this fixed. >>>> >>>> Regards, >>>> Jan >>>> >>>> >>>> On 19 November 2014 09:09, Jan Groenewald <[email protected]> wrote: >>>> >>>>> Hi >>>>> >>>>> I did >>>>> >>>>> $SAGE_INSTALL_GCC=yes make >>>>> >>>>> in the already built source tree, and it seemed to rebuild the >>>>> relevant parts without failing. Is that enough or should I try it in a >>>>> cleanly unpacked source tree? >>>>> >>>>> Regards, >>>>> Jan >>>>> >>>>> >>>>> On 18 November 2014 15:56, Jan Groenewald <[email protected]> wrote: >>>>> >>>>>> Will do. >>>>>> >>>>>> Regards, >>>>>> Jan >>>>>> >>>>>> >>>>>> On 18 November 2014 15:29, Volker Braun <[email protected]> wrote: >>>>>> >>>>>>> Try building with SAGE_INSTALL_GCC=yes, I'm pretty sure this is >>>>>>> causing the problem. >>>>>>> >>>>>>> On Tuesday, November 18, 2014 11:56:03 AM UTC, pipedream wrote: >>>>>>>> >>>>>>>> Hi >>>>>>>> >>>>>>>> This is strange, the error I see is: >>>>>>>> >>>>>>>> /home/buildbot/build/sage/snapperkob/sage_git/build/local/var/tmp/sage/build/r-3.1.1.p0/src/bin/exec/R: >>>>>>>> /usr/lib/x86_64-linux-gnu/libgomp.so.1: version `GOMP_4.0' not found >>>>>>>> (required by >>>>>>>> /home/buildbot/build/sage/snapperkob/sage_git/build/local/var/tmp/sage/build/r-3.1.1.p0/src/lib/libR.so) >>>>>>>> >>>>>>>> I have the same version of libgomp1 (4.8.2-19ubuntu1) installed on >>>>>>>> my 14.04 64bit desktop as that builder (snapperkob) and yet sage 6.4 >>>>>>>> built >>>>>>>> succesfully on my desktop yesterday: >>>>>>>> >>>>>>>> "Successfully installed r-3.1.1.p0" >>>>>>>> >>>>>>>> Regards, >>>>>>>> Jan >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On 18 November 2014 13:22, Volker Braun <[email protected]> wrote: >>>>>>>> >>>>>>>>> The build failed because R insists on using openmp for some >>>>>>>>> reason, but the openmp libraries are not installed (or of the wrong >>>>>>>>> version): >>>>>>>>> >>>>>>>>> http://build.sagedev.org/release/builders/Zbin%20%20fast% >>>>>>>>> 20AIMS%20snapperkob%20%28Ubuntu%2014.04%20x86_64%29%20binary >>>>>>>>> /builds/1/steps/compile_2/logs/r-project >>>>>>>>> >>>>>>>>> >>>>>>>>> On Tuesday, November 18, 2014 5:00:26 AM UTC, pipedream wrote: >>>>>>>>>> >>>>>>>>>> Hi >>>>>>>>>> >>>>>>>>>> I do not see the 14.04 Ubuntu binaries here. >>>>>>>>>> http://boxen.math.washington.edu/home/sagemath/sage-mirror/l >>>>>>>>>> inux/64bit/index.html >>>>>>>>>> >>>>>>>>>> Are they not automatically generated? >>>>>>>>>> >>>>>>>>>> Regards, >>>>>>>>>> Jan >>>>>>>>>> >>>>>>>>>> On 17 November 2014 17:17, kcrisman <[email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> The release notes have a broken link in them: >>>>>>>>>>>> >>>>>>>>>>>> http://boxen.math.washington.edu/home/release/sage-6.4/ >>>>>>>>>>>> tickets.html >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> Yes, that has been reported before... >>>>>>>>>>> >>>>>>>>>>> By the way, Jeroen, I think I finished all the changes I'm going >>>>>>>>>>> to for now. Long-term, it would be fun to do some database thingie >>>>>>>>>>> to >>>>>>>>>>> standardize names of a few very frequent contributors who have them >>>>>>>>>>> in a >>>>>>>>>>> couple different formats. >>>>>>>>>>> >>>>>>>>>>> >>>> -- >>>> .~. >>>> /V\ Jan Groenewald >>>> /( )\ www.aims.ac.za >>>> ^^-^^ >>>> >>> -- >>> You received this message because you are subscribed to the Google >>> Groups "sage-release" group. >>> To unsubscribe from this group and stop receiving emails from it, send >>> an email to [email protected] <javascript:>. >>> To post to this group, send email to [email protected] >>> <javascript:>. >>> Visit this group at http://groups.google.com/group/sage-release. >>> For more options, visit https://groups.google.com/d/optout. >>> >> >> >> >> -- >> .~. >> /V\ Jan Groenewald >> /( )\ www.aims.ac.za >> ^^-^^ >> > > > > -- > .~. > /V\ Jan Groenewald > /( )\ www.aims.ac.za > ^^-^^ > -- You received this message because you are subscribed to the Google Groups "sage-release" group. 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