# Problems Compiling Mothur on 64-bit CentOS
**URL:** https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292
**Category:** mothur bugs
**Created:** [July 20, 2010, 3:20pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292 "2010-07-20T15:20:16Z")
**Posts on this page:** 16
**Page:** 1
### Author:  [@twaddlac](https://forum.mothur.org/u/twaddlac)
#### Post date: [July 20, 2010, 3:20pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/1 "2010-07-20T15:20:16Z")
Hello,
I am having a bit of trouble compiling the mothur source code. After I use the make command I get the following output:
```nohighlight
g++ -O3 -DUSE_READLINE sharedutilities.cpp -c -I. -o ./sharedutilities.o
In file included from sharedutilities.h:12,
from sharedutilities.cpp:10:
mothur.h:60:33: error: readline/readline.h: No such file or directory
mothur.h:61:32: error: readline/history.h: No such file or directory
make: *** [sharedutilities.o] Error 1
```
Let me know if you have any ideas/suggestions! Thank you very much!
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [July 20, 2010, 5:32pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/2 "2010-07-20T17:32:58Z")
It appears mothur can’t find the readline library. Do you have the readline library installed? If not, you will want to either install it or modified the make file so that the line:
USEREADLINE ?= yes
is
USEREADLINE ?= no
---
### Author:  [@twaddlac](https://forum.mothur.org/u/twaddlac)
#### Post date: [July 20, 2010, 7:33pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/3 "2010-07-20T19:33:09Z")
Well that worked for one of the errors (installing readline, that is) but now I am getting:
```nohighlight
/usr/bin/ld: cannot find -lncurses
collect2: ld returned 1 exit status
make: *** [mothur] Error 1
```
Any more ideas?
p.s. thank you very much!
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [July 21, 2010, 10:46am UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/4 "2010-07-21T10:46:39Z")
Glad I could help. Ncurses is another library package. I suspect you will need to install that as well.
---
### Author:  [@twaddlac](https://forum.mothur.org/u/twaddlac)
#### Post date: [July 21, 2010, 2:02pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/5 "2010-07-21T14:02:28Z")
Well I thought that the problems were solved but I guess not. I am now getting this error:
```nohighlight
./mothur: error while loading shared libraries: libreadline.so.6: cannot open shared object file: No such file or directory
```
I have tried to install libreadline.so.6 via:
```nohighlight
yum install libreadline.so.6
```
Any suggestions? Thanks again!
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [July 21, 2010, 2:37pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/6 "2010-07-21T14:37:54Z")
Mothur can’t find the compiled library. You can search for the .dylib file to see if the library was installed properly.
---
### Author:  [@twaddlac](https://forum.mothur.org/u/twaddlac)
#### Post date: [July 21, 2010, 2:53pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/7 "2010-07-21T14:53:12Z")
Which .o file should I look for specifically? Also, how do I install the missing file if it is in fact missing?
Sorry for being difficult, I’m a noob at linux and mothur. 😑
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [July 21, 2010, 4:32pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/8 "2010-07-21T16:32:31Z")
It’s no problem. I am not too familiar with centos, but I will try my best to help. When you installed the readline library it should have made a .dylib file. It would be called libreadline.dylib. If you did indeed get it installed, mothur needs to be able to find it. It should be located with your other standard libraries, in /usr/lib.
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [July 21, 2010, 4:34pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/9 "2010-07-21T16:34:36Z")
The readline library is not required to to run mothur. It allows you to scroll through previous commands you have entered if you are running mothur in interactive mode.
---
### Author:  [@twaddlac](https://forum.mothur.org/u/twaddlac)
#### Post date: [July 21, 2010, 7:16pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/10 "2010-07-21T19:16:29Z")
I wasn’t able to find it, though libreadline is installed (I think). I have only found libreadline.so.5 and libreadline.so.5.1 in /usr/lib and I couldn’t compile either of them. Do I need to install a package or what?
