Halla install error

Downstream analysis and statistics HAllA
1

Hi there!

I ran pip install halla successfully in Ubuntu 18.04, but when I run halla, it gave the following error:

$ /home/jessie/.local/bin/halla --help
Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so: undefined symbol: ALTREP_LENGTH
Error: package or namespace load failed for ‘utils’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/utils/libs/utils.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/utils/libs/utils.so: undefined symbol: IS_ASCII
Error: package or namespace load failed for ‘grDevices’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: R_GE_linearGradientColour
Error: package or namespace load failed for ‘graphics’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: R_GE_linearGradientColour
Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: R_GE_linearGradientColour
Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so: undefined symbol: ALTREP_LENGTH
During startup - Warning messages:
1: package “methods” in options(“defaultPackages”) was not found
2: package ‘utils’ in options(“defaultPackages”) was not found
3: package ‘grDevices’ in options(“defaultPackages”) was not found
4: package ‘graphics’ in options(“defaultPackages”) was not found
5: package ‘stats’ in options(“defaultPackages”) was not found
6: package ‘methods’ in options(“defaultPackages”) was not found
R[write to console]: Error in dyn.load(file, DLLpath = DLLpath, …) :
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so: undefined symbol: ALTREP_LENGTH

Traceback (most recent call last):
File “/home/jessie/.local/bin/halla”, line 5, in
from scripts.halla import main
File “/home/jessie/.local/lib/python3.7/site-packages/scripts/halla.py”, line 10, in
from halla import HAllA, AllA
File “/home/jessie/.local/lib/python3.7/site-packages/halla/init.py”, line 1, in
from .main import HAllA, AllA
File “/home/jessie/.local/lib/python3.7/site-packages/halla/main.py”, line 2, in
from .hierarchy import HierarchicalTree
File “/home/jessie/.local/lib/python3.7/site-packages/halla/hierarchy.py”, line 1, in
from .utils.similarity import get_similarity_function, similarity2distance
File “/home/jessie/.local/lib/python3.7/site-packages/halla/utils/similarity.py”, line 6, in
from rpy2.robjects.packages import importr
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/robjects/init.py”, line 19, in
from rpy2.robjects.robject import RObjectMixin, RObject
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/robjects/robject.py”, line 58, in
class RObjectMixin(object):
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/robjects/robject.py”, line 70, in RObjectMixin
__show = _get_exported_value(‘methods’, ‘show’)
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py”, line 45, in _
cdata = function(*args, **kwargs)
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/rinterface.py”, line 680, in call
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, …) :
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so: undefined symbol: ALTREP_LENGTH

I googled this question, but still failed to solve it. Any suggestion will be greatly appreciated. Thanks in advance!

Best regards,
Jessie

2

Did you have R installed before installing HAllA? What output do you get from the following python code?

import rpy2.robjects as robjects
print(robjects.r(".libPaths()"))
3

Dear Andrew Ghazi,

Thank you for very much for your quick reply. I have installed R before installing HAIIA. And the following is the output for your code:

$ python
Python 3.7.7 (default, Mar 26 2020, 15:48:22)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type “help”, “copyright”, “credits” or “license” for more information.

import rpy2.robjects as robjects
Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so: undefined symbol: ALTREP_LENGTH
Error: package or namespace load failed for ‘utils’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/utils/libs/utils.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/utils/libs/utils.so: undefined symbol: IS_ASCII
Error: package or namespace load failed for ‘grDevices’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: R_GE_linearGradientColour
Error: package or namespace load failed for ‘graphics’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: R_GE_linearGradientColour
Error: package or namespace load failed for ‘stats’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/grDevices/libs/grDevices.so: undefined symbol: R_GE_linearGradientColour
Error: package or namespace load failed for ‘methods’ in dyn.load(file, DLLpath = DLLpath, …):
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so: undefined symbol: ALTREP_LENGTH
During startup - Warning messages:
1: package “methods” in options(“defaultPackages”) was not found
2: package ‘utils’ in options(“defaultPackages”) was not found
3: package ‘grDevices’ in options(“defaultPackages”) was not found
4: package ‘graphics’ in options(“defaultPackages”) was not found
5: package ‘stats’ in options(“defaultPackages”) was not found
6: package ‘methods’ in options(“defaultPackages”) was not found
R[write to console]: Error in dyn.load(file, DLLpath = DLLpath, …) :
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so: undefined symbol: ALTREP_LENGTH

Traceback (most recent call last):
File “”, line 1, in
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/robjects/init.py”, line 19, in
from rpy2.robjects.robject import RObjectMixin, RObject
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/robjects/robject.py”, line 58, in
class RObjectMixin(object):
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/robjects/robject.py”, line 70, in RObjectMixin
__show = _get_exported_value(‘methods’, ‘show’)
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/rinterface_lib/conversion.py”, line 45, in _
cdata = function(*args, **kwargs)
File “/home/jessie/.local/lib/python3.7/site-packages/rpy2/rinterface.py”, line 680, in call
raise embedded.RRuntimeError(_rinterface._geterrmessage())
rpy2.rinterface_lib.embedded.RRuntimeError: Error in dyn.load(file, DLLpath = DLLpath, …) :
unable to load shared object ‘/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so’:
/exeh_3/jessie/software/R-4.1.0/lib/R/library/methods/libs/methods.so: undefined symbol: ALTREP_LENGTH

print(robjects.r(“.libPaths()”))
Traceback (most recent call last):
File “”, line 1, in
NameError: name ‘robjects’ is not defined

