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.