Source: mothur Version: 1.22.1-1 Severity: serious Justification: fails to build from source Tags: patch
Hi, mothur FTBFS on the architecture except x86. https://buildd.debian.org/status/package.php?p=mothur http://buildd.debian-ports.org/status/package.php?p=mothur ----- g++ -O3 -DBIT_VERSION -DRELEASE_DATE="\"10/24/2011\"" -DVERSION="\"1.22.1\"" -I. -c -o whittaker.o whittaker.cpp cc -c -o fisher2.o fisher2.c cc -c -o metastats2.o metastats2.c cd uchime_src && ./mk && mv uchime .. && cd .. ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' ./mk: line 9: /dev/tty: No such device or address cc1plus: error: unrecognized command line option '-msse2' cc1plus: error: unrecognized command line option '-mfpmath=sse' g++: error: addtargets2.o: No such file or directory g++: error: alignchime.o: No such file or directory g++: error: alignchimel.o: No such file or directory g++: error: alnparams.o: No such file or directory g++: error: alpha.o: No such file or directory g++: error: alpha2.o: No such file or directory g++: error: fractid.o: No such file or directory g++: error: getparents.o: No such file or directory g++: error: globalalign2.o: No such file or directory g++: error: make3way.o: No such file or directory g++: error: mx.o: No such file or directory g++: error: myutils.o: No such file or directory g++: error: path.o: No such file or directory g++: error: searchchime.o: No such file or directory g++: error: seqdb.o: No such file or directory g++: error: setnucmx.o: No such file or directory g++: error: sfasta.o: No such file or directory g++: error: tracebackbit.o: No such file or directory g++: error: uchime_main.o: No such file or directory g++: error: usort.o: No such file or directory g++: error: viterbifast.o: No such file or directory g++: error: writechhit.o: No such file or directory g++: fatal error: no input files compilation terminated. strip: 'uchime': No such file ls: cannot access uchime: No such file or directory sum: uchime: No such file or directory make[2]: *** [uchime] Error 1 ----- I made a patch which revise this problem. Could you apply this patch? Best regards, Nobuhiro -- Nobuhiro Iwamatsu iwamatsu at {nigauri.org / debian.org} GPG ID: 40AD1FA6
diff --git a/uchime_src/mk b/uchime_src/mk index 42ce843..f00e93e 100755 --- a/uchime_src/mk +++ b/uchime_src/mk @@ -7,7 +7,7 @@ rm -f *.o mk.stdout mk.stderr tmp.stderr for CPPName in $CPPNames do echo $CPPName >> /dev/tty - g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr + g++ $ENV_GCC_OPTS -c -O2 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 $CPPName.cpp -o $CPPName.o >> mk.stdout 2>> tmp.stderr cat tmp.stderr cat tmp.stderr >> mk.stderr rm -f tmp.stderr