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [July 21, 2010, 7:28pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/11 "2010-07-21T19:28:19Z")
You don’t need to install it to run mother. If you set the USEREADLINE ?= no in the makefile, mothur will compile without the library.
---
### Author:  [@twaddlac](https://forum.mothur.org/u/twaddlac)
#### Post date: [July 21, 2010, 7:53pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/12 "2010-07-21T19:53:25Z")
How do I do that?
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [July 21, 2010, 10:41pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/13 "2010-07-21T22:41:35Z")
In the folder containing your mothur source files there is a file called makefile. You can open it in any text editor and you will see:
###################################################
#
# Makefile for mothur
# Creator [Xcode -\> Makefile Ver: Feb 14 2007 09:18:41]
# Created: April 16, 2010
#
###################################################
#
# Macros
#
CC = g++
CC\_OPTIONS = -O3
# if you do not want to use the readline library set to no, default yes.
# make sure you have the library installed
64BIT\_VERSION ?= no
ifeq ($(strip $(64BIT\_VERSION)),yes)
CC\_OPTIONS += -arch x86\_64
LNK\_OPTIONS += -arch x86\_64
endif
USEREADLINE ?= yes
ifeq ($(strip $(USEREADLINE)),yes)
CC\_OPTIONS += -DUSE\_READLINE
LNK\_OPTIONS +=
-lreadline
-lncurses
-L…/readline-6.0
endif
…
You want to change the USEREADLINE ?= yes to USEREADLINE ?= no. Since you are running a 64bit OS you should also change 64BIT\_VERSION ?= no to 64BIT\_VERSION ?= yes. Then save the file and run “make clean”, followed by “make”.
---
### Author:  [@twaddlac](https://forum.mothur.org/u/twaddlac)
#### Post date: [July 22, 2010, 8:20pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/14 "2010-07-22T20:20:55Z")
When I run make clean I get the following:
```nohighlight
rm: cannot remove `./sharedutilities.o': No such file or directory
rm: cannot remove `./treegroupscommand.o': No such file or directory
rm: cannot remove `./bootstrapsharedcommand.o': No such file or directory
rm: cannot remove `./matrixoutputcommand.o': No such file or directory
rm: cannot remove `./getoturepcommand.o': No such file or directory
rm: cannot remove `./screenseqscommand.o': No such file or directory
rm: cannot remove `./chimera.o': No such file or directory
rm: cannot remove `./decalc.o': No such file or directory
rm: cannot remove `./readotucommand.o': No such file or directory
rm: cannot remove `./readdistcommand.o': No such file or directory
rm: cannot remove `./commandfactory.o': No such file or directory
rm: cannot remove `./alignment.o': No such file or directory
rm: cannot remove `./alignmentcell.o': No such file or directory
rm: cannot remove `./gotohoverlap.o': No such file or directory
rm: cannot remove `./overlap.o': No such file or directory
rm: cannot remove `./needlemanoverlap.o': No such file or directory
rm: cannot remove `./blastalign.o': No such file or directory
rm: cannot remove `./noalign.o': No such file or directory
rm: cannot remove `./suffixdb.o': No such file or directory
rm: cannot remove `./suffixnodes.o': No such file or directory
rm: cannot remove `./suffixtree.o': No such file or directory
rm: cannot remove `./blastdb.o': No such file or directory
rm: cannot remove `./nast.o': No such file or directory
rm: cannot remove `./nastreport.o': No such file or directory
rm: cannot remove `./boneh.o': No such file or directory
rm: cannot remove `./efron.o': No such file or directory
rm: cannot remove `./solow.o': No such file or directory
rm: cannot remove `./unifracweightedcommand.o': No such file or directory
rm: cannot remove `./weighted.o': No such file or directory
rm: cannot remove `./unweighted.o': No such file or directory
rm: cannot remove `./unifracunweightedcommand.o': No such file or directory
rm: cannot remove `./getsabundcommand.o': No such file or directory
rm: cannot remove `./getrabundcommand.o': No such file or directory
