Make Linux condalock file
FrickTobias opened this issue · comments
Problem
Currently there is a conda problem giving an error when running condalock. When it is resolved the environment.linux.lock.yml
file should be remade using bash misc/condalock.sh linux
bash misc/condalock.sh osx
works as normal.
The current place holder linux file is just a copy of environment.yml
Error
Verifying transaction: failed
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
return func(*args, **kwargs)
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda_env/cli/main.py", line 80, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda_env/cli/main_create.py", line 118, in execute
result[installer_type] = installer.install(prefix, pkg_specs, args, env)
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda_env/installers/conda.py", line 40, in install
unlink_link_transaction.execute()
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda/core/link.py", line 244, in execute
self.verify()
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
return f(*args, **kwds)
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda/core/link.py", line 231, in verify
exceptions = self._verify(self.prefix_setups, self.prefix_action_groups)
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda/core/link.py", line 590, in _verify
for exc in self.verify_executor.map(UnlinkLinkTransaction._verify_individual_level,
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda/common/io.py", line 525, in map
yield func(thing)
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda/core/link.py", line 411, in _verify_individual_level
error_result = axn.verify()
File "/Users/tobiasfrick/miniconda/lib/python3.8/site-packages/conda/core/path_actions.py", line 323, in verify
source_size_in_bytes = getsize(self.source_full_path)
File "/Users/tobiasfrick/miniconda/lib/python3.8/genericpath.py", line 50, in getsize
return os.stat(filename).st_size
OSError: [Errno 62] Too many levels of symbolic links: '/Users/tobiasfrick/miniconda/pkgs/ncurses-6.2-h58526e2_4/share/terminfo/N/NCR260VT300WPP'
`$ /Users/tobiasfrick/miniconda/bin/conda-env create -n blrtmp-7778-linux -f environment.yml`
environment variables:
CIO_TEST=<not set>
CONDA_AUTO_UPDATE_CONDA=false
CONDA_DEFAULT_ENV=nd2tools
CONDA_EXE=/Users/tobiasfrick/miniconda/bin/conda
CONDA_PREFIX=/Users/tobiasfrick/miniconda/envs/nd2tools
CONDA_PROMPT_MODIFIER=(nd2tools)
CONDA_PYTHON_EXE=/Users/tobiasfrick/miniconda/bin/python
CONDA_ROOT=/Users/tobiasfrick/miniconda
CONDA_SHLVL=1
CURL_CA_BUNDLE=<not set>
PATH=/Users/tobiasfrick/miniconda/envs/nd2tools/bin:/usr/local/git/bin:/sw/
bin:/usr/local/bin:/usr/local:/usr/local/sbin:/usr/local/mysql/bin:/Us
ers/tobiasfrick/Library/Python/3.9/bin:/Users/tobiasfrick/external/cel
lranger-5.0.1:/Users/tobiasfrick/miniconda/condabin:/usr/local/bin:/us
r/bin:/bin:/usr/sbin:/sbin:/Users/tobiasfrick/external/sratoolkit.2.10
.9-mac64/bin:/usr/local/bin
REQUESTS_CA_BUNDLE=<not set>
SSL_CERT_FILE=<not set>
active environment : nd2tools
active env location : /Users/tobiasfrick/miniconda/envs/nd2tools
shell level : 1
user config file : /Users/tobiasfrick/.condarc
populated config files : /Users/tobiasfrick/.condarc
conda version : 4.9.2
conda-build version : not installed
python version : 3.8.5.final.0
virtual packages : __unix=0=0
__archspec=1=x86_64
base environment : /Users/tobiasfrick/miniconda (writable)
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://conda.anaconda.org/bioconda/linux-64
https://conda.anaconda.org/bioconda/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /Users/tobiasfrick/miniconda/pkgs
/Users/tobiasfrick/.conda/pkgs
envs directories : /Users/tobiasfrick/miniconda/envs
/Users/tobiasfrick/.conda/envs
platform : linux-64
user-agent : conda/4.9.2 requests/2.24.0 CPython/3.8.5 Darwin/20.3.0 OSX/10.16
UID:GID : 501:20
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
If submitted, this report will be used by core maintainers to improve
future releases of conda.
Moved to conda-lock