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astromatic / sextractor

Extract catalogs of sources from astronomical images
http://astromatic.net/software/sextractor
GNU General Public License v3.0
151 stars 44 forks source link

Installation crushed on Mac with "clang-12: error: linker command failed with exit code 1 " #32

Closed B1GeasY closed 1 year ago

B1GeasY commented 1 year ago

Hi, I want to install sextractor on my Inter Mac(MacOS 10.15). The configure is perfect. But an error showed when I tried to make it and the installation crushed.

Below is the output:

(base) k:sextractor-2.19.5 k$ make /Library/Developer/CommandLineTools/usr/bin/make all-recursive Making all in man make[2]: Nothing to be done for all'. Making all in src Making all in fits make[3]: Nothing to be done forall'. Making all in levmar make[3]: Nothing to be done for all'. Making all in wcs make[3]: Nothing to be done forall'. /bin/sh ../libtool --tag=CC --mode=link x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -isystem /Users/k/anaconda3/include -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/k/anaconda3/lib -L/Users/k/anaconda3/lib -o sex analyse.o assoc.o astrom.o back.o bpro.o catout.o check.o clean.o extract.o fft.o field.o filter.o fitswcs.o flag.o graph.o growth.o header.o image.o interpolate.o main.o makeit.o manobjlist.o misc.o neurro.o pattern.o pc.o photom.o plist.o prefs.o profit.o psf.o readimage.o refine.o retina.o scan.o som.o weight.o winpos.o xml.o ./fits/libfits.a ./wcs/libwcs_c.a ./levmar/liblevmar.a -L/usr/local/atlas/lib -llapack -lcblas -latlas -L/usr/local/fftw/lib -lfftw3f -lm libtool: link: x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong 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in: analyse.o profit.o duplicate symbol '_thepsfit' in: analyse.o psf.o duplicate symbol '_thedpsfit' in: analyse.o psf.o duplicate symbol '_thecat' in: analyse.o psf.o duplicate symbol '_prefs' in: analyse.o psf.o duplicate symbol '_gstr' in: analyse.o psf.o duplicate symbol '_thefilter' in: field.o psf.o duplicate symbol '_checkmask' in: analyse.o psf.o duplicate symbol '_flagobj' in: analyse.o psf.o duplicate symbol '_stg' in: analyse.o psf.o duplicate symbol '_ctg' in: analyse.o psf.o duplicate symbol '_bswapflag' in: analyse.o psf.o duplicate symbol '_thepsf' in: analyse.o psf.o duplicate symbol '_thedpsf' in: analyse.o psf.o duplicate symbol '_psf' in: analyse.o psf.o duplicate symbol '_flagobj2' in: analyse.o psf.o duplicate symbol '_thewfield2' in: analyse.o psf.o duplicate symbol '_thefield2' in: analyse.o psf.o duplicate symbol '_thewfield1' in: analyse.o psf.o duplicate symbol '_thefield1' in: analyse.o psf.o duplicate symbol '_thecat' in: analyse.o readimage.o duplicate symbol '_prefs' in: analyse.o readimage.o duplicate symbol '_gstr' in: analyse.o readimage.o duplicate symbol '_flagobj' in: analyse.o readimage.o duplicate symbol '_stg' in: analyse.o readimage.o duplicate symbol '_ctg' in: analyse.o readimage.o duplicate symbol '_bswapflag' in: analyse.o readimage.o duplicate symbol '_flagobj2' in: analyse.o readimage.o duplicate symbol '_thewfield2' in: analyse.o readimage.o duplicate symbol '_thefield2' in: analyse.o readimage.o duplicate symbol '_thewfield1' in: analyse.o readimage.o duplicate symbol '_thefield1' in: analyse.o readimage.o duplicate symbol '_thecat' in: analyse.o refine.o duplicate symbol '_prefs' in: analyse.o refine.o duplicate symbol '_gstr' in: analyse.o refine.o duplicate symbol '_plistexist_var' in: analyse.o refine.o duplicate symbol '_plistoff_var' in: analyse.o refine.o duplicate symbol '_dumscan' in: extract.o refine.o duplicate symbol '_flagobj' in: analyse.o refine.o duplicate symbol '_plistexist_dthresh' in: analyse.o refine.o duplicate symbol '_plistoff_dthresh' in: analyse.o refine.o duplicate symbol '_stg' in: analyse.o refine.o duplicate symbol '_ctg' in: analyse.o refine.o duplicate symbol '_plistexist_wflag' in: analyse.o refine.o duplicate symbol '_plistoff_wflag' in: analyse.o refine.o duplicate symbol '_bswapflag' in: analyse.o refine.o duplicate symbol '_plistexist_flag' in: analyse.o refine.o duplicate symbol '_plistoff_flag' in: analyse.o refine.o duplicate symbol '_plistsize' in: analyse.o refine.o duplicate symbol '_plistexist_cdvalue' in: analyse.o refine.o duplicate symbol '_plistoff_cdvalue' in: analyse.o refine.o duplicate symbol '_plistexist_dvalue' in: analyse.o refine.o duplicate symbol '_plistoff_dvalue' in: analyse.o refine.o duplicate symbol '_plistexist_value' in: analyse.o refine.o duplicate symbol '_plistoff_value' in: analyse.o refine.o duplicate symbol '_flagobj2' in: analyse.o refine.o duplicate symbol '_thewfield2' in: analyse.o refine.o duplicate symbol '_thefield2' in: analyse.o refine.o duplicate symbol '_thewfield1' in: analyse.o refine.o duplicate symbol '_thefield1' in: analyse.o refine.o duplicate symbol '_thecat' in: analyse.o retina.o duplicate symbol '_gstr' in: analyse.o retina.o duplicate symbol '_flagobj' in: analyse.o retina.o duplicate symbol '_stg' in: analyse.o retina.o duplicate symbol '_ctg' in: analyse.o retina.o duplicate symbol '_bswapflag' in: analyse.o retina.o duplicate symbol '_theretina' in: analyse.o retina.o duplicate symbol '_flagobj2' in: analyse.o retina.o duplicate symbol '_thewfield2' in: analyse.o retina.o duplicate symbol '_thefield2' in: analyse.o retina.o duplicate symbol '_thewfield1' in: analyse.o retina.o duplicate symbol '_thefield1' in: analyse.o retina.o duplicate symbol '_cleanobjlist' in: clean.o scan.o duplicate symbol '_thecat' in: analyse.o scan.o duplicate symbol '_prefs' in: analyse.o scan.o duplicate symbol '_gstr' in: analyse.o scan.o duplicate symbol '_thefilter' in: field.o scan.o duplicate symbol '_plistexist_var' in: analyse.o scan.o duplicate symbol '_plistoff_var' in: analyse.o scan.o duplicate symbol '_dumscan' in: extract.o scan.o duplicate symbol '_flagobj' in: analyse.o scan.o duplicate symbol '_plistexist_dthresh' in: analyse.o scan.o duplicate symbol '_plistoff_dthresh' in: analyse.o scan.o duplicate symbol '_stg' in: analyse.o scan.o duplicate symbol '_ctg' in: analyse.o scan.o duplicate symbol '_plistexist_wflag' in: analyse.o scan.o duplicate symbol '_plistoff_wflag' in: analyse.o scan.o duplicate symbol '_bswapflag' in: analyse.o scan.o duplicate symbol '_plistexist_flag' in: analyse.o scan.o duplicate symbol '_plistoff_flag' in: analyse.o scan.o duplicate symbol '_plistsize' in: analyse.o scan.o duplicate symbol '_plistexist_cdvalue' in: analyse.o scan.o duplicate symbol '_plistoff_cdvalue' in: analyse.o scan.o duplicate symbol '_plistexist_dvalue' in: analyse.o scan.o duplicate symbol '_plistoff_dvalue' in: analyse.o scan.o duplicate symbol '_plistexist_value' in: analyse.o scan.o duplicate symbol '_plistoff_value' in: analyse.o scan.o duplicate symbol '_flagobj2' in: analyse.o scan.o duplicate symbol '_thewfield2' in: analyse.o scan.o duplicate symbol '_thefield2' in: analyse.o scan.o duplicate symbol '_thewfield1' in: analyse.o scan.o duplicate symbol '_thefield1' in: analyse.o scan.o duplicate symbol '_thecat' in: analyse.o som.o duplicate symbol '_prefs' in: analyse.o som.o duplicate symbol '_gstr' in: analyse.o som.o duplicate symbol '_thesom' in: analyse.o som.o duplicate symbol '_flagobj' in: analyse.o som.o duplicate symbol '_stg' in: analyse.o som.o duplicate symbol '_ctg' in: analyse.o som.o duplicate symbol '_bswapflag' in: analyse.o som.o duplicate symbol '_flagobj2' in: analyse.o som.o duplicate symbol '_thewfield2' in: analyse.o som.o duplicate symbol '_thefield2' in: analyse.o som.o duplicate symbol '_thewfield1' in: analyse.o som.o duplicate symbol '_thefield1' in: analyse.o som.o duplicate symbol '_thecat' in: analyse.o weight.o duplicate symbol '_gstr' in: analyse.o weight.o duplicate symbol '_plistexist_var' in: analyse.o weight.o duplicate symbol '_plistoff_var' in: analyse.o weight.o duplicate symbol '_flagobj' in: analyse.o weight.o duplicate symbol '_plistexist_dthresh' in: analyse.o weight.o duplicate symbol '_plistoff_dthresh' in: analyse.o weight.o duplicate symbol '_stg' in: analyse.o weight.o duplicate symbol '_ctg' in: analyse.o weight.o duplicate symbol '_plistexist_wflag' in: analyse.o weight.o duplicate symbol '_plistoff_wflag' in: analyse.o weight.o duplicate symbol '_bswapflag' in: analyse.o weight.o duplicate symbol '_plistexist_flag' in: analyse.o weight.o duplicate symbol '_plistoff_flag' in: analyse.o weight.o duplicate symbol '_plistsize' in: analyse.o weight.o duplicate symbol '_plistexist_cdvalue' in: analyse.o weight.o duplicate symbol '_plistoff_cdvalue' in: analyse.o weight.o duplicate symbol '_plistexist_dvalue' in: analyse.o weight.o duplicate symbol '_plistoff_dvalue' in: analyse.o weight.o duplicate symbol '_plistexist_value' in: analyse.o weight.o duplicate symbol '_plistoff_value' in: analyse.o weight.o duplicate symbol '_flagobj2' in: analyse.o weight.o duplicate symbol '_thewfield2' in: analyse.o weight.o duplicate symbol '_thefield2' in: analyse.o weight.o duplicate symbol '_thewfield1' in: analyse.o weight.o duplicate symbol '_thefield1' in: analyse.o weight.o duplicate symbol '_thecat' in: analyse.o winpos.o duplicate symbol '_prefs' in: analyse.o winpos.o duplicate symbol '_gstr' in: analyse.o winpos.o duplicate symbol '_flagobj' in: analyse.o winpos.o duplicate symbol '_stg' in: analyse.o winpos.o duplicate symbol '_ctg' in: analyse.o winpos.o duplicate symbol '_bswapflag' in: analyse.o winpos.o duplicate symbol '_flagobj2' in: analyse.o winpos.o duplicate symbol '_thewfield2' in: analyse.o winpos.o duplicate symbol '_thefield2' in: analyse.o winpos.o duplicate symbol '_thewfield1' in: analyse.o winpos.o duplicate symbol '_thefield1' in: analyse.o winpos.o duplicate symbol '_thecat' in: analyse.o xml.o duplicate symbol '_prefs' in: analyse.o xml.o duplicate symbol '_gstr' in: analyse.o xml.o duplicate symbol '_flagobj' in: analyse.o xml.o duplicate symbol '_stg' in: analyse.o xml.o duplicate symbol '_ctg' in: analyse.o xml.o duplicate symbol '_bswapflag' in: analyse.o xml.o duplicate symbol '_flagobj2' in: analyse.o xml.o duplicate symbol '_thewfield2' in: analyse.o xml.o duplicate symbol '_thefield2' in: analyse.o xml.o duplicate symbol '_thewfield1' in: analyse.o xml.o duplicate symbol '_thefield1' in: analyse.o xml.o duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitsbody.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitsbody.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitscat.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitscat.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitscheck.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitscheck.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitscleanup.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitscleanup.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitsconv.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitsconv.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitshead.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitshead.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitskey.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitskey.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitsmisc.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitsmisc.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitsread.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitsread.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitstab.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitstab.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitsutil.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitsutil.o) duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitswrite.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitswrite.o) ld: 617 duplicate symbols for architecture x86_64 clang-12: error: linker command failed with exit code 1 (use -v to see invocation) make[3]: [sex] Error 1 make[2]: [all-recursive] Error 1 make[1]: [all-recursive] Error 1 make: [all] Error 2

