Cannot upgrade to newest renku version

Please let me know if you need access to that repo. Or if I should report this differently.

Thank you very much in advance!

As a new user, I can only post two links: here are two more:

Hi Lili, thanks for the question! Can you paste the old image version and the new image version? I don’t have access to your project!

Thanks,
Emma

with new renku version

 > Step 1/3 : FROM renku/renkulab:renku0.10.3-cuda10.0-tf1.14-0.6.2
>     33  ---> a075cbb7ca7b
>     34 Step 2/3 : COPY requirements.txt environment-conda.yml /tmp/
>     35  ---> fdb00595cbe5
>     36 Step 3/3 : RUN conda env update -q -f /tmp/environment-conda.yml &&     conda clean -y --all &&     conda env export -n "root"
>     37  ---> Running in 2ed19d6cb1ba
>     38 Collecting package metadata (repodata.json): ...working... done
>     39 Examining conflict for wheel tornado pandocfilters rdkit pysocks openpyxl nbconvert sqlalchemy prometheus_client mako python_abi blinker notebook jsonschema alembic zipp nbformat async_generator certifi pickleshare numpy mendeleev pycurl python-dateutil pyrsistent pamela tk traitlets backcall webencodings parso attrs json5 pycosat pygments testpath tqdm requests jupyterlab_server ruamel_yaml python-editor pyzmq jupyterlab jupyterhub-base decorator urllib3 umap-learn ptyprocess certipy metric-learn mistune markupsafe jupyter_core pyopenssl jupyterhub wcwidth ruamel.yaml.clib libcurl krb5 defusedxml prompt-toolkit entrypoints importlib-metadata seaborn terminado pexpect oauthlib jupyter_telemetry pip setuptools send2trash xlrd cryptography pandas conda-package-handling python pycparser chardet ipython_genutils pyjwt idna python-json-logger scipy six ipykernel cffi pubchempy jinja2 jedi conda ruamel.yaml bleach ipython matplotlib jupyter_client:   2%|▏         | 2/129 [00:00<01:03,  2.00it/s]
>     40 Found conflicts! Looking for incompatible packages.
>     41 This can take several minutes.  Press CTRL-C to abort.
>     42 failed
>     43                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
>     44 # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
>     45     Traceback (most recent call last):
>     46       File "/opt/conda/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
>     47         return func(*args, **kwargs)
>     48       File "/opt/conda/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
>     49         exit_code = getattr(module, func_name)(args, parser)
>     50       File "/opt/conda/lib/python3.7/site-packages/conda_env/cli/main_update.py", line 124, in execute
>     51         result[installer_type] = installer.install(prefix, specs, args, env)
>     52       File "/opt/conda/lib/python3.7/site-packages/conda_env/installers/conda.py", line 32, in install
>     53         prune=getattr(args, 'prune', False), update_modifier=UpdateModifier.FREEZE_INSTALLED)
>     54       File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
>     55         should_retry_solve)
>     56       File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
>     57         force_remove, should_retry_solve)
>     58       File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 281, in solve_final_state
>     59         ssc = self._run_sat(ssc)
>     60       File "/opt/conda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
>     61         return f(*args, **kwds)
>     62       File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 808, in _run_sat
>     63         should_retry_solve=ssc.should_retry_solve
>     64       File "/opt/conda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
>     65         return f(*args, **kwds)
>     66       File "/opt/conda/lib/python3.7/site-packages/conda/resolve.py", line 1318, in solve
>     67         self.find_conflicts(specs, specs_to_add, history_specs)
>     68       File "/opt/conda/lib/python3.7/site-packages/conda/resolve.py", line 347, in find_conflicts
>     69         bad_deps = self.build_conflict_map(specs, specs_to_add, history_specs)
>     70       File "/opt/conda/lib/python3.7/site-packages/conda/resolve.py", line 507, in build_conflict_map
>     71         root, search_node, dep_graph, num_occurances)
>     72       File "/opt/conda/lib/python3.7/site-packages/conda/resolve.py", line 369, in breadth_first_search_for_dep_graph
>     73         last_spec = MatchSpec.union((path[-1], target_paths[-1][-1]))[0]
>     74       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 481, in union
>     75         return cls.merge(match_specs, union=True)
>     76       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in merge
>     77         reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
>     78       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in <lambda>
>     79         reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
>     80       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 502, in _merge
>     81         final = this_component.union(that_component)
>     82       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 764, in union
>     83         return '|'.join(options)
>     84     TypeError: sequence item 0: expected str instance, Channel found
>     85 `$ /opt/conda/bin/conda-env update -q -f /tmp/environment-conda.yml`
>     86   environment variables:
>     87                  CIO_TEST=<not set>
>     88   CONDA_AUTO_UPDATE_CONDA=false
>     89                 CONDA_DIR=/opt/conda
>     90                CONDA_ROOT=/opt/conda
>     91             CONDA_VERSION=4.8.2
>     92           LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64
>     93              LIBRARY_PATH=/usr/local/cuda/lib64/stubs
>     94                      PATH=/usr/local/nvidia/bin:/usr/local/cuda/bin:/opt/conda/bin:/usr/local/sb
>     95                           in:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
>     96        REQUESTS_CA_BUNDLE=<not set>
>     97             SSL_CERT_FILE=<not set>
>     98      active environment : None
>     99        user config file : /home/jovyan/.condarc
>     100  populated config files : /opt/conda/.condarc
>     101           conda version : 4.8.2
>     102     conda-build version : not installed
>     103          python version : 3.7.6.final.0
>     104        virtual packages : __glibc=2.27
>     105        base environment : /opt/conda  (writable)
>     106            channel URLs : https://conda.anaconda.org/conda-forge/linux-64
>     107                           https://conda.anaconda.org/conda-forge/noarch
>     108                           https://repo.anaconda.com/pkgs/main/linux-64
>     109                           https://repo.anaconda.com/pkgs/main/noarch
>     110                           https://repo.anaconda.com/pkgs/r/linux-64
>     111                           https://repo.anaconda.com/pkgs/r/noarch
>     112           package cache : /opt/conda/pkgs
>     113                           /home/jovyan/.conda/pkgs
>     114        envs directories : /opt/conda/envs
>     115                           /home/jovyan/.conda/envs
>     116                platform : linux-64
>     117              user-agent : conda/4.8.2 requests/2.23.0 CPython/3.7.6 Linux/4.19.0-1.el7.elrepo.x86_64 ubuntu/18.04.4 glibc/2.27
>     118                 UID:GID : 1000:100
>     119              netrc file : None
>     120            offline mode : False
>     121 An unexpected error has occurred. Conda has prepared the above report.
>     122 The command '/bin/sh -c conda env update -q -f /tmp/environment-conda.yml &&     conda clean -y --all &&     conda env export -n "root"' returned a non-zero code: 1
>     126 ERROR: Job failed: exit code 1

