Conda install - ImportError: libicuuc.so.58: cannot open shared object file: No such file or directory
lowandrew opened this issue · 2 comments
lowandrew commented
Hello,
I attempted to install PlasFlow using conda as recommended in your README, but it looks like conda is having some issues with a dependency - when I try to run PlasFlow.py, I get the following ImportError:
PlasFlow.py --input /home/lowa/test.fasta --output classified.txt
Traceback (most recent call last):
File "/home/lowa/miniconda3/envs/plasflow/bin/PlasFlow.py", line 48, in <module>
from rpy2.robjects.packages import importr
File "/home/lowa/miniconda3/envs/plasflow/lib/python3.5/site-packages/rpy2/robjects/__init__.py", line 15, in <module>
import rpy2.rinterface as rinterface
File "/home/lowa/miniconda3/envs/plasflow/lib/python3.5/site-packages/rpy2/rinterface/__init__.py", line 99, in <module>
from rpy2.rinterface._rinterface import *
ImportError: libicuuc.so.58: cannot open shared object file: No such file or directory
The rpy2 module is definitely installed, as can be seen with conda list
, so I'm not sure what's going wrong. Any guidance on how to resolve this would be much appreciated. Thanks!
Output of conda list:
# packages in environment at /home/lowa/miniconda3/envs/plasflow:
#
bioconductor-biocgenerics 0.22.0 r3.3.2_0 bioconda
bioconductor-iranges 2.8.2 r3.3.2_0 bioconda
bioconductor-s4vectors 0.12.2 r3.3.2_0 bioconda
bioconductor-xvector 0.14.1 r3.3.2_0 bioconda
bioconductor-zlibbioc 1.20.0 r3.3.2_1 bioconda
biopython 1.70 py35_2 conda-forge
bzip2 1.0.6 1 conda-forge
ca-certificates 2017.11.5 0 conda-forge
cairo 1.14.8 0
certifi 2017.11.5 py35_0 conda-forge
curl 7.55.1 0 conda-forge
fontconfig 2.12.1 3
freetype 2.5.5 2
glib 2.50.2 1
gsl 2.1 2 conda-forge
harfbuzz 0.9.39 2
icu 54.1 0
intel-openmp 2018.0.0 hc7b2577_8
jpeg 9b 2 conda-forge
krb5 1.14.2 0 conda-forge
libffi 3.2.1 3 conda-forge
libgcc 7.2.0 h69d50b8_2
libgcc-ng 7.2.0 h7cc24e2_2
libgfortran 3.0.0 1
libiconv 1.14 4 conda-forge
libpng 1.6.34 0 conda-forge
libssh2 1.8.0 2 conda-forge
libstdcxx-ng 7.2.0 h7a57d05_2
libtiff 4.0.9 0 conda-forge
libxml2 2.9.4 0
mkl 2017.0.4 h4c4d0af_0
mock 2.0.0 py35_0 conda-forge
ncurses 5.9 10 conda-forge
numpy 1.11.3 py35_0
openssl 1.0.2n 0 conda-forge
pandas 0.22.0 py35_0 conda-forge
pango 1.40.3 1
pbr 3.1.1 py35_0 conda-forge
pcre 8.39 0 conda-forge
pip 9.0.1 py35_1 conda-forge
pixman 0.34.0 1 conda-forge
plasflow 1.0.7 py35_0 smaegol
protobuf 3.5.1 py35_3 conda-forge
python 3.5.4 2 conda-forge
python-dateutil 2.3 py35_0 bioconda
pytz 2017.3 py_2 conda-forge
r-base 3.3.2 1
readline 6.2 0 conda-forge
rpy2 2.7.8 py35r3.3.2_1 bioconda
scikit-learn 0.18.1 np111py35_1
scipy 0.19.0 np111py35_0
setuptools 38.4.0 py35_0 conda-forge
six 1.11.0 py35_1 conda-forge
sqlite 3.13.0 1 conda-forge
tensorflow 0.10.0rc0 np111py35_0
tk 8.5.19 2 conda-forge
wheel 0.30.0 py35_2 conda-forge
xz 5.2.3 0 conda-forge
zlib 1.2.11 0 conda-forge
lowandrew commented
Seems to be working as of today.
feilongzh commented
Seems to be working as of today.
How to deal with that ?I have the same question.