rm: cannot remove `./bellerophon.o': No such file or directory
rm: cannot remove `./pintail.o': No such file or directory
rm: cannot remove `./sharedanderbergs.o': No such file or directory
rm: cannot remove `./venncommand.o': No such file or directory
rm: cannot remove `./venn.o': No such file or directory
rm: cannot remove `./fullmatrix.o': No such file or directory
rm: cannot remove `./heatmap.o': No such file or directory
rm: cannot remove `./heatmapcommand.o': No such file or directory
rm: cannot remove `./libshuffcommand.o': No such file or directory
rm: cannot remove `./nocommands.o': No such file or directory
rm: cannot remove `./sharedbraycurtis.o': No such file or directory
rm: cannot remove `./sharedkulczynski.o': No such file or directory
rm: cannot remove `./sharedlennon.o': No such file or directory
rm: cannot remove `./sharedkulczynskicody.o': No such file or directory
rm: cannot remove `./sharedmorisitahorn.o': No such file or directory
rm: cannot remove `./sharedochiai.o': No such file or directory
rm: cannot remove `./readcolumn.o': No such file or directory
rm: cannot remove `./readotu.o': No such file or directory
rm: cannot remove `./readphylip.o': No such file or directory
rm: cannot remove `./consensuscommand.o': No such file or directory
rm: cannot remove `./heatmapsimcommand.o': No such file or directory
rm: cannot remove `./heatmapsim.o': No such file or directory
rm: cannot remove `./optionparser.o': No such file or directory
rm: cannot remove `./filterseqscommand.o': No such file or directory
rm: cannot remove `./goodscoverage.o': No such file or directory
rm: cannot remove `./sequencedb.o': No such file or directory
rm: cannot remove `./sharedjackknife.o': No such file or directory
rm: cannot remove `./sharedmarczewski.o': No such file or directory
rm: cannot remove `./aligncommand.o': No such file or directory
rm: cannot remove `./treemap.o': No such file or directory
rm: cannot remove `./parsimonycommand.o': No such file or directory
rm: cannot remove `./parsimony.o': No such file or directory
rm: cannot remove `./seqsummarycommand.o': No such file or directory
rm: cannot remove `./chimeraccodecommand.o': No such file or directory
rm: cannot remove `./chimerabellerophoncommand.o': No such file or directory
rm: cannot remove `./chimeracheckcommand.o': No such file or directory
rm: cannot remove `./chimeraslayercommand.o': No such file or directory
rm: cannot remove `./chimerapintailcommand.o': No such file or directory
rm: cannot remove `./chimeraseqscommand.o': No such file or directory
rm: cannot remove `./sharedlistvector.o': No such file or directory
rm: cannot remove `./tree.o': No such file or directory
rm: cannot remove `./readtree.o': No such file or directory
rm: cannot remove `./sharedsobscollectsummary.o': No such file or directory
rm: cannot remove `./deconvolutecommand.o': No such file or directory
rm: cannot remove `./listseqscommand.o': No such file or directory
rm: cannot remove `./getseqscommand.o': No such file or directory
rm: cannot remove `./removeseqscommand.o': No such file or directory
rm: cannot remove `./systemcommand.o': No such file or directory
rm: cannot remove `./binsequencecommand.o': No such file or directory
rm: cannot remove `./distancecommand.o': No such file or directory
rm: cannot remove `./ace.o': No such file or directory
rm: cannot remove `./averagelinkage.o': No such file or directory
rm: cannot remove `./bootstrap.o': No such file or directory
rm: cannot remove `./calculator.o': No such file or directory
rm: cannot remove `./chao1.o': No such file or directory
rm: cannot remove `./cluster.o': No such file or directory
rm: cannot remove `./clustercommand.o': No such file or directory
rm: cannot remove `./collect.o': No such file or directory
rm: cannot remove `./collectcommand.o': No such file or directory
rm: cannot remove `./collectsharedcommand.o': No such file or directory
rm: cannot remove `./commandoptionparser.o': No such file or directory
rm: cannot remove `./completelinkage.o': No such file or directory