trying to update conda

Step 1/5 : FROM renku/renkulab:renku0.10.3-py3.7-0.6.2
47 renku0.10.3-py3.7-0.6.2: Pulling from renku/renkulab
48 Digest: sha256:e04f83b71b9ae02a782745d5ede69a6ed5e7af1c34de13d3d301c346acc0d111
49 Status: Downloaded newer image for renku/renkulab:renku0.10.3-py3.7-0.6.2
50  ---> a3d45bf66436
51 Step 2/5 : COPY environment-conda.yml /tmp/
52  ---> 3686a30e2a93
53 Step 3/5 : ENV PATH /opt/conda/bin:$PATH
54  ---> Running in ab4eb1ee5497
55 Removing intermediate container ab4eb1ee5497
56  ---> f9d21d97ae42
57 Step 4/5 : RUN conda update -n base conda
58  ---> Running in 42ab9131da01
59 Collecting package metadata (current_repodata.json): ...working... done
60 Solving environment: ...working... done
61 ## Package Plan ##
62   environment location: /opt/conda
63   added / updated specs:
64     - conda
65 The following packages will be downloaded:
66     package                    |            build
67     ---------------------------|-----------------
68     alembic-1.4.2              |     pyh9f0ad1d_0         111 KB  conda-forge
69     bleach-3.1.5               |     pyh9f0ad1d_0         112 KB  conda-forge
70     brotlipy-0.7.0             |py37h8f50634_1000         346 KB  conda-forge
71     configurable-http-proxy-4.2.1|node13_he01fd0c_0         884 KB  conda-forge
72     cryptography-2.9.2         |   py37hb09aad4_0         622 KB  conda-forge
73     importlib-metadata-1.6.0   |   py37hc8dfbb8_0          43 KB  conda-forge
74     importlib_metadata-1.6.0   |                0           3 KB  conda-forge
75     ipykernel-5.3.0            |   py37h43977f1_0         164 KB  conda-forge
76     ipython-7.14.0             |   py37hc8dfbb8_0         1.1 MB  conda-forge
77     jedi-0.17.0                |   py37hc8dfbb8_0         807 KB  conda-forge
78     jinja2-2.11.2              |     pyh9f0ad1d_0          93 KB  conda-forge
79     jupyter_client-6.1.3       |             py_0          74 KB  conda-forge
80     jupyterlab_server-1.1.5    |             py_0          25 KB  conda-forge
81     krb5-1.17.1                |       h2fd8d38_0         1.5 MB  conda-forge
82     libcurl-7.69.1             |       hf7181ac_0         573 KB  conda-forge
83     libffi-3.2.1               |    he1b5a44_1007          47 KB  conda-forge
84     libssh2-1.9.0              |       hab1572f_2         298 KB  conda-forge
85     mistune-0.8.4              |py37h8f50634_1001          53 KB  conda-forge
86     nbconvert-5.6.1            |   py37hc8dfbb8_1         487 KB  conda-forge
87     nbformat-5.0.6             |             py_0          99 KB  conda-forge
88     nodejs-13.13.0             |       hf5d1a2b_0        15.8 MB  conda-forge
89     packaging-20.4             |     pyh9f0ad1d_0          32 KB  conda-forge
90     pandoc-2.9.2.1             |                0        18.7 MB  conda-forge
91     parso-0.7.0                |     pyh9f0ad1d_0          67 KB  conda-forge
92     pip-20.1.1                 |             py_1         1.1 MB  conda-forge
93     prometheus_client-0.8.0    |     pyh9f0ad1d_0          44 KB  conda-forge
94     prompt-toolkit-3.0.5       |             py_0         232 KB  conda-forge
95     pyparsing-2.4.7            |     pyh9f0ad1d_0          60 KB  conda-forge
96     pyrsistent-0.16.0          |   py37h8f50634_0          89 KB  conda-forge
97     python-3.7.6               |h8356626_5_cpython        52.9 MB  conda-forge
98     pyzmq-19.0.1               |   py37hac76be4_0         519 KB  conda-forge
99     setuptools-47.1.0          |   py37hc8dfbb8_0         636 KB  conda-forge
100     six-1.15.0                 |     pyh9f0ad1d_0          14 KB  conda-forge
101     sqlalchemy-1.3.17          |   py37h8f50634_0         1.8 MB  conda-forge
102     tqdm-4.46.0                |     pyh9f0ad1d_0          50 KB  conda-forge
103     urllib3-1.25.9             |             py_0          92 KB  conda-forge
104     wcwidth-0.1.9              |     pyh9f0ad1d_0          20 KB  conda-forge
105     xz-5.2.5                   |       h516909a_0         430 KB  conda-forge
