itsmeludo
commented
4 years ago Hi,
sorry to hear about that.
there seems to be a problem with the recent versions of scikit.
you may have to downgrade the version oh joblib in your conda env.
Closed sadikmu closed 3 years ago
itsmeludo
commented
4 years ago Hi,
sorry to hear about that.
there seems to be a problem with the recent versions of scikit.
you may have to downgrade the version oh joblib in your conda env.
sadikmu
commented
4 years ago hi @itsmeludo
Thanks for the suggestion. I did try with all python 3 supporting joblib installations sadly it do not seem to help.
itsmeludo
commented
4 years ago Hi!
Here is a list of all the versionning of my conda env that is known to run. Please adjust the version of your environment to these versions, it will ensure that the program works.
you should al least try in the conda env to launch :
conda create -n phyloligo
conda activate phyloligo
conda install scikit-learn=0.19.1=py37hedc7406_0
conda instsall -c itsmeludo phyloligo
# packages in environment at /global/conda/envs/phyloligo:
#
# Name Version Build Channel
_r-mutex 1.0.0 anacondar_1
atk 2.25.90 hf2eb9ee_1001 conda-forge
binutils_impl_linux-64 2.28.1 had2808c_3
binutils_linux-64 7.2.0 had2808c_27
biopython 1.73 py37h14c3975_0 conda-forge
blas 1.0 mkl
bwidget 1.9.11 1
bzip2 1.0.6 h14c3975_1002 conda-forge
ca-certificates 2018.11.29 ha4d7672_0 conda-forge
cairo 1.14.12 h80bd089_1005 conda-forge
certifi 2018.11.29 py37_1000 conda-forge
curl 7.62.0 hbc83047_0
cycler 0.10.0 py_1 conda-forge
cython 0.29.5 py37hf484d3e_0 conda-forge
dbus 1.13.2 h714fa37_1
emboss 6.6.0 h6debe1e_0 bioconda
expat 2.2.5 hf484d3e_1002 conda-forge
fontconfig 2.13.1 h2176d3f_1000 conda-forge
freetype 2.9.1 h94bbf69_1005 conda-forge
gcc_impl_linux-64 7.2.0 habb00fd_3
gcc_linux-64 7.2.0 h550dcbe_27
gdk-pixbuf 2.36.12 h4f1c04b_1001 conda-forge
gettext 0.19.8.1 h9745a5d_1001 conda-forge
gfortran_impl_linux-64 7.2.0 hdf63c60_3
gfortran_linux-64 7.2.0 h550dcbe_27
giflib 5.1.4 h14c3975_1001 conda-forge
glib 2.56.2 had28632_1001 conda-forge
gmp 6.1.2 hf484d3e_1000 conda-forge
gobject-introspection 1.56.1 py37h9e29830_1001 conda-forge
graphite2 1.3.13 hf484d3e_1000 conda-forge
greenlet 0.4.15 py37h7b6447c_0
gst-plugins-base 1.14.0 hbbd80ab_1
gstreamer 1.14.0 hb453b48_1
gtk2 2.24.31 h5baeb44_1000 conda-forge
gxx_impl_linux-64 7.2.0 hdf63c60_3
gxx_linux-64 7.2.0 h550dcbe_27
h5py 2.9.0 nompi_py37hf008753_1102 conda-forge
harfbuzz 1.9.0 he243708_1001 conda-forge
hdbscan 0.8.19 py37h3010b51_0 conda-forge
hdf5 1.10.4 nompi_h11e915b_1105 conda-forge
icu 58.2 hf484d3e_1000 conda-forge
igraph 0.7.1 h2166141_1005 conda-forge
intel-openmp 2019.1 144
jpeg 9c h14c3975_1001 conda-forge
kiwisolver 1.0.1 py37h6bb024c_1002 conda-forge
krb5 1.16.3 h05b26f9_1001 conda-forge
libcurl 7.62.0 h20c2e04_0
libdeflate 1.0 h14c3975_1 bioconda
libedit 3.1.20170329 hf8c457e_1001 conda-forge
libffi 3.2.1 hf484d3e_1005 conda-forge
libgcc-ng 7.3.0 hdf63c60_0 conda-forge
libgd 2.2.5 h0d07dcb_1005 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3 conda-forge
libiconv 1.15 h14c3975_1004 conda-forge
