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TimoLassmann / kalign

A fast multiple sequence alignment program.
GNU General Public License v3.0
128 stars 28 forks source link

Issue with installation using make #27

Closed mtva0001 closed 3 years ago

mtva0001 commented 3 years ago

Hi!

I got the following when I run 'make' (following your installation guide; Host system: aarch64-apple-darwin20.6.0):

Making all in src /Applications/Xcode.app/Contents/Developer/usr/bin/make all-am gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT run_kalign.o -MD -MP -MF .deps/run_kalign.Tpo -c -o run_kalign.o run_kalign.c mv -f .deps/run_kalign.Tpo .deps/run_kalign.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT idata.o -MD -MP -MF .deps/idata.Tpo -c -o idata.o idata.c mv -f .deps/idata.Tpo .deps/idata.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT tldevel.o -MD -MP -MF .deps/tldevel.Tpo -c -o tldevel.o tldevel.c mv -f .deps/tldevel.Tpo .deps/tldevel.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT tlmisc.o -MD -MP -MF .deps/tlmisc.Tpo -c -o tlmisc.o tlmisc.c mv -f .deps/tlmisc.Tpo .deps/tlmisc.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT esl_stopwatch.o -MD -MP -MF .deps/esl_stopwatch.Tpo -c -o esl_stopwatch.o esl_stopwatch.c mv -f .deps/esl_stopwatch.Tpo .deps/esl_stopwatch.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT tlrng.o -MD -MP -MF .deps/tlrng.Tpo -c -o tlrng.o tlrng.c mv -f .deps/tlrng.Tpo .deps/tlrng.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT parameters.o -MD -MP -MF .deps/parameters.Tpo -c -o parameters.o parameters.c mv -f .deps/parameters.Tpo .deps/parameters.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT alphabet.o -MD -MP -MF .deps/alphabet.Tpo -c -o alphabet.o alphabet.c mv -f .deps/alphabet.Tpo .deps/alphabet.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT alignment_parameters.o -MD -MP -MF .deps/alignment_parameters.Tpo -c -o alignment_parameters.o alignment_parameters.c mv -f .deps/alignment_parameters.Tpo .deps/alignment_parameters.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT pick_anchor.o -MD -MP -MF .deps/pick_anchor.Tpo -c -o pick_anchor.o pick_anchor.c mv -f .deps/pick_anchor.Tpo .deps/pick_anchor.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT bisectingKmeans.o -MD -MP -MF .deps/bisectingKmeans.Tpo -c -o bisectingKmeans.o bisectingKmeans.c mv -f .deps/bisectingKmeans.Tpo .deps/bisectingKmeans.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT sequence_distance.o -MD -MP -MF .deps/sequence_distance.Tpo -c -o sequence_distance.o sequence_distance.c mv -f .deps/sequence_distance.Tpo .deps/sequence_distance.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT euclidean_dist.o -MD -MP -MF .deps/euclidean_dist.Tpo -c -o euclidean_dist.o euclidean_dist.c mv -f .deps/euclidean_dist.Tpo .deps/euclidean_dist.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT weave_alignment.o -MD -MP -MF .deps/weave_alignment.Tpo -c -o weave_alignment.o weave_alignment.c mv -f .deps/weave_alignment.Tpo .deps/weave_alignment.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT rwalign.o -MD -MP -MF .deps/rwalign.Tpo -c -o rwalign.o rwalign.c mv -f .deps/rwalign.Tpo .deps/rwalign.Po gcc -DHAVE_CONFIG_H -I. -D_FORTIFY_SOURCE=2 -ffunction-sections -fdata-sections -O3 -std=gnu11 -MT misc.o -MD -MP -MF .deps/misc.Tpo -c -o misc.o misc.c In file included from misc.c:33: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/immintrin.h:13: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/x86gprintrin.h:15: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/hresetintrin.h:42:27: error: invalid input constraint 'a' in asm asm ("hreset $0" :: "a"(eax)); ^ In file included from misc.c:33: In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/immintrin.h:17: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:50:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_vec_init_v2si(i, 0); ^~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:129:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_packsswb((v4hi)m1, (v4hi)m2); ^~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:159:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_packssdw((v2si)m1, (v2si)m2); ^~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:189:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_packuswb((v4hi)m1, (v4hi)m2); ^~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:216:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_punpckhbw((v8qi)m1, (v8qi)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:239:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_punpckhwd((v4hi)m1, (v4hi)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:260:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_punpckhdq((v2si)m1, (v2si)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:287:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_punpcklbw((v8qi)m1, (v8qi)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:310:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_punpcklwd((v4hi)m1, (v4hi)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:331:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_punpckldq((v2si)m1, (v2si)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:352:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_paddb((v8qi)m1, (v8qi)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:373:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_paddw((v4hi)m1, (v4hi)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:394:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_paddd((v2si)m1, (v2si)m2); ^~~~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:416:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_paddsb((v8qi)m1, (v8qi)m2); ^~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:439:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_paddsw((v4hi)m1, (v4hi)m2); ^~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:461:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_paddusb((v8qi)m1, (v8qi)m2); ^~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:483:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_paddusw((v4hi)m1, (v4hi)m2); ^~~~~~~~~~~~~ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/13.0.0/include/mmintrin.h:504:12: error: invalid conversion between vector type 'm64' (vector of 1 'long long' value) and integer type 'int' of different size return (m64)builtin_ia32_psubb((v8qi)m1, (v8qi)m2); ^~~~~~~~~~~~~~~ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. make[2]: [misc.o] Error 1 make[1]: [all] Error 2 make: *** [all-recursive] Error 1

TimoLassmann commented 3 years ago

Hi,

Thanks for reporting! I presume this error happens on one of the new(ish) M1 macs?

The error points to the fact that I seem to have forgotten to wrap a header include in a check. I now fixed this - could you do a pull and try to compile again?

Thanks, Timo

mtva0001 commented 3 years ago

It worked, thank you so much for your quick help!