106     yaml-0.2.4                 |       h516909a_0          82 KB  conda-forge
107     ------------------------------------------------------------
108                                            Total:        99.8 MB
109 The following NEW packages will be INSTALLED:
110   brotlipy           conda-forge/linux-64::brotlipy-0.7.0-py37h8f50634_1000
111   packaging          conda-forge/noarch::packaging-20.4-pyh9f0ad1d_0
112   pyparsing          conda-forge/noarch::pyparsing-2.4.7-pyh9f0ad1d_0
113 The following packages will be REMOVED:
114   prompt_toolkit-3.0.4-0
115 The following packages will be UPDATED:
116   alembic                                        1.4.1-py_0 --> 1.4.2-pyh9f0ad1d_0
117   bleach                                 3.1.3-pyh8c360ce_0 --> 3.1.5-pyh9f0ad1d_0
118   configurable-http~                4.2.0-node13_he01fd0c_2 --> 4.2.1-node13_he01fd0c_0
119   cryptography                           2.8-py37hb09aad4_2 --> 2.9.2-py37hb09aad4_0
120   importlib-metadata                   1.5.0-py37hc8dfbb8_1 --> 1.6.0-py37hc8dfbb8_0
121   importlib_metadata                                1.5.0-1 --> 1.6.0-0
122   ipykernel                            5.1.4-py37h5ca1d4c_0 --> 5.3.0-py37h43977f1_0
123   ipython                             7.13.0-py37h5ca1d4c_0 --> 7.14.0-py37hc8dfbb8_0
124   jedi                                0.16.0-py37hc8dfbb8_1 --> 0.17.0-py37hc8dfbb8_0
125   jinja2                                        2.11.1-py_0 --> 2.11.2-pyh9f0ad1d_0
126   jupyter_client                                 6.0.0-py_0 --> 6.1.3-py_0
127   jupyterlab_server                              1.0.7-py_0 --> 1.1.5-py_0
128   krb5                                    1.16.4-h2fd8d38_0 --> 1.17.1-h2fd8d38_0
129   libcurl                                 7.68.0-hda55be3_0 --> 7.69.1-hf7181ac_0
130   libffi                                3.2.1-he1b5a44_1006 --> 3.2.1-he1b5a44_1007
131   libssh2                                  1.8.2-h22169c7_2 --> 1.9.0-hab1572f_2
132   mistune                           0.8.4-py37h516909a_1000 --> 0.8.4-py37h8f50634_1001
133   nbconvert                                    5.6.1-py37_0 --> 5.6.1-py37hc8dfbb8_1
134   nbformat                                       5.0.4-py_0 --> 5.0.6-py_0
135   nodejs                                 13.10.1-hf5d1a2b_0 --> 13.13.0-hf5d1a2b_0
136   pandoc                                            2.9.2-0 --> 2.9.2.1-0
137   parso                                          0.6.2-py_0 --> 0.7.0-pyh9f0ad1d_0
138   pip                                           20.0.2-py_2 --> 20.1.1-py_1
139   prometheus_client                              0.7.1-py_0 --> 0.8.0-pyh9f0ad1d_0
140   prompt-toolkit                                 3.0.4-py_0 --> 3.0.5-py_0
141   pyrsistent                          0.15.7-py37h8f50634_1 --> 0.16.0-py37h8f50634_0
142   python                           3.7.6-h357f687_4_cpython --> 3.7.6-h8356626_5_cpython
143   pyzmq                               19.0.0-py37hac76be4_1 --> 19.0.1-py37hac76be4_0
144   setuptools                          46.0.0-py37hc8dfbb8_2 --> 47.1.0-py37hc8dfbb8_0
145   six                                           1.14.0-py_1 --> 1.15.0-pyh9f0ad1d_0
146   sqlalchemy                          1.3.15-py37h8f50634_1 --> 1.3.17-py37h8f50634_0
147   tqdm                                          4.43.0-py_0 --> 4.46.0-pyh9f0ad1d_0
148   urllib3            conda-forge/linux-64::urllib3-1.25.7-~ --> conda-forge/noarch::urllib3-1.25.9-py_0
149   wcwidth                                        0.1.8-py_0 --> 0.1.9-pyh9f0ad1d_0
150   xz                                    5.2.4-h14c3975_1001 --> 5.2.5-h516909a_0
151   yaml                                     0.2.2-h516909a_1 --> 0.2.4-h516909a_0
152 Proceed ([y]/n)? 
153 Downloading and Extracting Packages
154 ipykernel-5.3.0      | 164 KB    | ########## | 100% 
155 nbconvert-5.6.1      | 487 KB    | ########## | 100% 
156 parso-0.7.0          | 67 KB     | ########## | 100% 
157 yaml-0.2.4           | 82 KB     | ########## | 100% 