I want to know how to fix it. Thanks in advance!

B1GeasY commented 1 year ago

Sorry for the long long log. It seems that it got stucked in duplicating symbol '_gstr' and '_bswapflag'

hbouy commented 1 year ago

I think I recall that Mac OS make does not work. Try with e.g. homebrew make instead, it might solve the issues.

B1GeasY commented 1 year ago

Thanks a lot for your reply! However gmake is not helping. :( The error still shows:

duplicate symbol '_gstr' in: analyse.o ./fits/libfits.a(fitswrite.o) duplicate symbol '_bswapflag' in: analyse.o ./fits/libfits.a(fitswrite.o) ld: 617 duplicate symbols for architecture x86_64 clang-12: error: linker command failed with exit code 1 (use -v to see invocation) gmake[3]: [Makefile:454: sex] Error 1 gmake[3]: Leaving directory '/Users/k/Documents/sextractor-2.19.5/src' gmake[2]: [Makefile:537: all-recursive] Error 1 gmake[2]: Leaving directory '/Users/k/Documents/sextractor-2.19.5/src' gmake[1]: [Makefile:442: all-recursive] Error 1 gmake[1]: Leaving directory '/Users/k/Documents/sextractor-2.19.5' gmake: [Makefile:350: all] Error 2

B1GeasY commented 1 year ago

I have sextractor installed on my pc and it worked for now. But I don't think I solved this error. The clang error kept showing so I tried "make -t" and "make -e" for several times. Finally "sex" command worked in terminal but there is no "bin" and "src" folders in the prefix. So I copied these folders from others, put them into prefix and set the environment in .bash_profile. Now "sex" works on my pc though I don't know why.