# Halla install error

**URL:** <https://forum.biobakery.org/t/halla-install-error/2513>\
**Category:** HAllA\
**Created:** [August 27, 2021, 10:12am UTC](https://forum.biobakery.org/t/halla-install-error/2513 "2021-08-27T10:12:18Z")\
**Posts on this page:** 7\
**Page:** 1

<div class="post-metadata">

**Author:** ![Jinpao\_Hou](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jinpao_hou/32/985_2.png) [@Jinpao\_Hou](https://forum.biobakery.org/u/Jinpao_Hou)\
**Post date:** [August 27, 2021, 10:12am UTC](https://forum.biobakery.org/t/halla-install-error/2513/1 "2021-08-27T10:12:18Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![andrewGhazi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrewghazi/32/2950_2.png) [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)\
**Post date:** [August 27, 2021, 11:46am UTC](https://forum.biobakery.org/t/halla-install-error/2513/2 "2021-08-27T11:46:25Z")

</div>

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

```auto
import rpy2.robjects as robjects
print(robjects.r(".libPaths()"))

```

---

<div class="post-metadata">

**Author:** ![Jinpao\_Hou](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jinpao_hou/32/985_2.png) [@Jinpao\_Hou](https://forum.biobakery.org/u/Jinpao_Hou)\
**Post date:** [August 27, 2021, 4:46pm UTC](https://forum.biobakery.org/t/halla-install-error/2513/3 "2021-08-27T16:46:11Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![andrewGhazi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrewghazi/32/2950_2.png) [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)\
**Post date:** [August 27, 2021, 5:40pm UTC](https://forum.biobakery.org/t/halla-install-error/2513/4 "2021-08-27T17:40:45Z")

</div>

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](https://rpy2.github.io/doc/v2.9.x/html/robjects_rpackages.html#installing-removing-r-packages)

---

<div class="post-metadata">

**Author:** ![Jinpao\_Hou](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jinpao_hou/32/985_2.png) [@Jinpao\_Hou](https://forum.biobakery.org/u/Jinpao_Hou)\
**Post date:** [August 28, 2021, 5:50am UTC](https://forum.biobakery.org/t/halla-install-error/2513/5 "2021-08-28T05:50:46Z")

</div>

> [@Jinpao\_Hou](#):
>
> import rpy2.robjects as robjects

Dear Andrew Ghazi,

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

```auto
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

---

<div class="post-metadata">

**Author:** ![Jinpao\_Hou](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/jinpao_hou/32/985_2.png) [@Jinpao\_Hou](https://forum.biobakery.org/u/Jinpao_Hou)\
**Post date:** [August 28, 2021, 6:16am UTC](https://forum.biobakery.org/t/halla-install-error/2513/6 "2021-08-28T06:16:34Z")

</div>

> [@Jinpao\_Hou](#):
>
> /home/jessie/.local/bin/halla

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

---

<div class="post-metadata">

**Author:** ![andrewGhazi](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/andrewghazi/32/2950_2.png) [@andrewGhazi](https://forum.biobakery.org/u/andrewGhazi)\
**Post date:** [August 30, 2021, 4:24pm UTC](https://forum.biobakery.org/t/halla-install-error/2513/7 "2021-08-30T16:24:54Z")

</div>

> [@Jinpao\_Hou](#):
>
> 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

Great, glad you were able to get it sorted.