158 configurable-http-pr | 884 KB    | ########## | 100% 
159 prompt-toolkit-3.0.5 | 232 KB    | ########## | 100% 
160 six-1.15.0           | 14 KB     | ########## | 100% 
161 tqdm-4.46.0          | 50 KB     | ########## | 100% 
162 importlib_metadata-1 | 3 KB      | ########## | 100% 
163 pip-20.1.1           | 1.1 MB    | ########## | 100% 
164 setuptools-47.1.0    | 636 KB    | ########## | 100% 
165 jupyterlab_server-1. | 25 KB     | ########## | 100% 
166 jedi-0.17.0          | 807 KB    | ########## | 100% 
167 prometheus_client-0. | 44 KB     | ########## | 100% 
168 ipython-7.14.0       | 1.1 MB    | ########## | 100% 
169 pyzmq-19.0.1         | 519 KB    | ########## | 100% 
170 libssh2-1.9.0        | 298 KB    | ########## | 100% 
171 brotlipy-0.7.0       | 346 KB    | ########## | 100% 
172 cryptography-2.9.2   | 622 KB    | ########## | 100% 
173 krb5-1.17.1          | 1.5 MB    | ########## | 100% 
174 nodejs-13.13.0       | 15.8 MB   | ########## | 100% 
175 libcurl-7.69.1       | 573 KB    | ########## | 100% 
176 xz-5.2.5             | 430 KB    | ########## | 100% 
177 libffi-3.2.1         | 47 KB     | ########## | 100% 
178 pyrsistent-0.16.0    | 89 KB     | ########## | 100% 
179 bleach-3.1.5         | 112 KB    | ########## | 100% 
180 nbformat-5.0.6       | 99 KB     | ########## | 100% 
181 packaging-20.4       | 32 KB     | ########## | 100% 
182 sqlalchemy-1.3.17    | 1.8 MB    | ########## | 100% 
183 mistune-0.8.4        | 53 KB     | ########## | 100% 
184 jinja2-2.11.2        | 93 KB     | ########## | 100% 
185 importlib-metadata-1 | 43 KB     | ########## | 100% 
186 pandoc-2.9.2.1       | 18.7 MB   | ########## | 100% 
187 urllib3-1.25.9       | 92 KB     | ########## | 100% 
188 wcwidth-0.1.9        | 20 KB     | ########## | 100% 
189 pyparsing-2.4.7      | 60 KB     | ########## | 100% 
190 jupyter_client-6.1.3 | 74 KB     | ########## | 100% 
191 alembic-1.4.2        | 111 KB    | ########## | 100% 
192 python-3.7.6         | 52.9 MB   | ########## | 100% 
193 Preparing transaction: ...working... done
194 Verifying transaction: ...working... done
195 Executing transaction: ...working... done
196 ==> WARNING: A newer version of conda exists. <==
197   current version: 4.8.2
198   latest version: 4.8.3
199 Please update conda by running
200     $ conda update -n base conda
201 Removing intermediate container 42ab9131da01
202  ---> 501c253f8ca7
203 Step 5/5 : RUN conda env update -q -f /tmp/environment-conda.yml &&     conda clean -y --all &&     conda env export -n "root"
204  ---> Running in 1e575beeac8f
205 Collecting package metadata (repodata.json): ...working... done
206                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
207 Found conflicts! Looking for incompatible packages.
208 This can take several minutes.  Press CTRL-C to abort.
209 failed
210 # >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
211     Traceback (most recent call last):
212       File "/opt/conda/lib/python3.7/site-packages/conda/exceptions.py", line 1079, in __call__
213         return func(*args, **kwargs)
214       File "/opt/conda/lib/python3.7/site-packages/conda_env/cli/main.py", line 80, in do_call
215         exit_code = getattr(module, func_name)(args, parser)
216       File "/opt/conda/lib/python3.7/site-packages/conda_env/cli/main_update.py", line 124, in execute
217         result[installer_type] = installer.install(prefix, specs, args, env)
218       File "/opt/conda/lib/python3.7/site-packages/conda_env/installers/conda.py", line 32, in install
219         prune=getattr(args, 'prune', False), update_modifier=UpdateModifier.FREEZE_INSTALLED)
220       File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 117, in solve_for_transaction
221         should_retry_solve)
222       File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 158, in solve_for_diff
223         force_remove, should_retry_solve)
224       File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 281, in solve_final_state
