almost there on my octave udpates. Just nan-atlas-octave364 isn't playing nicely. Output below, not sure what is going wrong, could it be a case-sensitive file system problem??
many thanks, -- Viv ________________________________________________ Dr Viv Kendon http://quantum.leeds.ac.uk/~viv tel: +44 113 343 4864 Physics and Astronomy Quantum Information Group University of Leeds The following package will be installed or updated: nan-atlas-oct364 Setting runtime build-lock... dpkg-deb -b /sw/src/fink.build/root-fink-buildlock-nan-atlas-oct364-2.5.5-8 /sw/src/fink.build dpkg-deb: building package `fink-buildlock-nan-atlas-oct364-2.5.5-8' in `/sw/src/fink.build/fink-buildlock-nan-atlas-oct364-2.5.5-8_2013.10.03-12.36.13_darwin-x86_64.deb'. Installing build-lock package... /sw/bin/dpkg-lockwait -i /sw/src/fink.build/fink-buildlock-nan-atlas-oct364-2.5.5-8_2013.10.03-12.36.13_darwin-x86_64.deb Selecting previously deselected package fink-buildlock-nan-atlas-oct364-2.5.5-8. (Reading database ... 266034 files and directories currently installed.) Unpacking fink-buildlock-nan-atlas-oct364-2.5.5-8 (from .../fink-buildlock-nan-atlas-oct364-2.5.5-8_2013.10.03-12.36.13_darwin-x86_64.deb) ... Setting up fink-buildlock-nan-atlas-oct364-2.5.5-8 (2013.10.03-12.36.13) ... env LANG=C LC_ALL=C /sw/bin/tar --no-same-owner --no-same-permissions -xvf /sw/src/nan-2.5.5.tar.gz NaN/ NaN/inst/ NaN/inst/hist2res.m NaN/inst/moment.m NaN/inst/mean.m NaN/inst/xval.m NaN/inst/classify.m NaN/inst/geomean.m NaN/inst/nantest.m NaN/inst/var.m NaN/inst/nanfft.m NaN/inst/zscore.m NaN/inst/tcdf.m NaN/inst/statistic.m NaN/inst/norminv.m NaN/inst/spearman.m NaN/inst/median.m NaN/inst/normpdf.m NaN/inst/meansq.m NaN/inst/naninsttest.m NaN/inst/kurtosis.m NaN/inst/trimean.m NaN/inst/tinv.m NaN/inst/range.m NaN/inst/ranks.m NaN/inst/ttest.m NaN/inst/meandev.m NaN/inst/normcdf.m NaN/inst/nansum.m NaN/inst/row_col_deletion.m NaN/inst/train_lda_sparse.m NaN/inst/rms.m NaN/inst/cov.m NaN/inst/flag_implicit_skip_nan.m NaN/inst/cdfplot.m NaN/inst/nanstd.m NaN/inst/nanmean.m NaN/inst/harmmean.m NaN/inst/nanconv.m NaN/inst/corrcoef.m NaN/inst/nanfilter.m NaN/inst/cat2bin.m NaN/inst/sem.m NaN/inst/ecdf.m NaN/inst/flag_nans_occured.m NaN/inst/test_sc.m NaN/inst/std.m NaN/inst/train_sc.m NaN/inst/covm.m NaN/inst/partcorrcoef.m NaN/inst/decovm.m NaN/inst/mad.m NaN/inst/rankcorr.m NaN/inst/trimmean.m NaN/inst/mahal.m NaN/inst/cumsumskipnan.m NaN/inst/coefficient_of_variation.m NaN/inst/prctile.m NaN/inst/flag_implicit_significance.m NaN/inst/tpdf.m NaN/inst/tiedrank.m NaN/inst/cor.m NaN/inst/xptopen.m NaN/inst/bland_altman.m NaN/inst/load_fisheriris.m NaN/inst/center.m NaN/inst/flag_accuracy_level.m NaN/inst/gscatter.m NaN/inst/iqr.m NaN/inst/zScoreMedian.m NaN/inst/skewness.m NaN/inst/detrend.m NaN/inst/percentile.m NaN/inst/medAbsDev.m NaN/inst/fss.m NaN/inst/quantile.m NaN/inst/xcovf.m NaN/inst/ttest2.m NaN/inst/sumsq.m NaN/inst/sumskipnan.m NaN/inst/nanfilter1uc.m NaN/inst/kappa.m NaN/DESCRIPTION NaN/INDEX NaN/src/ NaN/src/kth_element.mexa64 NaN/src/make.m NaN/src/kth_element.mexw32 NaN/src/train.mexa64 