I have Miniconda installed with 2 environments: base and gis. Packages in gis were installed from coda-forge. I have 2 questions:
Q1) want to update all packages in gis environment only from conda-forge. Am I using correct command ?
Q2) Why it is downgrading numpy-base ? It is updating other packages and when conda-forge still has several newer versions of 1.15.3 of numpy-base, why it is being downgraded ?
(gis) [arnuld@arch64 ~]$ conda update --all -c conda-forge
Solving environment: donePackage Plan
environment location: /home/arnuld/.local/miniconda/envs/gis
The following packages will be downloaded:
package | build ---------------------------|----------------- matplotlib-3.0.1 | h8a2030e_1 6 KB conda-forge openblas-0.3.3 | ha44fe06_1 13.7 MB conda-forge libopenblas-0.2.20 | h9ac9557_7 8.8 MB numpy-base-1.14.3 | py36h0ea5e3f_1 4.1 MB blas-1.1 | openblas 1 KB conda-forge krb5-1.16.2 | hbb41f41_0 1.4 MB conda-forge scipy-1.1.0 |py36_blas_openblashb06ca3d_202 39.8 MB conda-forge mkl_random-1.0.2 | py36_0 1.3 MB conda-forge numpy-1.15.3 |py36_blas_openblashb06ca3d_0 9.4 MB conda-forge matplotlib-base-3.0.1 | py36hc039c98_1 9.2 MB conda-forge ------------------------------------------------------------ Total: 87.6 MBThe following NEW packages will be INSTALLED:
libopenblas: 0.2.20-h9ac9557_7 matplotlib-base: 3.0.1-py36hc039c98_1 conda-forge openblas: 0.3.3-ha44fe06_1 conda-forgeThe following packages will be UPDATED:
blas: 1.0-mkl --> 1.1-openblas conda-forge krb5: 1.16.1-hbb41f41_0 conda-forge --> 1.16.2-hbb41f41_0 conda-forge matplotlib: 2.2.3-py36h8e2386c_0 conda-forge --> 3.0.1-h8a2030e_1 conda-forge mkl_random: 1.0.1-py36_0 conda-forge --> 1.0.2-py36_0 conda-forge numpy: 1.15.0-py36h1b885b7_0 --> 1.15.3-py36_blas_openblashb06ca3d_0 conda-forge [blas_openblas] scipy: 1.1.0-py36hc49cb51_0 --> 1.1.0-py36_blas_openblashb06ca3d_202 conda-forge [blas_openblas]The following packages will be DOWNGRADED:
numpy-base: 1.15.0-py36h3dfced4_0 --> 1.14.3-py36h0ea5e3f_1Proceed ([y]/n)? n
[arnuld@arch64 ~]$ conda list -n gis
# packages in environment at /home/arnuld/.local/miniconda/envs/gis:
#
# Name Version Build Channel
attrs 18.2.0 py_0 conda-forge
backcall 0.1.0 py_0 conda-forge
blas 1.0 mkl
bleach 3.0.2 py_0 conda-forge
boost-cpp 1.67.0 h3a22d5f_0 conda-forge
bzip2 1.0.6 h470a237_2 conda-forge
ca-certificates 2018.10.15 ha4d7672_0 conda-forge
cairo 1.14.12 he6fea26_5 conda-forge
certifi 2018.10.15 py36_1000 conda-forge
click 7.0 py_0 conda-forge
click-plugins 1.0.4 py_0 conda-forge
cligj 0.5.0 py_0 conda-forge
curl 7.62.0 h74213dd_0 conda-forge
cycler 0.10.0 py_1 conda-forge
dbus 1.13.0 h3a4f0e9_0 conda-forge
decorator 4.3.0 py_0 conda-forge
descartes 1.1.0 py_2 conda-forge
entrypoints 0.2.3 py36_1002 conda-forge
expat 2.2.5 hfc679d8_2 conda-forge
fiona 1.8.0 py36hfc77a4a_0 conda-forge
fontconfig 2.13.1 h65d0f4c_0 conda-forge
