installment seems successful, but encounter errors running majiq

YINI LI

unread,

Mar 15, 2022, 11:45:41 PM3/15/22

to majiq_voila

I am using a macOS Big Sur system.

The error message I received when running majiq -

(env) (base) kittybunny@Yinis-iMac ~ % majiq

Traceback (most recent call last):

File "/Users/kittybunny/env/bin/majiq", line 5, in <module>

from rna_majiq.run_majiq import main

File "/Users/kittybunny/env/lib/python3.8/site-packages/rna_majiq/run_majiq.py", line 12, in <module>

from rna_majiq.src.build import build

ImportError: dlopen(/Users/kittybunny/env/lib/python3.8/site-packages/rna_majiq/src/build.cpython-38-darwin.so, 2): Symbol not found: _GOMP_parallel

Referenced from: /Users/kittybunny/env/lib/python3.8/site-packages/rna_majiq/src/build.cpython-38-darwin.so

Expected in: flat namespace

in /Users/kittybunny/env/lib/python3.8/site-packages/rna_majiq/src/build.cpython-38-darwin.so

I installed with the following lines (seems successful)-

export HTSLIB_LIBRARY_DIR=/usr/local/lib

export HTSLIB_INCLUDE_DIR=/usr/local/include

export CC=/usr/local/bin/gcc-11

export CXX=/usr/local/bin/g++-11

pip install git+https://bitbucket.org/biociphers/majiq_academic.git

The messages received upon installation -

(env) (base) kittybunny@Yinis-iMac ~ % pip install git+https://bitbucket.org/biociphers/majiq_academic.git

Collecting git+https://bitbucket.org/biociphers/majiq_academic.git

Cloning https://bitbucket.org/biociphers/majiq_academic.git to /private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo

Running command git clone --filter=blob:none --quiet https://bitbucket.org/biociphers/majiq_academic.git /private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo

warning: filtering not recognized by server, ignoring

Resolved https://bitbucket.org/biociphers/majiq_academic.git to commit 85d07819f55b182c830bdc69296c1485f51b3100

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Processing /private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Processing /private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/majiq

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... done

Requirement already satisfied: numpy>=1.18.1 in ./env/lib/python3.8/site-packages (from rna-majiq@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/majiq/->rna-majiq-meta==2.4.dev3+g85d07819) (1.22.3)

Requirement already satisfied: smmap2==2.0.5 in ./env/lib/python3.8/site-packages (from rna-majiq@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/majiq/->rna-majiq-meta==2.4.dev3+g85d07819) (2.0.5)

Requirement already satisfied: scipy>=1.4.1 in ./env/lib/python3.8/site-packages (from rna-majiq@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/majiq/->rna-majiq-meta==2.4.dev3+g85d07819) (1.8.0)

Requirement already satisfied: Flask==1.0.2 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (1.0.2)

Requirement already satisfied: Flask-Session==0.3.1 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (0.3.1)

Requirement already satisfied: h5py==2.10.0 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (2.10.0)

Requirement already satisfied: six==1.14.0 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (1.14.0)

Requirement already satisfied: Werkzeug==0.16.0 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (0.16.0)

Requirement already satisfied: WTForms==2.2.1 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (2.2.1)

Requirement already satisfied: Click>=7.0 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (8.0.4)

Requirement already satisfied: gunicorn==19.9.0 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (19.9.0)

Requirement already satisfied: MarkupSafe==1.1.1 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (1.1.1)

Requirement already satisfied: Flask-WTF==0.14.2 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (0.14.2)

Requirement already satisfied: waitress==1.1.0 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (1.1.0)

Requirement already satisfied: itsdangerous==1.1.0 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (1.1.0)

Requirement already satisfied: networkx==2.5 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (2.5)

Requirement already satisfied: GitPython==3.0.5 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (3.0.5)

Requirement already satisfied: Jinja2==2.11.1 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (2.11.1)

Requirement already satisfied: psutil==5.6.7 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (5.6.7)

Requirement already satisfied: gitdb2==2.0.6 in ./env/lib/python3.8/site-packages (from rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (2.0.6)

Requirement already satisfied: decorator>=4.3.0 in ./env/lib/python3.8/site-packages (from networkx==2.5->rna-voila@ file://localhost/private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-req-build-6gp0g3yo/voila/->rna-majiq-meta==2.4.dev3+g85d07819) (5.1.1)

