Your message dated Thu, 10 Nov 2011 08:48:09 +0000
with message-id <[email protected]>
and subject line Bug#648255: fixed in mothur 1.22.2-1
has caused the Debian Bug report #648255,
regarding mothur: FTBFS: cc1plus: error: unrecognized command line option
'-msse2'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
648255: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=648255
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Source: mothur
Source-Version: 1.22.2-1
We believe that the bug you reported is fixed in the latest version of
mothur, which is due to be installed in the Debian FTP archive:
mothur_1.22.2-1.debian.tar.gz
to main/m/mothur/mothur_1.22.2-1.debian.tar.gz
mothur_1.22.2-1.dsc
to main/m/mothur/mothur_1.22.2-1.dsc
mothur_1.22.2-1_amd64.deb
to main/m/mothur/mothur_1.22.2-1_amd64.deb
mothur_1.22.2.orig.tar.gz
to main/m/mothur/mothur_1.22.2.orig.tar.gz
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated mothur package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Format: 1.8
Date: Thu, 10 Nov 2011 08:38:32 +0100
Source: mothur
Binary: mothur
Architecture: source amd64
Version: 1.22.2-1
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
mothur - sequence analysis suite for research on microbiota
Closes: 648255
Changes:
mothur (1.22.2-1) unstable; urgency=low
.
* New upstream version
* debian/patches/drop_sse_option.patch: Fix for FTBFS: unrecognized
command line option '-msse2' (Thanks for the patch to
Nobuhiro Iwamatsu <[email protected]>)
Closes: #648255
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Files:
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--- End Message ---
