R only uses our ATLAS if X development stuff is installed. The whole logic in the spkg-install is suspicious...
On Friday, November 21, 2014 7:02:52 PM UTC, pipedream wrote: > > Hi > > I didn't set SAGE_FAT_BINARY on either. > > Actually, I have atlas on muizenberg not snapperkob: > > 0 root@muizenberg:~#dpkg -l |grep atlas > ii libatlas3-base > 3.10.1-4 amd64 > Automatically Tuned Linear Algebra Software, generic shared > 0 root@muizenberg:~# > > > 1 jan@snapperkob:~/sage-6.4$dpkg -l |grep atlas > 1 jan@snapperkob:~/sage-6.4$ > > > Regards, > Jan > > On 21 November 2014 14:54, Volker Braun <[email protected] <javascript:>> > wrote: > >> 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]> 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]> 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%20A >>>>>>>>>>> IMS%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]. >>>>> To post to this group, send email to [email protected]. >>>>> 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. >> 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 > ^^-^^ > -- 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]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/sage-release. For more options, visit https://groups.google.com/d/optout.