NaN/src/histo_mex.cpp NaN/src/xptopen.cpp NaN/src/str2array.mexw64 NaN/src/linear.cpp NaN/src/svm_model_matlab.c NaN/src/svmpredict_mex.mexw32 NaN/src/svmpredict_mex.cpp NaN/src/str2array.mexw32 NaN/src/covm_mex.mexw32 NaN/src/train.mexw64 NaN/src/svmtrain_mex.mexw32 NaN/src/str2array.mexa64 NaN/src/covm_mex.mexa64 NaN/src/sumskipnan_mex.cpp NaN/src/svm.cpp NaN/src/covm_mex.mexw64 NaN/src/kth_element.mexw64 NaN/src/str2array.cpp NaN/src/svmpredict_mex.mexw64 NaN/src/sumskipnan_mex.mexa64 NaN/src/svm_model_matlab.h NaN/src/svmpredict_mex.mexa64 NaN/src/predict.c NaN/src/sumskipnan_mex.mexw32 NaN/src/linear.h NaN/src/kth_element.cpp NaN/src/svmtrain_mex.cpp NaN/src/linear_model_matlab.h NaN/src/tron.h NaN/src/svmtrain_mex.mexw64 NaN/src/histo_mex.mexw64 NaN/src/svmtrain_mex.mexa64 NaN/src/train.mexw32 NaN/src/train.c NaN/src/Makefile NaN/src/xptopen.mexw32 NaN/src/histo_mex.mexa64 NaN/src/histo_mex.mexw32 NaN/src/xptopen.mexw64 NaN/src/sumskipnan_mex.mexw64 NaN/src/svm.h NaN/src/tron.cpp NaN/src/covm_mex.cpp NaN/src/xptopen.mexa64 NaN/src/linear_model_matlab.c NaN/COPYING NaN/doc/ NaN/doc/INSTALL NaN/doc/README.TXT NaN/test/ NaN/test/test_mex_accuracy.m NaN/test/test_classify.m NaN/test/test_perf_skipnan.m NaN/test/test_xval.m NaN/test/test_fss.m NaN/test/test_train_sc.m NaN/test/test_xptopen.m NaN/VERSION [ -r /sw/fink/dists/stable/main/finkinfo/sci/nan-oct.patch ] /tmp/fink.1wFDF #!/bin/sh -ev sed -e 's|@FINKPREFIX@|/sw|g' \ -e 's|@OCTVERSION@|3.6.4|g' \ -e "s|@BLAS_LIBS@|`mkoctfile -p BLAS_LIBS`|" \ -e 's|@GCC@|4.7|' \ /sw/fink/dists/stable/main/finkinfo/sci/nan-oct.patch | patch -p1 mkoctfile -p BLAS_LIBS patching file src/xptopen.cpp patching file src/Makefile cd src rm *.mexw64 *.mexw32 *.mexa64 /tmp/fink.ytRj1 #!/bin/sh -ev if [ type_pkg[oct] -ge 343 ] then pkgsrc=NaN else pkgsrc=nan fi /tmp/fink.ytRj1: line 3: [: type_pkg[oct]: integer expression expected /sw/share/fink-octave-scripts/octave-forge-patch.sh nan 2.5.5 3.6.4 /sw/src/fink.build/nan-atlas-oct364-2.5.5-8/NaN /sw/src/fink.build/root-nan-atlas-oct364-2.5.5-8/sw $pkgsrc #!/bin/sh -ev if [ $UID -ne 0 ] then echo "$1 cannot be built with --build-as-nobody" exit 1 fi octvers=$3 subst1="s,@PKG@,$1,g" subst2="s,@PKGVERS@,$2,g" subst3="s,@OCTVERS@,$octvers,g" subst4="s,@BUILDDIR@,$4,g" subst5="s,@INSTDIR@,$5,g" subst6="s,@PKGSRC@,$6,g" for scriptfile in octave-forge-install.sh octave-forge-inst \ octave-forge-postinst.sh octave-forge-postinst \ octave-forge-prerm.sh octave-forge-prerm; do sed -e $subst1 -e $subst2 -e $subst3 -e $subst4 -e $subst5 /sw/share/fink-octave-scripts/$scriptfile.in > $scriptfile chmod a+x $scriptfile done if [[ "$octvers" > "3.4.0" ]] ; then oc_shell_script="/sw/share/fink-octave-scripts/octave-forge-compile-3.4.3.sh.in" oc_oct_script="/sw/share/fink-octave-scripts/octave-forge-comp-3.4.3.in" else oc_shell_script="/sw/share/fink-octave-scripts/octave-forge-compile-3.0.5.sh.in" oc_oct_script="/sw/share/fink-octave-scripts/octave-forge-comp-3.0.5.in" fi sed -e $subst1 -e $subst3 -e $subst4 -e $subst6 $oc_shell_script > octave-forge-compile.sh sed -e $subst1 -e $subst3 -e $subst6 $oc_oct_script > octave-forge-comp sed -e $subst3 -e $subst4 /sw/share/fink-octave-scripts/genmkoctfile.sh.in > genmkoctfile.sh chmod a+x octave-forge-comp* chmod a+x genmkoctfile.sh # needs to use gcc47 to build, so stash a special mkoctfile in %b/bin ./genmkoctfile.sh 4.7 #!