plink2: no file/directory libgfortran, search has found libgfortran
1
0
Entering edit mode
4 months ago

I used plink2 numerous times last month and the months preceding that, however, there has been a month time since then and now when I trry to use plink2 I get this error message:

plink2: error while loading shared libraries: libgfortran.so.3: cannot open shared object file: No such file or directory

however

 find ./ -iname 'libgfortran'
 ./anaconda3/pkgs/libgfortran-ng-7.2.0-hdf63c60_3/share/licenses/libgfortran
./anaconda3/pkgs/libgfortran-ng-7.5.0-hdf63c60_6/share/licenses/libgfortran
./anaconda3/share/licenses/libgfortran
./anaconda3/envs/Conda-Env-R/share/licenses/libgfortran

but

 which libgfortran
    /usr/bin/which: no libgfortran in (/storage/home/jok119/anaconda3/bin:/storage/home/jok119/anaconda3/condabin:/storage/home/jok119/perl5/bin:/storage/home/jok119/anaconda3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin export PATH=usr/bin/perl:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/storage/home/jok119/.local/bin:/storage/home/jok119/bin)

I tried uninstalling and reinstalling plink2 via

conda install plink2

and installing libgfortran

conda install libgfortran

Should be the right one: https://anaconda.org/anaconda/libgfortran/files esp since I have used plink2 before

plink genetics vcf sequencing WES • 255 views
ADD COMMENT
0
Entering edit mode

libgfortran is a library, not an executable, so which libgfortran won't give you anything - it's not in the $PATH.

Try creating a new conda environment and installing plink2 there. From my experience, I'd not recommend installing conda packages in the base environment as managing them becomes a pain sooner or later.

ADD REPLY
0
Entering edit mode

Ugh, yea, I should stop using base, I must have messed something up in the base env cuhz downloading plink in a new env worked. bleh. thanks so much.

ADD REPLY
0
Entering edit mode
4 months ago
Mensur Dlakic ★ 10k

The program needs libgfortran.so.3 specifically, not libgfortran. Chances are that you updated the library and you don't have the so.3 version any more.

Try these two commands:

locate libgfortran.so.3
locate libgfortran

If you manage to locate libgfortran.so.3, you can make a symbolic link to it inside a known library directory. If you find this library but it ends in a higher number than 3, say libgfortran.so.4, go to that directory and make a symbolic link :

ln -s libgfortran.so.4 libgfortran.so.3

This won't work if you find the library that ends in a smaller number than 3.

ADD COMMENT
0
Entering edit mode

thanks so much, really helpful in understanding and will be helpful in the future. I took the easy way out in the end (_r_am solution)

ADD REPLY

Login before adding your answer.

Traffic: 1927 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6