I downloaded 1.24.1 as an executable for Linux and attempted to install in in Ubuntu. I get the message “./mothur: error while loading shared libraries: libreadline.so.5: cannot open shared object file: No such file or directory” when trying to run. I get it in both 32 and 64 bit. The executable without readline works fine. I assume this is because I am running readline6, so the .5 file is replaced by a .6?
Trying to compile from source, I get the following:
georgia@georgia-U56E:~/mothur/Mothur.source$ make
gfortran -c -m64 *.f
g++ -O3 -mtune=native -march=native -m64 -DBIT_VERSION -DRELEASE_DATE="“3/16/2012"” -DVERSION="“1.24.1"” -DMOTHUR_FILES=""/home/georgia/mothur"" -DUSE_READLINE -I. -c -o ace.o ace.cpp
In file included from calculator.h:5:0,
from ace.h:16,
from ace.cpp:10:
mothur.h:66:33: fatal error: readline/readline.h: No such file or directory
compilation terminated.
Which I assume is related to the above error. I really love using readline in interactive mode, would like to see this fixed
It seems mothur is not able to find where you have readline installed on your machine. Can you tell me what “apt-file search readline/readline.h” returns?
I am experiencing the same problem with the install of the new mothur 1.26 whereas I never had this problem before.
I am running mothur on a 64 bit 24-core system with Ubuntu 12.04 LTS server installed.
The result of apt-file search readline/readline.h is:
You can mark this issue as resolved: after digging somewhat deeper I found out that although there apparently are links to the readline.h it wasn’t there.
I found out that I didn’t have the libreadline-dev installed. I had it previously installed on ubuntu 11.10 (former OS of the server) and somehow it got removed when updating to 12.04 LTS without removing the links I guess (my best guess, wouldn’t know how I was ever able to compile mothur 1.24 from source if this was not the case).
So after executing apt-get install libreadline-dev the installation didn’t give the issue anymore.
Sorry for bothering you all.
I hope this post might help other people with the same question as me resolve this issue in the future.
Thank you for your reply.
I’m not quite sure if I have ncurses installed.
As I am saying, when compiling mothur 1.24 from source I never experienced any issue however I switched the OS on my server from ubuntu server 11.10 to 12.04 LTS.
When I tried sudo apt-get install ncurses I get the following output:
Package ncurses is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
E: Package ‘ncurses’ has no installation candidate
If anyone knows how to install the correct package refering to ncurses, feel free to let me know (i have a 64-bit system).
Thank you very much!
lib64ncurses5-dev solved the issue.
Mothur 1.26 is up and running and I immediately could make use of the new get.coremcrobiome for my upcoming paper (which will, of course, include proper referencing to Mothur).