225         ssc = self._run_sat(ssc)
226       File "/opt/conda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
227         return f(*args, **kwds)
228       File "/opt/conda/lib/python3.7/site-packages/conda/core/solve.py", line 808, in _run_sat
229         should_retry_solve=ssc.should_retry_solve
230       File "/opt/conda/lib/python3.7/site-packages/conda/common/io.py", line 88, in decorated
231         return f(*args, **kwds)
232       File "/opt/conda/lib/python3.7/site-packages/conda/resolve.py", line 1318, in solve
233         self.find_conflicts(specs, specs_to_add, history_specs)
234       File "/opt/conda/lib/python3.7/site-packages/conda/resolve.py", line 347, in find_conflicts
235         bad_deps = self.build_conflict_map(specs, specs_to_add, history_specs)
236       File "/opt/conda/lib/python3.7/site-packages/conda/resolve.py", line 507, in build_conflict_map
237         root, search_node, dep_graph, num_occurances)
238       File "/opt/conda/lib/python3.7/site-packages/conda/resolve.py", line 369, in breadth_first_search_for_dep_graph
239         last_spec = MatchSpec.union((path[-1], target_paths[-1][-1]))[0]
240       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 481, in union
241         return cls.merge(match_specs, union=True)
242       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in merge
243         reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
244       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 475, in <lambda>
245         reduce(lambda x, y: x._merge(y, union), group) if len(group) > 1 else group[0]
246       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 502, in _merge
247         final = this_component.union(that_component)
248       File "/opt/conda/lib/python3.7/site-packages/conda/models/match_spec.py", line 764, in union
249         return '|'.join(options)
250     TypeError: sequence item 0: expected str instance, Channel found
251 `$ /opt/conda/bin/conda-env update -q -f /tmp/environment-conda.yml`
252   environment variables:
253                  CIO_TEST=<not set>
254   CONDA_AUTO_UPDATE_CONDA=false
255                 CONDA_DIR=/opt/conda
256                CONDA_ROOT=/opt/conda
257             CONDA_VERSION=4.8.2
258                      PATH=/opt/conda/bin:/opt/conda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin
259                           :/usr/bin:/sbin:/bin
260        REQUESTS_CA_BUNDLE=<not set>
261             SSL_CERT_FILE=<not set>
262      active environment : None
263        user config file : /home/jovyan/.condarc
264  populated config files : /opt/conda/.condarc
265           conda version : 4.8.2
266     conda-build version : not installed
267          python version : 3.7.6.final.0
268        virtual packages : __glibc=2.27
269        base environment : /opt/conda  (writable)
270            channel URLs : https://conda.anaconda.org/conda-forge/linux-64
271                           https://conda.anaconda.org/conda-forge/noarch
272                           https://repo.anaconda.com/pkgs/main/linux-64
273                           https://repo.anaconda.com/pkgs/main/noarch
274                           https://repo.anaconda.com/pkgs/r/linux-64
275                           https://repo.anaconda.com/pkgs/r/noarch
276           package cache : /opt/conda/pkgs
277                           /home/jovyan/.conda/pkgs
278        envs directories : /opt/conda/envs
279                           /home/jovyan/.conda/envs
280                platform : linux-64
281              user-agent : conda/4.8.2 requests/2.23.0 CPython/3.7.6 Linux/4.19.0-1.el7.elrepo.x86_64 ubuntu/18.04.4 glibc/2.27
282                 UID:GID : 1000:100
283              netrc file : None
284            offline mode : False
285 An unexpected error has occurred. Conda has prepared the above report.
286 The command '/bin/sh -c conda env update -q -f /tmp/environment-conda.yml &&     conda clean -y --all &&     conda env export -n "root"' returned a non-zero code: 1
290 ERROR: Job failed: exit code 1

