Compilation failing

Commands in mothur
1

Hi,

I am attempting to compile mother 1.24.1 on a 64 bit SUSE linux (gcc version 4.1.2 ) and getting the following error, which is about uchime.

cd uchime_src && ./mk && mv uchime … && cd …
addtargets2
cc1plus: error: unrecognized command line option “-msse2”
cc1plus: error: unrecognized command line option “-mfpmath=sse”
alignchime
cc1plus: error: unrecognized command line option “-msse2”
cc1plus: error: unrecognized command line option “-mfpmath=sse”
alignchimel
cc1plus: error: unrecognized command line option “-msse2”
cc1plus: error: unrecognized command line option “-mfpmath=sse”
.
.
.
.
strip: ‘uchime’: No such file
ls: uchime: 그런 파일이나 ë””ë ‰í† ë¦¬ê°€ 없음
sum: uchime: 그런 파일이나 ë””ë ‰í† ë¦¬ê°€ 없음
make: *** [uchime] 오류 1


Thanks for any help.

Hyungz.

2

You could change the following line in the makefile from:

mothur : fortranSource $(OBJECTS) uchime
$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)

to

mothur : fortranSource $(OBJECTS)
$(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)

Then mothur will build, but you won’t have the uchime executable. The uchime executable is included in the executable distribution of mothur, http://www.mothur.org/wiki/Download_mothur.

3

Thank you very much, Westcott.

I have one more question.

Because the SUSE linux is 64 bit, I changed

64BIT_VERSION ?= no

#if you are a mac user use the following line
TARGET_ARCH += -arch x86_64

#if you are a linux user use the following line
#CXXFLAGS += -mtune=native -march=native -m64

to

64BIT_VERSION ?= yes

#if you are a mac user use the following line
#TARGET_ARCH += -arch x86_64

#if you are a linux user use the following line
CXXFLAGS += -mtune=native -march=native -m64

in makefile and obtained following error.

gfortran -c -m64 *.f
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
f951: error: unrecognized command line option “-m64”
make: *** [fortranSource] 오류 1


Thank you for your concern.
hyungz.
4

Have you tried running the executable version of mothur instead of building from source?

5

I tried already, but it did not work.

The executable version was runned on Redhat linux, which has been installed in anonther server computer, but it was not runned on SUSE linux, I don’t know why.

hyungz

6

I am not familiar with the specific differences between SUSE Linux and CentOS Linux. You could try building the 32bit version?

7

Thank you, Westcott,

I could compile and install mothur from the source code with 32 bit version, and it works now.

But when I copies and pasted uchim executable and ran uchime, I obtained the following massage.

mothur > chimera.uchime(fasta=chim1.fasta, reference=self)


uchime by Robert C. Edgar http://drive5.com/uchime This code is donated to the public domain.

Checking sequences from chim1.fasta …

No namesfile given, running unique.seqs command to generate one.

/******************************************/
Running command: unique.seqs(fasta=chim1.fasta)
[WARNING]: This command can take a namefile and you did not provide one. The current namefile is chim1.names which seems to match chim1.fasta.
1000 643
2000 1274
3000 1974
4000 2734
4164 2882

Output File Names:
chim1.unique.fasta
chim1.names

/******************************************/
sh: …/…/…/mothur/Mothur.source/uchime: 허가 거부됨 (This means “not permitted”)

It took 0 secs to check 1 sequences. 0 chimeras were found.

Output File Names:
chim1.uchime.chimera
chim1.uchime.accnos