Comments (4)
Adding ncurses to environment.yml did not help and resulted in a bunch of inconsistencies:
The following packages are causing the inconsistency:
- defaults/osx-64::jupyter_console==6.0.0=py36_0
- defaults/osx-64::jupyterlab_server==0.2.0=py36_0
- defaults/osx-64::widgetsnbextension==3.4.2=py36_0
- pyviz/label/dev/noarch::holoviews==1.10.9=py_0
- defaults/osx-64::nb_conda_kernels==2.2.0=py36_1
- conda-forge/osx-64::bqplot==0.11.2=py36_1000
- defaults/osx-64::ipython==7.2.0=py36h39e3cac_0
- defaults/osx-64::jupyterlab==0.35.4=py36hf63ae98_0
- defaults/osx-64::jupyter==1.0.0=py36_7
- defaults/osx-64::ipywidgets==7.4.2=py36_0
- defaults/osx-64::jupyterlab_launcher==0.13.1=py36_0
- defaults/osx-64::qtconsole==4.4.3=py36_0
- defaults/noarch::intake==0.4.4=py_0
- defaults/osx-64::notebook==5.7.4=py36_0
- defaults/osx-64::ipykernel==5.1.0=py36h39e3cac_0
- intake/noarch::intake-xarray==0.2.4=py_0
failed
UPD: inconsistencies existed in the env prior to addition of ncurses
from binder.
Similar problem arose in the independent conda environment from EAGER which also includes samtools 1.9. This was installed on Sanger farm3. Error message:
samtools: error while loading shared libraries: libtinfow.so.5: cannot open shared object file: No such file or directory
Googling also indicates the role of ncurses.
from binder.
Working MacOS test example:
Env:
name: samtoolstest
channels:
- defaults
- pyviz/label/dev
- bokeh/label/dev
- intake
- bioconda
- conda-forge
dependencies:
- samtools=1.9
- conda-forge::ncurses
Installed packages
# packages in environment at /Users/am60/malaria/malariagen/binder/conda/envs/samtoolstest:
#
# Name Version Build Channel
bzip2 1.0.6 h1de35cc_5
ca-certificates 2019.5.15 0
curl 7.64.1 ha441bb4_0
krb5 1.16.1 hddcf347_7
libcurl 7.64.1 h051b688_0
libcxx 4.0.1 hcfea43d_1
libcxxabi 4.0.1 hcfea43d_1
libdeflate 1.0 h1de35cc_1 bioconda
libedit 3.1.20181209 hb402a30_0
libssh2 1.8.2 ha12b0ac_0
ncurses 6.1 h0a44026_1002 conda-forge
openssl 1.1.1c h1de35cc_1
samtools 1.9 h7c4ea83_11 bioconda
tk 8.6.8 ha441bb4_0
xz 5.2.4 h1de35cc_4
zlib 1.2.11 h1de35cc_3
Adding - conda-forge::ncurses
to binder environment also worked, so this should be a reasonable way to go forward (probably we need to fix the version, though). Previously I had some temporary issue during resolving dependencies.
from binder.
Happy to see a PR adding conda-forge::ncurses to requirements-conda.txt if that still works and would be useful.
from binder.
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