conda seems to be pinned to 4.8.2

 Step 1/6 : FROM renku/renkulab:renku0.10.3-py3.7-0.6.2
    28  ---> a3d45bf66436
    29 Step 2/6 : COPY environment-conda.yml /tmp/
    30  ---> Using cache
    31  ---> 3686a30e2a93
    32 Step 3/6 : RUN conda config --show-sources
    33  ---> Using cache
    34  ---> 5cb183364353
    35 Step 4/6 : ENV PATH /opt/conda/bin:$PATH
    36  ---> Using cache
    37  ---> 890f66a77126
    38 Step 5/6 : RUN conda update -n base conda -c defaults
    39  ---> Running in a408da387b01
    40 Collecting package metadata (current_repodata.json): ...working... done
    41 Solving environment: ...working... WARNING conda.core.solve:_add_specs(601): pinned spec conda==4.8.2 conflicts with explicit specs.  Overriding pinned spec.
    42 failed with repodata from current_repodata.json, will retry with next repodata source.
    43 Solving environment: ...working... WARNING conda.core.solve:_add_specs(601): pinned spec conda==4.8.2 conflicts with explicit specs.  Overriding pinned spec.
    44 failed with repodata from current_repodata.json, will retry with next repodata source.
    45 Collecting package metadata (repodata.json): ...working... done
    46 Solving environment: ...working... failed
    47                                                              
    48 Found conflicts! Looking for incompatible packages.
    49 This can take several minutes.  Press CTRL-C to abort.
    50 failed
    51 UnsatisfiableError: The following specifications were found
    52 to be incompatible with the existing python installation in your environment:
    53 Specifications:
    54   - conda==4.8.2 -> python[version='2.7.*|>=3.5,<3.6.0a0|3.6.*|3.5.*|3.4.*']
    55 Your python: python=3.7
    56 If python is on the left-most side of the chain, that's the version you've asked for.
    57 When python appears to the right, that indicates that the thing on the left is somehow
    58 not available for the python version you are constrained to. Note that conda will not
    59 change your python version to a different minor version unless you explicitly specify
    60 that.
    61 The following specifications were found to be incompatible with a past
    62 explicit spec that is not an explicit spec in this operation (conda):
    63   - conda
    64 The following specifications were found to be incompatible with each other:
    65 Output in format: Requested package -> Available versions
    66 Package pypy3.6 conflicts for:
    67 conda==4.8.2 -> setuptools[version='>=31.0.1'] -> pypy3.6[version='7.3.0.*|7.3.1.*|>=7.3.1']
    68 conda -> pypy3.6[version='>=7.3.1']
    69 jupyterhub=1.1.0 -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.0.*|7.3.1.*|>=7.3.1']
    70 notebook=6.0.3 -> ipykernel -> pypy3.6[version='7.3.0.*|7.3.1.*|>=7.3.1']
    71 certifi -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*']
    72 jupyterlab=2.0.1 -> python[version='>=3.5'] -> pypy3.6[version='7.3.0.*|7.3.1.*|>=7.3.1']
    73 conda -> python[version='>=3.6,<3.7.0a0'] -> pypy3.6[version='7.3.*|7.3.0.*|7.3.1.*']
    74 Package ca-certificates conflicts for:
    75 certifi -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
    76 python=3.7 -> openssl[version='>=1.1.1g,<1.1.2a'] -> ca-certificates
    77 conda -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
    78 openssl -> ca-certificates
    79 conda==4.8.2 -> python[version='>=2.7,<2.8.0a0'] -> ca-certificates
    80 Package _libgcc_mutex conflicts for:
    81 tini=0.18.0 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main']
    82 openssl -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main']
    83 python=3.7 -> libgcc-ng[version='>=7.3.0'] -> _libgcc_mutex[version='*|0.1',build='conda_forge|main']
    84 Package libstdcxx-ng conflicts for:
    85 conda==4.8.2 -> python[version='>=2.7,<2.8.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    86 jupyterlab=2.0.1 -> python[version='>=3.5'] -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    87 gxx_linux-64 -> libstdcxx-ng==7.2.0=h24385c6_1
    88 jupyterhub=1.1.0 -> python[version='>=3.8,<3.9.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    89 python=3.7 -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    90 certifi -> python[version='>=3.8,<3.9.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    91 notebook=6.0.3 -> python[version='>=3.7,<3.8.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    92 conda -> python[version='>=3.7,<3.8.0a0'] -> libstdcxx-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    93 Package markupsafe conflicts for:
    94 notebook=6.0.3 -> jinja2 -> markupsafe[version='>=0.23']
    95 jupyterhub=1.1.0 -> jinja2 -> markupsafe[version='>=0.23']
    96 jupyterlab=2.0.1 -> jinja2[version='>=2.10'] -> markupsafe[version='>=0.23']
    97 Package openssl conflicts for:
    98 jupyterlab=2.0.1 -> python[version='>=3.5'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.1.1f,<1.1.2a']
    99 jupyterhub=1.1.0 -> python[version='>=3.8,<3.9.0a0'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.1.1b,<1.1.2a|1.0.2.*']