/bin/sh -ev mkdir -p /sw/src/fink.build/nan-atlas-oct364-2.5.5-8/NaN/bin pushd /sw/src/fink.build/nan-atlas-oct364-2.5.5-8/NaN/bin /sw/src/fink.build/nan-atlas-oct364-2.5.5-8/NaN/bin /sw/src/fink.build/nan-atlas-oct364-2.5.5-8/NaN # generate Fink-gcc enabled mkoctfile cp "/sw/bin/mkoctfile-3.6.4" "mkoctfile-3.6.4-gcc$1" perl -pi -e " s,oct\-cc,/sw/bin/gcc-fsf-$1,g; \ s,oct\-cxx,/sw/bin/g++-fsf-$1,g" \ "mkoctfile-3.6.4-gcc$1" # create convenience symlink ln -s "mkoctfile-3.6.4-gcc$1" "mkoctfile-gcc$1" popd /sw/src/fink.build/nan-atlas-oct364-2.5.5-8/NaN chmod a+x bin/mkoctfile* export PATH="/sw/src/fink.build/nan-atlas-oct364-2.5.5-8/NaN/bin:$PATH" ./octave-forge-compile.sh #!/bin/sh -ev # repack tarball, since octave-3.4.0+ appears not to want to install # from directories cd .. tar -cf nan.tar nan tar: nan: Cannot stat: No such file or directory tar: Exiting with failure status due to previous errors ### execution of /tmp/fink.ytRj1 failed, exit code 2 Removing runtime build-lock... Removing build-lock package... /sw/bin/dpkg-lockwait -r fink-buildlock-nan-atlas-oct364-2.5.5-8 (Reading database ... 266035 files and directories currently installed.) Removing fink-buildlock-nan-atlas-oct364-2.5.5-8 ... Failed: phase compiling: nan-atlas-oct364-2.5.5-8 failed Before reporting any errors, please run "fink selfupdate" and try again. If you continue to have issues, please check to see if the FAQ on Fink's website solves the problem. If not, ask on one (not both, please) of these mailing lists: The Fink Users List <[email protected]> The Fink Beginners List <[email protected]>, with a carbon copy to the maintainer: Alexander Hansen <[email protected]> Note that this is preferable to emailing just the maintainer directly, since most fink package maintainers do not have access to all possible hardware and software configurations. Please try to include the complete error message in your report. This generally consists of a compiler line starting with e.g. "gcc" or "g++" followed by the actual error output from the compiler. Also include the following system information: Package manager version: 0.35.2 Distribution version: selfupdate-rsync Thu Oct 3 11:20:26 2013, 10.7, x86_64 Trees: local/main stable/main Xcode.app: 4.6.1 Xcode command-line tools: 4.6.0.0.1.1362189000 nan-atlas-oct364-2.5.5-8 is set to build with only one job. ------------------------------------------------------------------------------ October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register > http://pubads.g.doubleclick.net/gampad/clk?id=60134791&iu=/4140/ostg.clktrk _______________________________________________ Fink-users mailing list [email protected] List archive: http://news.gmane.org/gmane.os.macosx.fink.user Subscription management: https://lists.sourceforge.net/lists/listinfo/fink-users