Building wheels for collected packages: rna-majiq, rna-voila

Building wheel for rna-majiq (pyproject.toml) ... done

Created wheel for rna-majiq: filename=rna_majiq-2.4.dev3+g85d07819-cp38-cp38-macosx_10_9_x86_64.whl size=6838874 sha256=ef29e4ecf459f4c63de0c418322d4d066eb7145e427d0a04e19109e1a0ebb70c

Stored in directory: /private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-ephem-wheel-cache-klwhm1n1/wheels/35/b1/f4/45e6969eddd76bb76cf99d0ef471e494e9a683c127fee131f6

Building wheel for rna-voila (pyproject.toml) ... done

Created wheel for rna-voila: filename=rna_voila-2.4.dev3+g85d07819-py3-none-any.whl size=2451745 sha256=2c250dfd227bd46e92ecdba8e1696b5566ca90e89327f332455ef49aabd03406

Stored in directory: /private/var/folders/qk/m6v59dts2qg8tvndw4w26p3w0000gn/T/pip-ephem-wheel-cache-klwhm1n1/wheels/fb/06/3f/4e452cf6bc16652a686d958cfdf7ea0e1cbc1f10d1a418445c

Successfully built rna-majiq rna-voila

Installing collected packages: rna-voila, rna-majiq

Attempting uninstall: rna-voila

Found existing installation: rna-voila 2.4.dev3+g85d07819

Uninstalling rna-voila-2.4.dev3+g85d07819:

Successfully uninstalled rna-voila-2.4.dev3+g85d07819

Attempting uninstall: rna-majiq

Found existing installation: rna-majiq 2.4.dev3+g85d07819

Uninstalling rna-majiq-2.4.dev3+g85d07819:

Successfully uninstalled rna-majiq-2.4.dev3+g85d07819

Successfully installed rna-majiq-2.4.dev3+g85d07819 rna-voila-2.4.dev3+g85d07819

--

Any suggestions? Hope someone can help me out. Thanks in advance!

Yini

Paul Jewell

unread,

Mar 17, 2022, 2:45:57 PM3/17/22

to majiq_voila

Hello Yini,

Have you created a virtualenv or conda env before installation?

Can you brew install gcc-8 and check if you have any difference using this gcc/g++ version in your exports?

Xiao Lei

unread,

Jun 30, 2024, 6:11:38 PMJun 30

to Biociphers

I have the same problem. Installation seems successful but majiq build failed (error attached). I installed Majiq with instructions on the website: 1) python3 -m venv env; 2) source env/bin/activate; and 3) pip install git+https://bitbucket.org/biociphers/majiq_academic.git. I also did brew install gcc-8 in the same virtual env after installation. I use a Macstudio with M1 Chip. I appreciate any inputs to fix the problem.

Error:

majiq build /Users/bieniaszlab/Documents/Xiao/CLIP/index/hg38/gencode.v44.annotation.gff3 -o /Users/bieniaszlab/Documents/Xiao/CLIP/CLIP58/nxsq/CLIP58_keepuntrimmed/PARalyzer_CLIP58_keepuntrimmed/env/output/test/build -c /Users/bieniaszlab/Documents/Xiao/CLIP/CLIP58/nxsq/CLIP58_keepuntrimmed/PARalyzer_CLIP58_keepuntrimmed/env/

Traceback (most recent call last):

File "/Users/bieniaszlab/Documents/Xiao/CLIP/CLIP58/nxsq/CLIP58_keepuntrimmed/PARalyzer_CLIP58_keepuntrimmed/env/bin/majiq", line 5, in <module>
from rna_majiq.run_majiq import main
File "/Users/bieniaszlab/Documents/Xiao/CLIP/CLIP58/nxsq/CLIP58_keepuntrimmed/PARalyzer_CLIP58_keepuntrimmed/env/lib/python3.9/site-packages/rna_majiq/run_majiq.py", line 12, in <module>
from rna_majiq.src.build import build
ImportError: dlopen(/Users/bieniaszlab/Documents/Xiao/CLIP/CLIP58/nxsq/CLIP58_keepuntrimmed/PARalyzer_CLIP58_keepuntrimmed/env/lib/python3.9/site-packages/rna_majiq/src/build.cpython-39-darwin.so, 0x0002): symbol not found in flat namespace (___kmpc_barrier)