    100 conda==4.8.2 -> python[version='>=2.7,<2.8.0a0'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.1.1g,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1f,<1.1.2a']
    101 conda -> python[version='>=3.7,<3.8.0a0'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.0.2l,<1.0.3a']
    102 python=3.7 -> openssl[version='>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1b,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a']
    103 certifi -> python[version='>=3.8,<3.9.0a0'] -> openssl[version='1.0.*|>=1.0.2m,<1.0.3a|>=1.0.2n,<1.0.3a|>=1.0.2o,<1.0.3a|>=1.0.2p,<1.0.3a|>=1.1.1a,<1.1.2a|>=1.1.1d,<1.1.2a|>=1.1.1e,<1.1.2a|>=1.1.1g,<1.1.2a|>=1.1.1f,<1.1.2a|>=1.1.1c,<1.1.2a|>=1.0.2l,<1.0.3a|>=1.1.1b,<1.1.2a']
    104 Package libgcc-ng conflicts for:
    105 jupyterhub=1.1.0 -> python[version='>=3.8,<3.9.0a0'] -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    106 conda -> conda-package-handling[version='>=1.3.0'] -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    107 python=3.7 -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    108 openssl -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    109 tini=0.18.0 -> libgcc-ng[version='>=4.9|>=7.3.0']
    110 jupyterlab=2.0.1 -> python[version='>=3.5'] -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    111 certifi -> python[version='>=3.8,<3.9.0a0'] -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    112 notebook=6.0.3 -> python[version='>=3.7,<3.8.0a0'] -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    113 conda==4.8.2 -> conda-package-handling[version='>=1.3.0'] -> libgcc-ng[version='>=4.9|>=7.2.0|>=7.3.0']
    114 Package enum34 conflicts for:
    115 jupyterhub=1.1.0 -> traitlets[version='>=4.3.2'] -> enum34
    116 notebook=6.0.3 -> traitlets[version='>=4.2.1'] -> enum34
    117 conda==4.8.2 -> enum34
    118 conda -> enum34
    119 Package futures conflicts for:
    120 notebook=6.0.3 -> tornado[version='>=5.0'] -> futures
    121 jupyterhub=1.1.0 -> tornado[version='>=5.0'] -> futures
    122 conda -> futures[version='>=3.0.0']
    123 jupyterlab=2.0.1 -> tornado[version='!=6.0.0,!=6.0.1,!=6.0.2'] -> futures
    124 conda==4.8.2 -> conda-package-handling[version='>=1.3.0'] -> futures
    125 conda==4.8.2 -> futures[version='>=3.0.0']
    126 Package setuptools conflicts for:
    127 conda==4.8.2 -> setuptools[version='>=31.0.1']
    128 jupyterhub=1.1.0 -> jinja2 -> setuptools
    129 python=3.7 -> pip -> setuptools
    130 conda -> ruamel_yaml -> setuptools
    131 notebook=6.0.3 -> jinja2 -> setuptools
    132 jupyterlab=2.0.1 -> jinja2[version='>=2.10'] -> setuptools
    133 conda -> setuptools[version='>=31.0.1']
    134 Package certifi conflicts for:
    135 conda==4.8.2 -> requests[version='>=2.18.4,<3'] -> certifi[version='>=2016.09|>=2016.9.26|>=2017.4.17']
    136 jupyterhub=1.1.0 -> requests -> certifi[version='>=2017.4.17']
    137 conda -> requests[version='>=2.18.4,<3'] -> certifi[version='>=2016.09|>=2016.9.26|>=2017.4.17']
    138 jupyterlab=2.0.1 -> tornado[version='!=6.0.0,!=6.0.1,!=6.0.2'] -> certifi
    139 Package tornado conflicts for:
    140 notebook=6.0.3 -> tornado[version='>=5.0']
    141 notebook=6.0.3 -> ipykernel -> tornado[version='>=4|>=4.0|>=4.2|>=4.1']
    142 Package idna conflicts for:
    143 conda==4.8.2 -> requests[version='>=2.18.4,<3'] -> idna[version='>=2.5,<2.6|>=2.5,<2.7|>=2.5,<2.8|>=2.5,<2.9|>=2.5,<3']
    144 conda -> requests[version='>=2.18.4,<3'] -> idna[version='>=2.5,<2.6|>=2.5,<2.7|>=2.5,<2.8|>=2.5,<2.9|>=2.5,<3']
    145 jupyterhub=1.1.0 -> requests -> idna[version='>=2.5,<2.6|>=2.5,<2.7|>=2.5,<2.8|>=2.5,<2.9|>=2.5,<3']
    146 Package python_abi conflicts for:
    147 notebook=6.0.3 -> ipykernel -> python_abi[version='2.7.*|3.6',build='*_cp27mu|*_pypy36_pp73']
    148 notebook=6.0.3 -> python_abi[version='3.6.*|3.7.*|3.8.*',build='*_cp37m|*_cp36m|*_cp38']
    149 Package traitlets conflicts for:
    150 notebook=6.0.3 -> traitlets[version='>=4.2.1']
    151 notebook=6.0.3 -> ipykernel -> traitlets[version='>=4.1|>=4.2']
    152 Package notebook conflicts for:
    153 jupyterlab=2.0.1 -> notebook[version='>=4.3.1']
    154 jupyterlab=2.0.1 -> jupyterlab_server[version='>=1.0.0,<2.0.0'] -> notebook[version='>=4.2.0']
    155 Package entrypoints conflicts for:
    156 notebook=6.0.3 -> jupyter_client[version='>=5.3.4'] -> entrypoints[version='>=0.2.2']
    157 jupyterhub=1.1.0 -> entrypoints
    158 Package requests conflicts for:
    159 jupyterhub=1.1.0 -> requests
    160 jupyterlab=2.0.1 -> jupyterlab_server[version='>=1.0.0,<2.0.0'] -> requests
    161 conda -> requests[version='>=2.12.4|>=2.12.4,<3|>=2.18.4,<3|>=2.14.2,<3|>=2.5.3']
    162 conda==4.8.2 -> requests[version='>=2.18.4,<3']
    163 Note that strict channel priority may have removed packages required for satisfiability.
    164 The command '/bin/sh -c conda update -n base conda -c defaults' returned a non-zero code: 1
    168 ERROR: Job failed: exit code 1