freetype 2.9.1 h6debe1e_4 conda-forge
freexl 1.0.5 h470a237_2 conda-forge
gdal 2.3.2 py36hb00a9d7_0 conda-forge
geopandas 0.4.0 py_1 conda-forge
geos 3.6.2 hfc679d8_3 conda-forge
geotiff 1.4.2 h700e5ad_5 conda-forge
gettext 0.19.8.1 h5e8e0c9_1 conda-forge
giflib 5.1.4 h470a237_1 conda-forge
glib 2.55.0 h464dc38_2 conda-forge
gmp 6.1.2 hfc679d8_0 conda-forge
gst-plugins-base 1.12.5 hde13a9d_0 conda-forge
gstreamer 1.12.5 h61a6719_0 conda-forge
hdf4 4.2.13 h951d187_2 conda-forge
hdf5 1.10.3 hc401514_2 conda-forge
icu 58.2 hfc679d8_0 conda-forge
intel-openmp 2019.0 118
ipykernel 5.1.0 pyh24bf2e0_0 conda-forge
ipython 7.1.1 py36h24bf2e0_1000 conda-forge
ipython_genutils 0.2.0 py_1 conda-forge
jedi 0.13.1 py36_1000 conda-forge
jinja2 2.10 py_1 conda-forge
jpeg 9c h470a237_1 conda-forge
json-c 0.12.1 h470a237_1 conda-forge
jsonschema 3.0.0a3 py36_1000 conda-forge
jupyter_client 5.2.3 py_1 conda-forge
jupyter_core 4.4.0 py_0 conda-forge
kealib 1.4.10 hb88cf67_0 conda-forge
kiwisolver 1.0.1 py36h2d50403_2 conda-forge
krb5 1.16.1 hbb41f41_0 conda-forge
libcurl 7.62.0 hbdb9355_0 conda-forge
libdap4 3.19.1 h8fe5423_1 conda-forge
libedit 3.1.20170329 haf1bffa_1 conda-forge
libffi 3.2.1 hfc679d8_5 conda-forge
libgcc-ng 7.2.0 hdf63c60_3 conda-forge
libgdal 2.3.2 hc73897a_0 conda-forge
libgfortran 3.0.0 1 conda-forge
libgfortran-ng 7.2.0 hdf63c60_3 conda-forge
libiconv 1.15 h470a237_3 conda-forge
libkml 1.3.0 hccc92b1_8 conda-forge
libnetcdf 4.6.1 h9cd6fdc_11 conda-forge
libpng 1.6.35 ha92aebf_2 conda-forge
libpq 10.5 he29860b_0 conda-forge
libsodium 1.0.16 h470a237_1 conda-forge
libspatialindex 1.8.5 hfc679d8_3 conda-forge
libspatialite 4.3.0a hdfcc80b_23 conda-forge
libssh2 1.8.0 h5b517e9_2 conda-forge
libstdcxx-ng 7.2.0 hdf63c60_3 conda-forge
libtiff 4.0.9 he6b73bb_2 conda-forge
libuuid 2.32.1 h470a237_2 conda-forge
libxcb 1.13 h470a237_2 conda-forge
libxml2 2.9.8 h422b904_5 conda-forge
markupsafe 1.0 py36h470a237_1 conda-forge
matplotlib 2.2.3 py36h8e2386c_0 conda-forge
mistune 0.8.4 py36h470a237_0 conda-forge
mkl 2019.0 118
mkl_fft 1.0.6 py36_0 conda-forge
mkl_random 1.0.1 py36_0 conda-forge
munch 2.3.2 py_0 conda-forge
nbconvert 5.3.1 py_1 conda-forge
nbformat 4.4.0 py_1 conda-forge
ncurses 6.1 hfc679d8_1 conda-forge
notebook 5.7.0 py36_1000 conda-forge
numpy 1.15.0 py36h1b885b7_0
numpy-base 1.15.0 py36h3dfced4_0
openjpeg 2.3.0 h0e734dc_3 conda-forge
openssl 1.0.2p h470a237_1 conda-forge
pandas 0.23.4 py36hf8a1672_0 conda-forge
pandoc 2.3.1 0 conda-forge
pandocfilters 1.4.2 py_1 conda-forge
parso 0.3.1 py_0 conda-forge
pcre 8.41 hfc679d8_3 conda-forge
pexpect 4.6.0 py36_1000 conda-forge
pickleshare 0.7.5 py36_1000 conda-forge
pip 18.1 py36_1000 conda-forge
pixman 0.34.0 h470a237_3 conda-forge
poppler 0.67.0 h4d7e492_3 conda-forge
poppler-data 0.4.9 0 conda-forge
postgresql 10.5 h66035e0_0 conda-forge