My R sessionInfo is:

library(eva)
library(XICOR)
sessionInfo()
R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
[1] LC_CTYPE=en_HK.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_HK.UTF-8 LC_COLLATE=en_HK.UTF-8
[5] LC_MONETARY=en_HK.UTF-8 LC_MESSAGES=en_HK.UTF-8
[7] LC_PAPER=en_HK.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_HK.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] XICOR_0.3.3 eva_0.2.6

loaded via a namespace (and not attached):
[1] compiler_4.1.0 Matrix_1.3-3 parallel_4.1.0 grid_4.1.0
[5] lattice_0.20-44

Many thanks again!

Best regards,
Jessie

4

It seems your rpy2 installation is broken, try reinstalling that then manually using rpy2 to install eva and XICOR like so: R packages — rpy2 2.9.4 documentation

5

Dear Andrew Ghazi,

I tried your method but still failed. I installed rpy2 from source by typing:

tar -zxf rpy2-3.4.5.tar.gz
cd rpy2-3.4.5
python setup.py build install

The above commands run smoothly. However, when I run import rpy2.robjects as robjects in python. The same errors occured.

To debug, I typed:
$ python -m rpy2.situation
rpy2 version:
3.4.5
Python version:
3.7.7 (default, Mar 26 2020, 15:48:22)
[GCC 7.3.0]
Looking for R’s HOME:
Environment variable R_HOME: None
Calling R RHOME: /exeh_3/jessie/software/R-4.1.0/lib/R
Environment variable R_LIBS_USER: None
R’s additions to LD_LIBRARY_PATH:
/home/jessie/src/software/openssl/lib/:/home/jessie/src/software/openssl/lib/
R version:
In the PATH: R version 4.1.0 (2021-05-18) – “Camp Pontanezen”
Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
include:
[‘/exeh_3/jessie/software/R-4.1.0/lib/R/include’]
libraries:
[‘R’, ‘pcre’, ‘lzma’, ‘bz2’, ‘z’, ‘rt’, ‘dl’, ‘m’, ‘icuuc’, ‘icui18n’]
library_dirs:
[‘/usr/local/lib’, ‘/exeh_3/jessie/software/R-4.1.0/lib/R/lib’]
extra_compile_args:

extra_link_args:
[‘-Wl,–export-dynamic’, ‘-fopenmp’]

I noted the LD_LIBRARY_PATH is /home/jessie/src/software/openssl/lib/:/home/jessie/src/software/openssl/lib/, which turned out an invalid path (this path does not exist) that were included my .bashrc file. Therefore, I commented this line in .bashrc file and restarted a session. Then I reinstalled rpy2 using the same commands as above. This time the command ‘python -m rpy2.situation’ give the following output:
$ python -m rpy2.situation
rpy2 version:
3.4.5
Python version:
3.7.7 (default, Mar 26 2020, 15:48:22)
[GCC 7.3.0]
Looking for R’s HOME:
Environment variable R_HOME: None
Calling R RHOME: /exeh_3/jessie/software/R-4.1.0/lib/R
Environment variable R_LIBS_USER: None
R’s additions to LD_LIBRARY_PATH:
/exeh_3/jessie/software/R-4.1.0/lib/R/lib:/usr/local/lib:/exeh_3/jessie/src/jdk-16.0.1/lib/server
R version:
In the PATH: R version 4.1.0 (2021-05-18) – “Camp Pontanezen”
Loading R library from rpy2: OK
Additional directories to load R packages from:
None
C extension compilation:
include:
[‘/exeh_3/jessie/software/R-4.1.0/lib/R/include’]
libraries:
[‘R’, ‘pcre’, ‘lzma’, ‘bz2’, ‘z’, ‘rt’, ‘dl’, ‘m’, ‘icuuc’, ‘icui18n’]
library_dirs:
[‘/usr/local/lib’, ‘/exeh_3/jessie/software/R-4.1.0/lib/R/lib’]
extra_compile_args:

extra_link_args:
[‘-Wl,–export-dynamic’, ‘-fopenmp’]

The LD_LIBRARY_PATH became /exeh_3/jessie/software/R-4.1.0/lib/R/lib:/usr/local/lib:/exeh_3/jessie/src/jdk-16.0.1/lib/server

After this change, I ran ‘import rpy2.robjects as robjects’ in python, but still got the same error. I have no idea currently. How to install rpy2 correctly?

Thank you very much for your time and patience.

Best regards,
Jessie

6

Dear Andrew Ghazi,

I finally made it by changing the LD_LIBRARY_PATH in my ~/.bashrc file:
export LD_LIBRARY_PATH=“/exeh_3/jessie/software/R-4.1.0/lib/R/lib:/usr/local/lib:$LD_LIBRARY_PATH”

Now HAllA can be used normally. Many thanks for your guidance!

Best regards,
Jessie

7

Great, glad you were able to get it sorted.