Thanks! Can you paste the FROM line from your old Dockerfile and from your new Dockerfile? There’s a “new” new renku version also (renku/renkulab-cuda10.0-tf1.14:renku0.10.4-0.6.3); https://github.com/SwissDataScienceCenter/renkulab-docker#cuda100-tf114

(the reason i’m asking for the pasted lines from your Dockerfile instead of the log output is because you have a few different flavors of image posted; are you intending to use the cuda or not?)

The old Dockerfile: FROM renku/singleuser:0.4.4-renku0.9.0
The new Dockerfile: FROM renku/renkulab:renku0.10.3-py3.7-0.6.2

I don’t need cuda.

Ok, good to know! The line you pasted from the log contained cuda:

The latest python is renku/renkulab-py:3.7-renku0.10.4-0.6.3 from:
(https://github.com/SwissDataScienceCenter/renkulab-docker#py37)

Hey! As a follow up, is there an image with the latest renku, but with python 3.6? Would it become a catastrophe for renku if I replace python 3.7 in the dockerfile?

Hey @mitch, no we don’t have python 3.6 images. You could try by putting

RUN conda install python==3.6 

in your Dockerfile, though not everything is installed through conda so some things may not work properly.

yeah, sorry, I’ve seen only now https://github.com/SwissDataScienceCenter/renkulab-docker. But thanks for the answer, I was planning to downgrade via conda and see what happens… thanks @rrrrrok !

Just tried this - powerline-shell is installed via pip so you need to install that again (otherwise the terminal doesn’t work). E.g.

RUN conda install python==3.6 && \
    pip install powerline-shell
1 Like