Closed serge2016 closed 1 year ago
Hello!
Could you help me, please, to fix this with new versions of Ubuntu 22.04?
R -e "library(basilisk); source('R/basilisk.R'); basiliskStart(env_azimuth)" #44 0.450 R version 4.3.1 (2023-06-16) -- "Beagle Scouts" #44 0.450 Copyright (C) 2023 The R Foundation for Statistical Computing #44 0.450 Platform: x86_64-pc-linux-gnu (64-bit) ... #44 0.537 > library(basilisk); source('R/basilisk.R'); basiliskStart(env_azimuth) #44 1.652 trying URL 'https://repo.anaconda.com/miniconda/Miniconda3-py310_23.5.0-3-Linux-x86_64.sh' #44 2.086 Content type 'application/x-sh' length 95815836 bytes (91.4 MB) #44 2.189 ================================================== #44 6.373 downloaded 91.4 MB #44 6.373 #44 6.387 PREFIX=/home/rstudio/.cache/R/basilisk/1.13.3/0 #44 6.627 Unpacking payload ... ... #44 178.5 added / updated specs: #44 178.5 - python=2.7 #44 178.5 #44 178.5 #44 178.5 The following packages will be downloaded: #44 178.5 #44 178.5 package | build #44 178.5 ---------------------------|----------------- #44 178.5 _libgcc_mutex-0.1 | conda_forge 3 KB conda-forge #44 178.5 _openmp_mutex-4.5 | 2_gnu 23 KB conda-forge #44 178.5 ca-certificates-2023.7.22 | hbcca054_0 146 KB conda-forge #44 178.5 certifi-2019.11.28 | py27h8c360ce_1 149 KB conda-forge #44 178.5 ld_impl_linux-64-2.40 | h41732ed_0 688 KB conda-forge #44 178.5 libffi-3.2.1 | he1b5a44_1007 47 KB conda-forge #44 178.5 libgcc-ng-13.1.0 | he5830b7_0 758 KB conda-forge #44 178.5 libgomp-13.1.0 | he5830b7_0 409 KB conda-forge #44 178.5 libsqlite-3.42.0 | h2797004_0 809 KB conda-forge #44 178.5 libstdcxx-ng-13.1.0 | hfd8a6a1_0 3.7 MB conda-forge #44 178.5 libzlib-1.2.13 | hd590300_5 60 KB conda-forge #44 178.5 ncurses-6.4 | hcb278e6_0 860 KB conda-forge #44 178.5 openssl-1.1.1v | hd590300_0 1.9 MB conda-forge #44 178.5 pip-20.1.1 | pyh9f0ad1d_0 1.1 MB conda-forge #44 178.5 python-2.7.15 |h5a48372_1011_cpython 12.2 MB conda-forge #44 178.5 python_abi-2.7 | 1_cp27mu 4 KB conda-forge #44 178.5 readline-8.2 | h8228510_1 275 KB conda-forge #44 178.5 setuptools-44.0.0 | py27_0 663 KB conda-forge #44 178.5 sqlite-3.42.0 | h2c6b66d_0 799 KB conda-forge #44 178.5 tk-8.6.12 | h27826a3_0 3.3 MB conda-forge #44 178.5 wheel-0.37.1 | pyhd8ed1ab_0 31 KB conda-forge #44 178.5 zlib-1.2.13 | hd590300_5 91 KB conda-forge #44 178.5 ------------------------------------------------------------ #44 178.5 Total: 27.8 MB #44 178.5 #44 178.5 The following NEW packages will be INSTALLED: #44 178.5 #44 178.5 _libgcc_mutex conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge #44 178.5 _openmp_mutex conda-forge/linux-64::_openmp_mutex-4.5-2_gnu #44 178.5 ca-certificates conda-forge/linux-64::ca-certificates-2023.7.22-hbcca054_0 #44 178.5 certifi conda-forge/linux-64::certifi-2019.11.28-py27h8c360ce_1 #44 178.5 ld_impl_linux-64 conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0 #44 178.5 libffi conda-forge/linux-64::libffi-3.2.1-he1b5a44_1007 #44 178.5 libgcc-ng conda-forge/linux-64::libgcc-ng-13.1.0-he5830b7_0 #44 178.5 libgomp conda-forge/linux-64::libgomp-13.1.0-he5830b7_0 #44 178.5 libsqlite conda-forge/linux-64::libsqlite-3.42.0-h2797004_0 #44 178.5 libstdcxx-ng conda-forge/linux-64::libstdcxx-ng-13.1.0-hfd8a6a1_0 #44 178.5 libzlib conda-forge/linux-64::libzlib-1.2.13-hd590300_5 #44 178.5 ncurses conda-forge/linux-64::ncurses-6.4-hcb278e6_0 #44 178.5 openssl conda-forge/linux-64::openssl-1.1.1v-hd590300_0 #44 178.5 pip conda-forge/noarch::pip-20.1.1-pyh9f0ad1d_0 #44 178.5 python conda-forge/linux-64::python-2.7.15-h5a48372_1011_cpython #44 178.5 python_abi conda-forge/linux-64::python_abi-2.7-1_cp27mu #44 178.5 readline conda-forge/linux-64::readline-8.2-h8228510_1 #44 178.5 setuptools conda-forge/linux-64::setuptools-44.0.0-py27_0 #44 178.5 sqlite conda-forge/linux-64::sqlite-3.42.0-h2c6b66d_0 #44 178.5 tk conda-forge/linux-64::tk-8.6.12-h27826a3_0 #44 178.5 wheel conda-forge/noarch::wheel-0.37.1-pyhd8ed1ab_0 #44 178.5 zlib conda-forge/linux-64::zlib-1.2.13-hd590300_5 ... #44 787.8 Processing /home/rstudio/R/library/crisprScore/python/azimuth #44 787.9 Requirement already satisfied: scipy<=1.2.1 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.2.1) #44 787.9 Requirement already satisfied: numpy<=1.14 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.11.3) #44 787.9 Requirement already satisfied: matplotlib in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (2.2.3) #44 788.0 Requirement already satisfied: nose in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.3.7) #44 788.0 Requirement already satisfied: scikit-learn<0.18,>=0.17.1 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (0.17.1) #44 788.0 Requirement already satisfied: pandas in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (0.23.4) #44 788.0 Requirement already satisfied: biopython<=1.76 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from Azimuth==2.0) (1.74) #44 788.0 Requirement already satisfied: cycler>=0.10 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (0.10.0) #44 788.0 Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2.4.7) #44 788.0 Requirement already satisfied: python-dateutil>=2.1 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2.8.1) #44 788.0 Requirement already satisfied: pytz in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (2020.1) #44 788.0 Requirement already satisfied: six>=1.10 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.15.0) #44 788.0 Requirement already satisfied: kiwisolver>=1.0.1 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.1.0) #44 788.0 Requirement already satisfied: backports.functools_lru_cache in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (1.6.1) #44 788.0 Requirement already satisfied: subprocess32 in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from matplotlib->Azimuth==2.0) (3.5.4) #44 788.0 Requirement already satisfied: setuptools in /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib->Azimuth==2.0) (44.0.0.post20200102) #44 788.0 Building wheels for collected packages: Azimuth #44 788.0 Building wheel for Azimuth (setup.py): started #44 788.2 Building wheel for Azimuth (setup.py): finished with status 'done' #44 788.2 Created wheel for Azimuth: filename=Azimuth-2.0-py2-none-any.whl size=163884 sha256=cb56e2d7a8bad3018036c51eaa65e25109f5668f4c195acd3477d5618d491688 #44 788.2 Stored in directory: /tmp/pip-ephem-wheel-cache-KOxihB/wheels/56/4b/66/e075652909d01dd3d766e57ba0d9a334f4ddbcce926d80fe70 #44 788.2 Successfully built Azimuth #44 788.2 Installing collected packages: Azimuth #44 788.3 Successfully installed Azimuth-2.0 #44 789.3 Error: PyType_GetFlags - /home/rstudio/.cache/R/basilisk/1.13.3/crisprScore/1.3.4/azimuth_basilisk/lib/libpython2.7.so: undefined symbol: PyType_GetFlags #44 789.3 In addition: Warning message: #44 789.3 In py_initialize(config$python, config$libpython, config$pythonhome, : #44 789.3 Python 2 reached EOL on January 1, 2020. Python 2 compatability will be removed in an upcoming reticulate release. #44 789.3 Execution halted #44 ERROR: process "/bin/sh -c cd \"$SOFT/crisprScore\" && R -e \"library(basilisk); source('R/basilisk.R'); basiliskStart(env_azimuth)\"" did not complete successfully: exit code: 1
Maybe this is a reason: https://foss.heptapod.net/pypy/pypy/-/issues/3173#note_160826 ?
I suppose, that some versions should be updated maybe here: https://github.com/crisprVerse/crisprScore/blob/master/R/basilisk.R#L1
P.S.: First I asked here: https://github.com/crisprVerse/crisprScore/issues/8
Please don't cross-post issues, you'll just end up with semi-duplicate answers.
I'm going to close this, continue discussion at https://github.com/crisprVerse/crisprScore/issues/8.
Hello!
Could you help me, please, to fix this with new versions of Ubuntu 22.04?
Maybe this is a reason: https://foss.heptapod.net/pypy/pypy/-/issues/3173#note_160826 ?
I suppose, that some versions should be updated maybe here: https://github.com/crisprVerse/crisprScore/blob/master/R/basilisk.R#L1
P.S.: First I asked here: https://github.com/crisprVerse/crisprScore/issues/8