proj4 4.9.3 h470a237_8 conda-forge
prometheus_client 0.4.2 py_0 conda-forge
prompt_toolkit 2.0.7 py_0 conda-forge
psycopg2 2.7.5 py36hdffb7b8_2 conda-forge
pthread-stubs 0.4 h470a237_1 conda-forge
ptyprocess 0.6.0 py36_1000 conda-forge
pygments 2.2.0 py_1 conda-forge
pyparsing 2.3.0 py_0 conda-forge
pyproj 1.9.5.1 py36h508ed2a_6 conda-forge
pyqt 5.6.0 py36h8210e8a_7 conda-forge
pyrsistent 0.14.5 py36h470a237_1 conda-forge
pysal 1.14.4.post2 py36_1001 conda-forge
python 3.6.6 h5001a0f_3 conda-forge
python-dateutil 2.7.5 py_0 conda-forge
pytz 2018.7 py_0 conda-forge
pyzmq 17.1.2 py36hae99301_1 conda-forge
qt 5.6.2 hf70d934_9 conda-forge
readline 7.0 haf1bffa_1 conda-forge
rtree 0.8.3 py36_1000 conda-forge
scipy 1.1.0 py36hc49cb51_0
send2trash 1.5.0 py_0 conda-forge
setuptools 40.5.0 py36_0 conda-forge
shapely 1.6.4 py36h164cb2d_1 conda-forge
sip 4.18.1 py36hfc679d8_0 conda-forge
six 1.11.0 py36_1001 conda-forge
sqlalchemy 1.2.13 py36h470a237_0 conda-forge
sqlite 3.25.2 hb1c47c0_0 conda-forge
terminado 0.8.1 py36_1001 conda-forge
testpath 0.4.2 py36_1000 conda-forge
tk 8.6.8 ha92aebf_0 conda-forge
tornado 5.1.1 py36h470a237_0 conda-forge
traitlets 4.3.2 py36_1000 conda-forge
wcwidth 0.1.7 py_1 conda-forge
webencodings 0.5.1 py_1 conda-forge
wheel 0.32.2 py36_0 conda-forge
xerces-c 3.2.0 h5d6a6da_2 conda-forge
xorg-kbproto 1.0.7 h470a237_2 conda-forge
xorg-libice 1.0.9 h470a237_4 conda-forge
xorg-libsm 1.2.3 h8c8a85c_0 conda-forge
xorg-libx11 1.6.6 h470a237_0 conda-forge
xorg-libxau 1.0.8 h470a237_6 conda-forge
xorg-libxdmcp 1.1.2 h470a237_7 conda-forge
xorg-libxext 1.3.3 h470a237_4 conda-forge
xorg-libxrender 0.9.10 h470a237_2 conda-forge
xorg-renderproto 0.11.1 h470a237_2 conda-forge
xorg-xextproto 7.3.0 h470a237_2 conda-forge
xorg-xproto 7.0.31 h470a237_7 conda-forge
xz 5.2.4 h470a237_1 conda-forge
zeromq 4.2.5 hfc679d8_6 conda-forge
zlib 1.2.11 h470a237_3 conda-forge
[arnuld@arch64 ~]$
Yes, that's the right command. However, some of your packages aren't in conda-forge, e.g., numpy-base:
conda search conda-forge::numpy-base
turns up empty, same for libopenblas. They are falling back to updating from the defaults channel.
Don't know for sure, but it seems your BLAS libraries are involved too. Namely, libopenblas also has 0.3.3 version available in defaults, whereas here it shows installing 0.2.2. This happens to be a dependency of numpy-base, and specifically version 1.15.3 requires libopenblas>=0.3.3.
Could have something to do with the mkl to openblas switch that happens when prioritizing conda-forge. I think we'd need to know the other libraries installed (not being changed during update) to precisely answer this question as posed.
It looks like this script for searching the conda dependency graph could be useful for further inspection if you're really interested in assigning the blame.