libpng 1.6.36 h84994c4_1000 conda-forge
libsodium 1.0.16 h14c3975_1001 conda-forge
libssh2 1.8.0 1 conda-forge
libstdcxx-ng 7.3.0 hdf63c60_0 conda-forge
libtiff 4.0.10 h648cc4a_1001 conda-forge
libuuid 2.32.1 h14c3975_1000 conda-forge
libwebp 1.0.2 h576950b_1 conda-forge
libxcb 1.13 h14c3975_1002 conda-forge
libxml2 2.9.8 h143f9aa_1005 conda-forge
make 4.2.1 h14c3975_2004 conda-forge
matplotlib 3.0.2 py37_1002 conda-forge
matplotlib-base 3.0.2 py37h167e16e_1002 conda-forge
mkl 2018.0.3 1
ncurses 6.1 hf484d3e_1002 conda-forge
numpy 1.11.3 py37h1d66e8a_10
numpy-base 1.11.3 py37h81de0dd_10
openssl 1.1.1b h14c3975_0 conda-forge
pandas 0.23.4 py37h637b7d7_1000 conda-forge
pango 1.40.14 hf0c64fd_1003 conda-forge
patsy 0.5.1 py_0 conda-forge
pcre 8.42 h439df22_0
phyloligo v1.0 1c27c7c itsmeludo
pip 19.0.2 py37_0 conda-forge
pixman 0.34.0 h14c3975_1003 conda-forge
pthread-stubs 0.4 h14c3975_1001 conda-forge
pyparsing 2.3.1 py_0 conda-forge
pyqt 5.6.0 py37h13b7fb3_1008 conda-forge
python 3.7.2 h0371630_0
python-dateutil 2.8.0 py_0 conda-forge
pytz 2018.9 py_0 conda-forge
pyzmq 17.1.2 py37h6afc9c9_1001 conda-forge
qt 5.6.3 h8bf5577_3
r-ape 5.2 r351h29659fb_0 conda-forge
r-base 3.5.1 he45234b_1005 conda-forge
r-bitops 1.0_6 r351h96ca727_1002 conda-forge
r-catools 1.17.1.1 r351h29659fb_1002 conda-forge
r-gdata 2.18.0 r351h6115d3f_1001 conda-forge
r-getopt 1.20.2 r351_2001 conda-forge
r-gplots 3.0.1.1 r351h6115d3f_0 conda-forge
r-gtools 3.8.1 r351h96ca727_1002 conda-forge
r-igraph 1.2.4 r351h80f5a37_0 conda-forge
r-kernsmooth 2.23_15 r351ha65eedd_1002 conda-forge
r-lattice 0.20_38 r351h96ca727_1000 conda-forge
r-magrittr 1.5 r351h6115d3f_1001 conda-forge
r-matrix 1.2_15 r351h96ca727_1000 conda-forge
r-nlme 3.1_137 r351ha65eedd_1000 conda-forge
r-pkgconfig 2.0.2 r351h6115d3f_1001 conda-forge
r-rcpp 1.0.0 r351h29659fb_1000 conda-forge
readline 7.0 hf8c457e_1001 conda-forge
samtools 1.9 h91753b0_5 bioconda
scikit-learn 0.19.1 py37hedc7406_0
scipy 1.1.0 py37hc49cb51_0
scoop 0.7.1.1 pyh2d50403_2 bioconda
seaborn 0.9.0 py_0 conda-forge
setuptools 40.8.0 py37_0 conda-forge
sip 4.18.1 py37hf484d3e_1000 conda-forge
six 1.12.0 py37_1000 conda-forge
sqlite 3.26.0 h67949de_1000 conda-forge
statsmodels 0.9.0 py37h3010b51_1000 conda-forge
tk 8.6.9 h84994c4_1000 conda-forge
tktable 2.10 h14c3975_0
tornado 5.1.1 py37h14c3975_1000 conda-forge
wheel 0.33.0 py37_0 conda-forge
xorg-kbproto 1.0.7 h14c3975_1002 conda-forge
xorg-libice 1.0.9 h14c3975_1004 conda-forge
xorg-libsm 1.2.3 h4937e3b_1000 conda-forge
xorg-libx11 1.6.7 h14c3975_1000 conda-forge
xorg-libxau 1.0.9 h14c3975_0 conda-forge
xorg-libxdmcp 1.1.2 h14c3975_1007 conda-forge
xorg-libxext 1.3.3 h14c3975_1004 conda-forge
xorg-libxrender 0.9.10 h14c3975_1002 conda-forge
xorg-libxt 1.1.5 h14c3975_1002 conda-forge
xorg-renderproto 0.11.1 h14c3975_1002 conda-forge
xorg-xextproto 7.3.0 h14c3975_1002 conda-forge
xorg-xproto 7.0.31 h14c3975_1007 conda-forge
xz 5.2.4 h14c3975_1001 conda-forge
zeromq 4.2.5 hf484d3e_1006 conda-forge
zlib 1.2.11 h14c3975_1004 conda-forge
Hi I got the following issue. any fix please. phyloligo.py -h