installation issue

[Rhonnesss]

I got the error when i'm trying to install Fred2 so i'm novice. Thanks in advance for the help sapo@jgm-Ubuntu:~$ sudo pip3 install git+https://github.com/FRED-2/Fred2 The directory '/home/sapo/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag. The directory '/home/sapo/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag. Collecting git+https://github.com/FRED-2/Fred2 Cloning https://github.com/FRED-2/Fred2 to /tmp/pip-1qlp5lwg-build Collecting PyMySQL (from Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/ed/39/15045ae46f2a123019aa968dfcba0396c161c20f855f11dea6796bcaae95/PyMySQL-0.9.3-py2.py3-none-any.whl (47kB) 100% |████████████████████████████████| 51kB 1.1MB/s Collecting biopython (from Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/83/3d/e0c8a993dbea1136be90c31345aefc5babdd5046cd52f81c18fc3fdad865/biopython-1.76-cp36-cp36m-manylinux1_x86_64.whl (2.3MB) 100% |████████████████████████████████| 2.3MB 400kB/s Collecting mhcflurry (from Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/ef/95/cc8cc7324f4fdf7f32d8882fc4d25ae208038561e46cf0e7061f9dd88594/mhcflurry-1.6.0-py3-none-any.whl (133kB) 100% |████████████████████████████████| 143kB 1.0MB/s Collecting mhcnuggets (from Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/21/ca/f2bd3c9e3bdbbe8230a6975383d0712d924becddd90cfb8e9b256959726c/mhcnuggets-2.3.2.tar.gz (33.1MB) 100% |████████████████████████████████| 33.1MB 33kB/s Collecting pandas (from Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/bb/71/8f53bdbcbc67c912b888b40def255767e475402e9df64050019149b1a943/pandas-1.0.3-cp36-cp36m-manylinux1_x86_64.whl (10.0MB) 100% |████████████████████████████████| 10.0MB 106kB/s Collecting pyVCF (from Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/20/b6/36bfb1760f6983788d916096193fc14c83cce512c7787c93380e09458c09/PyVCF-0.6.8.tar.gz Collecting pyomo>=4.0 (from Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/17/12/a6270a9153d767787ccde6f3166cab01ea99c6c7dd60ee261d8925402f85/Pyomo-5.6.9-py2.py3-none-any.whl (2.5MB) 100% |████████████████████████████████| 2.5MB 372kB/s Requirement already satisfied: setuptools>=18.2 in /usr/lib/python3/dist-packages (from Fred2==2.0.6) Requirement already satisfied: svmlight in /usr/local/lib/python3.6/dist-packages (from Fred2==2.0.6) Collecting numpy (from biopython->Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/07/08/a549ba8b061005bb629b76adc000f3caaaf881028b963c2e18f811c6edc1/numpy-1.18.2-cp36-cp36m-manylinux1_x86_64.whl (20.2MB) 100% |████████████████████████████████| 20.2MB 52kB/s Collecting tqdm (from mhcflurry->Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/4a/1c/6359be64e8301b84160f6f6f7936bbfaaa5e9a4eab6cbc681db07600b949/tqdm-4.45.0-py2.py3-none-any.whl (60kB) 100% |████████████████████████████████| 61kB 2.2MB/s Collecting scikit-learn (from mhcflurry->Fred2==2.0.6) Downloading https://files.pythonhosted.org/packages/5e/d8/312e03adf4c78663e17d802fe2440072376fee46cada1404f1727ed77a32/scikit_learn-0.22.2.post1-cp36-cp36m-manylinux1_x86_64.whl (7.1MB) 100% |████████████████████████████████| 7.1MB 158kB/s Collecting tensorflow<2.0.0,>=1.15.0 (from mhcflurry->Fred2==2.0.6) Could not find a version that satisfies the requirement tensorflow<2.0.0,>=1.15.0 (from mhcflurry->Fred2==2.0.6) (from versions: 0.12.1, 1.0.0, 1.0.1, 1.1.0rc0, 1.1.0rc1, 1.1.0rc2, 1.1.0, 1.2.0rc0, 1.2.0rc1, 1.2.0rc2, 1.2.0, 1.2.1, 1.3.0rc0, 1.3.0rc1, 1.3.0rc2, 1.3.0, 1.4.0rc0, 1.4.0rc1, 1.4.0, 1.4.1, 1.5.0rc0, 1.5.0rc1, 1.5.0, 1.5.1, 1.6.0rc0, 1.6.0rc1, 1.6.0, 1.7.0rc0, 1.7.0rc1, 1.7.0, 1.7.1, 1.8.0rc0, 1.8.0rc1, 1.8.0, 1.9.0rc0, 1.9.0rc1, 1.9.0rc2, 1.9.0, 1.10.0rc0, 1.10.0rc1, 1.10.0, 1.10.1, 1.11.0rc0, 1.11.0rc1, 1.11.0rc2, 1.11.0, 1.12.0rc0, 1.12.0rc1, 1.12.0rc2, 1.12.0, 1.12.2, 1.12.3, 1.13.0rc0, 1.13.0rc1, 1.13.0rc2, 1.13.1, 1.13.2, 1.14.0rc0, 1.14.0rc1, 1.14.0, 2.0.0a0, 2.0.0b0, 2.0.0b1) No matching distribution found for tensorflow<2.0.0,>=1.15.0 (from mhcflurry->Fred2==2.0.6)

[christopher-mohr]

Hi @Rhonnesss, it looks like something has changed in the dependencies of FRED2. So far we could not identify the reason yet but we will keep you posted. Thanks for reporting this.

[Rhonnesss]

Thanks in advance for your feedback.

[christopher-mohr]

Sorry that there hasn't been an update on this for a long time. I think this was related to a new MHCflurry version. Therefore we restricted the version in the setup.py.