rm: cannot remove `./database.o': No such file or directory
rm: cannot remove `./engine.o': No such file or directory
rm: cannot remove `./fastamap.o': No such file or directory
rm: cannot remove `./fileoutput.o': No such file or directory
rm: cannot remove `./globaldata.o': No such file or directory
rm: cannot remove `./groupmap.o': No such file or directory
rm: cannot remove `./helpcommand.o': No such file or directory
rm: cannot remove `./makegroupcommand.o': No such file or directory
rm: cannot remove `./chopseqscommand.o': No such file or directory
rm: cannot remove `./clearcutcommand.o': No such file or directory
rm: cannot remove `./catchallcommand.o': No such file or directory
rm: cannot remove `./splitabundcommand.o': No such file or directory
rm: cannot remove `./splitmatrix.o': No such file or directory
rm: cannot remove `./clustersplitcommand.o': No such file or directory
rm: cannot remove `./weightedlinkage.o': No such file or directory
rm: cannot remove `./inputdata.o': No such file or directory
rm: cannot remove `./jackknife.o': No such file or directory
rm: cannot remove `./kmer.o': No such file or directory
rm: cannot remove `./kmerdb.o': No such file or directory
rm: cannot remove `./listvector.o': No such file or directory
rm: cannot remove `./mothur.o': No such file or directory
rm: cannot remove `./nameassignment.o': No such file or directory
rm: cannot remove `./npshannon.o': No such file or directory
rm: cannot remove `./ordervector.o': No such file or directory
rm: cannot remove `./progress.o': No such file or directory
rm: cannot remove `./quitcommand.o': No such file or directory
rm: cannot remove `./rabundvector.o': No such file or directory
rm: cannot remove `./rarecalc.o': No such file or directory
rm: cannot remove `./raredisplay.o': No such file or directory
rm: cannot remove `./rarefact.o': No such file or directory
rm: cannot remove `./rarefactcommand.o': No such file or directory
rm: cannot remove `./rarefactsharedcommand.o': No such file or directory
rm: cannot remove `./sabundvector.o': No such file or directory
rm: cannot remove `./sequence.o': No such file or directory
rm: cannot remove `./shannon.o': No such file or directory
rm: cannot remove `./sharedace.o': No such file or directory
rm: cannot remove `./sharedchao1.o': No such file or directory
rm: cannot remove `./sharedcommand.o': No such file or directory
rm: cannot remove `./sharedjabund.o': No such file or directory
rm: cannot remove `./sharedjclass.o': No such file or directory
rm: cannot remove `./sharedjest.o': No such file or directory
rm: cannot remove `./sharedordervector.o': No such file or directory
rm: cannot remove `./sharedrabundvector.o': No such file or directory
rm: cannot remove `./sharedsabundvector.o': No such file or directory
rm: cannot remove `./sharedsobs.o': No such file or directory
rm: cannot remove `./sharedsorabund.o': No such file or directory
rm: cannot remove `./sharedsorclass.o': No such file or directory
rm: cannot remove `./sharedsorest.o': No such file or directory
rm: cannot remove `./sharedthetan.o': No such file or directory
rm: cannot remove `./sharedthetayc.o': No such file or directory
rm: cannot remove `./simpson.o': No such file or directory
rm: cannot remove `./singlelinkage.o': No such file or directory
rm: cannot remove `./sparsematrix.o': No such file or directory
rm: cannot remove `./summarycommand.o': No such file or directory
rm: cannot remove `./summarysharedcommand.o': No such file or directory
rm: cannot remove `./uvest.o': No such file or directory
rm: cannot remove `./validcalculator.o': No such file or directory
rm: cannot remove `./validparameter.o': No such file or directory
rm: cannot remove `./treenode.o': No such file or directory
rm: cannot remove `./readtreecommand.o': No such file or directory
rm: cannot remove `./reversecommand.o': No such file or directory
rm: cannot remove `./trimseqscommand.o': No such file or directory
rm: cannot remove `./slibshuff.o': No such file or directory
