ImportError: libgfortran.so.1

[sean-ocall]

Hi guys,
I'm getting an error when I try to run the spheroid test. Full error message here:

(sm)ubuntu@vagrant-ubuntu-trusty-64:/opt/dev/sm$ scripts/run.sh scripts/run_molecule_search.py spheroid /opt/dev/sm/tests/data/sci_test_search_job_spheroid_dataset/ /opt/dev/sm/tests/data/sci_test_search_job_spheroid_dataset/config.json
ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
ERROR: ld.so: object '/usr/lib/x86_64-linux-gnu/libgfortran.so.3' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored.
Traceback (most recent call last):
File "scripts/run_molecule_search.py", line 10, in
from sm.engine.search_job import SearchJob
File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/sm/engine/search_job.py", line 15, in
from sm.engine.msm_basic.msm_basic_search import MSMBasicSearch
File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/sm/engine/msm_basic/msm_basic_search.py", line 2, in
from sm.engine.msm_basic.formula_img_validator import sf_image_metrics, sf_image_metrics_est_fdr
File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/sm/engine/msm_basic/formula_img_validator.py", line 8, in
from pyImagingMSpec.image_measures import isotope_image_correlation, isotope_pattern_match
File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/pyImagingMSpec/image_measures.py", line 2, in
import scipy.stats
File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/scipy/stats/init.py", line 321, in
from .stats import *
File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/scipy/stats/stats.py", line 180, in
import scipy.special as special
File "/opt/dev/miniconda/envs/sm/lib/python2.7/site-packages/scipy/special/init.py", line 601, in
from ._ufuncs import *
ImportError: libgfortran.so.1: cannot open shared object file: No such file or directory

Looks like it's some sort of scipy issue from a quick google search.

[lomereiter]

Hi, I googled a bit and it looks like ContinuumIO/anaconda-issues#686

The suggested workaround is to run conda install -f libgfortran==1

[sean-ocall]

Hi,

I should have said - I did try that (and have done so again), unfortunately it doesn't fix it, and the error message is the same.
Thanks,
Sean

[lomereiter]

Hi,
Apparently some nasty package sets LD_PRELOAD to point to system-wide installation of libgfortran3, and it is not installed. Please try running apt-get install libgfortran3, hopefully it'll help.

[sean-ocall]

Yes, that did it!