there is no package called ‘cowplot’ #21
Description
I am running into the following error when using NanoMod:
/home/pengj1/.local/share/r-miniconda/envs/py27nanomod/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: Error in loadNamespace(name) : there is no package called ‘cowplot’
warnings.warn(x, RRuntimeWarning)
Number of files in /mnt/isilon/wang_lab/jackie/project/long-read_tutorial/samples/meth1/NB01/is 16249
Start sorting
SaveTest 1
Finish SaveTest
Test data is saved in mRes//mod_sign_test.txt
Traceback (most recent call last):
File "/mnt/isilon/wang_lab/jackie/project/long-read_tutorial/NanoMod/bin/NanoMod.py", line 468, in <module>
args.func(args);
File "/mnt/isilon/wang_lab/jackie/project/long-read_tutorial/NanoMod/bin/NanoMod.py", line 178, in mDetect
myDetect.mDetect(moptions)
File "/mnt/isilon/wang_lab/jackie/project/long-read_tutorial/NanoMod/bin/scripts/myDetect.py", line 643, in mDetect
mboxplot(moptions)
File "/mnt/isilon/wang_lab/jackie/project/long-read_tutorial/NanoMod/bin/scripts/myDetect.py", line 264, in mboxplot
importr('cowplot')
File "/home/pengj1/.local/share/r-miniconda/envs/py27nanomod/lib/python2.7/site-packages/rpy2/robjects/packages.py", line 453, in importr
env = _get_namespace(rname)
rpy2.rinterface.RRuntimeError: Error in loadNamespace(name) : there is no package called ‘cowplot’
I created the conda environment using conda env create -f env.py27nanomod.yml, however, it seems like the cowplot package is required to use NanoMod but it is missing.
I tried installing cowplot using conda install -c r r-cowplot, however, I still get the error below (even when I also do conda install -c r r-stringr r-stringi):
/home/pengj1/.local/share/r-miniconda/envs/py27nanmod_manual/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: Error: package or namespace load failed for ‘stringr’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/pengj1/.local/share/r-miniconda/envs/py27nanmod_manual/lib/R/library/stringi/libs/stringi.so':
libicui18n.so.58: cannot open shared object file: No such file or directory
warnings.warn(x, RRuntimeWarning)
/home/pengj1/.local/share/r-miniconda/envs/py27nanmod_manual/lib/python2.7/site-packages/rpy2/rinterface/__init__.py:186: RRuntimeWarning: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/pengj1/.local/share/r-miniconda/envs/py27nanmod_manual/lib/R/library/stringi/libs/stringi.so':
libicui18n.so.58: cannot open shared object file: No such file or directory
warnings.warn(x, RRuntimeWarning)
Number of files in /mnt/isilon/wang_lab/jackie/project/long-read_tutorial/samples/meth1/NB01/is 16249
Start sorting
SaveTest 1
Finish SaveTest
Test data is saved in mRes//mod_sign_test.txt
Traceback (most recent call last):
File "/mnt/isilon/wang_lab/jackie/project/long-read_tutorial/NanoMod/bin/NanoMod.py", line 468, in <module>
args.func(args);
File "/mnt/isilon/wang_lab/jackie/project/long-read_tutorial/NanoMod/bin/NanoMod.py", line 178, in mDetect
myDetect.mDetect(moptions)
File "/mnt/isilon/wang_lab/jackie/project/long-read_tutorial/NanoMod/bin/scripts/myDetect.py", line 643, in mDetect
mboxplot(moptions)
File "/mnt/isilon/wang_lab/jackie/project/long-read_tutorial/NanoMod/bin/scripts/myDetect.py", line 265, in mboxplot
importr('stringr')
File "/home/pengj1/.local/share/r-miniconda/envs/py27nanmod_manual/lib/python2.7/site-packages/rpy2/robjects/packages.py", line 453, in importr
env = _get_namespace(rname)
rpy2.rinterface.RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/home/pengj1/.local/share/r-miniconda/envs/py27nanmod_manual/lib/R/library/stringi/libs/stringi.so':
libicui18n.so.58: cannot open shared object file: No such file or directory
Could you please help me with this error? Thanks!