rm: cannot remove `./libshuff.o': No such file or directory
rm: cannot remove `./dlibshuff.o': No such file or directory
rm: cannot remove `./mergefilecommand.o': No such file or directory
rm: cannot remove `./coverage.o': No such file or directory
rm: cannot remove `./whittaker.o': No such file or directory
rm: cannot remove `./preclustercommand.o': No such file or directory
rm: cannot remove `./otuhierarchycommand.o': No such file or directory
rm: cannot remove `./setdircommand.o': No such file or directory
rm: cannot remove `./getgroupcommand.o': No such file or directory
rm: cannot remove `./getlabelcommand.o': No such file or directory
rm: cannot remove `./secondarystructurecommand.o': No such file or directory
rm: cannot remove `./mothurout.o': No such file or directory
rm: cannot remove `./parselistscommand.o': No such file or directory
rm: cannot remove `./readblast.o': No such file or directory
rm: cannot remove `./chimeracheckrdp.o': No such file or directory
rm: cannot remove `./hclustercommand.o': No such file or directory
rm: cannot remove `./hcluster.o': No such file or directory
rm: cannot remove `./getlistcountcommand.o': No such file or directory
rm: cannot remove `./readcluster.o': No such file or directory
rm: cannot remove `./ccode.o': No such file or directory
rm: cannot remove `./taxonomyequalizer.o': No such file or directory
rm: cannot remove `./phylotypecommand.o': No such file or directory
rm: cannot remove `./classifyseqscommand.o': No such file or directory
rm: cannot remove `./classifyotucommand.o': No such file or directory
rm: cannot remove `./parsesffcommand.o': No such file or directory
rm: cannot remove `./classify.o': No such file or directory
rm: cannot remove `./phylotree.o': No such file or directory
rm: cannot remove `./phylodiversity.o': No such file or directory
rm: cannot remove `./phylodiversitycommand.o': No such file or directory
rm: cannot remove `./bayesian.o': No such file or directory
rm: cannot remove `./phylosummary.o': No such file or directory
rm: cannot remove `./alignmentdb.o': No such file or directory
rm: cannot remove `./knn.o': No such file or directory
rm: cannot remove `./distancedb.o': No such file or directory
rm: cannot remove `./chimeraslayer.o': No such file or directory
rm: cannot remove `./slayer.o': No such file or directory
rm: cannot remove `./pcacommand.o': No such file or directory
rm: cannot remove `./formatcolumn.o': No such file or directory
rm: cannot remove `./formatphylip.o': No such file or directory
rm: cannot remove `./mgclustercommand.o': No such file or directory
rm: cannot remove `./getsharedotucommand.o': No such file or directory
rm: cannot remove `./maligner.o': No such file or directory
rm: cannot remove `./chimerarealigner.o': No such file or directory
rm: cannot remove `./bergerparker.o': No such file or directory
rm: cannot remove `./bstick.o': No such file or directory
rm: cannot remove `./sharedkstest.o': No such file or directory
rm: cannot remove `./qstat.o': No such file or directory
rm: cannot remove `./shen.o': No such file or directory
rm: cannot remove `./logsd.o': No such file or directory
rm: cannot remove `./geom.o': No such file or directory
rm: cannot remove `./setlogfilecommand.o': No such file or directory
rm: cannot remove `mothur': No such file or directory
make: *** [clean] Error 1
```
---
### Author:  [@westcott](https://forum.mothur.org/u/westcott)
#### Post date: [July 23, 2010, 2:19am UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/15 "2010-07-23T02:19:23Z")
You can ignore those. The make clean removes anything that may have compiled, so you can start fresh. Anytime you change the makefile it’s a good idea to do a make clean. Now you just need to run make.
---
### Author:  [@twaddlac](https://forum.mothur.org/u/twaddlac)
#### Post date: [July 26, 2010, 4:40pm UTC](https://forum.mothur.org/t/problems-compiling-mothur-on-64-bit-centos/292/16 "2010-07-26T16:40:59Z")
Ahh it works now! Thanks a lot for your help!! 😃