gabefair
commented
5 years ago Did you ever figure this out?
Open Hofphi opened 5 years ago
gabefair
commented
5 years ago Did you ever figure this out?
Hofphi
commented
5 years ago Hey gabefair,
unfortunately I could not resolve the issue yet. I tried removing miniconda and reinstalling but without any success. The error message changed to this here:
# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
Traceback (most recent call last):
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/exceptions.py", line 819, in __call__
return func(*args, **kwargs)
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda_env/cli/main.py", line 74, in do_call
exit_code = getattr(module, func_name)(args, parser)
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda_env/cli/main_create.py", line 108, in execute
installer.install(prefix, pkg_specs, args, env)
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda_env/installers/conda.py", line 39, in install
unlink_link_transaction.execute()
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/core/link.py", line 223, in execute
self.verify()
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/common/io.py", line 46, in decorated
return f(*args, **kwds)
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/core/link.py", line 210, in verify
exceptions = self._verify(self.prefix_setups, self.prefix_action_groups)
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/core/link.py", line 486, in _verify
cls._verify_transaction_level(prefix_setups),
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/core/link.py", line 481, in <genexpr>
exceptions = tuple(exc for exc in concatv(
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/core/link.py", line 334, in _verify_individual_level
error_result = axn.verify()
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/core/path_actions.py", line 428, in verify
create_link(self.source_full_path, self.intermediate_path, LinkType.copy)
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/gateways/disk/create.py", line 334, in create_link
copy(src, dst)
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/gateways/disk/create.py", line 272, in copy
_do_copy(src, dst)
File "/home/hofphi00/miniconda3/lib/python3.6/site-packages/conda/gateways/disk/create.py", line 286, in _do_copy
copyfileobj(fsrc, fdst, buffer_size)
ProcessLookupError: [Errno 3] No such process
`$ /home/hofphi00/miniconda3/bin/conda-env create --file /scratch/hofphi00/dropSeqPipe/.snakemake/conda/13723821.yaml --prefix /scratch/hofphi00/dropSeqPipe/.snakemake/conda/13723821`I tried executing this line here:
/home/hofphi00/miniconda3/bin/conda-env create --file /scratch/hofphi00/dropSeqPipe/.snakemake/conda/13723821.yaml --prefix /scratch/hofphi00/dropSeqPipe/.snakemake/conda/13723821
which gave me the same error. I am really clueless on how to deal with this error. Any suggestions are very welcome!
youlimlee
commented
5 years ago I have a same problem.
ERROR conda.core.link:_execute(507): An error occurred while installing package 'defaults::tensorflow-base-1.12.0-eigen_py36h45df0d8_0'. PermissionError(13, 'Permission denied') Attempting to roll back. Rolling back transaction: done PermissionError(13, 'Permission denied')
Does anyone knows how can I solve this?
MASE13
commented
5 years ago same issue on two different win10 devices running anaconda
KuhnHuge
commented
5 years ago same issue on two different win10 devices running anaconda
I had the same issue ,and I just solve it .But I'm not good at English. 只需要以管理员身份打开就好了。（Just open as an administrator.） 3101142694@qq.com
matrpyth
commented
5 years ago I have the same problem and even opening the command window as an administrator did not work for me.
ERROR conda.core.link:_execute(507): An error occurred while installing package 'conda-forge::openssl-1.0.2o-vc9_0'. PermissionError(13, 'Permission denied') Attempting to roll back. Rolling back transaction: done PermissionError(13, 'Permission denied')
Is there another way than trying the admin cmd?
Nathan-Furnal
commented
5 years ago Same problem on a windows 10 machine
ERROR conda.core.link:_execute(507): An error occurred while uninstalling package 'anaconda::openssl-1.1.1-he774522_0'
giangnguyen2412
commented
5 years ago Following this fixed the problem: https://github.com/conda/conda/issues/3448 Uninstall miniconda and install again using Just me(Not everyone).
fromSun2Moon
commented
5 years ago if you use over window 8 , try command line Run as administrator! In my case, I go over it.
lindafa
commented
5 years ago I had the same problem today. I am using win10. You just have to run the anaconda Prompt as administrator, it should work.
fpetruccelli
commented
5 years ago RUN as ADMIN. RUN as ADMIN. It will work.
eavandoorn
commented
5 years ago Similar error today. It occurs when provisioning a Vagrant Ubuntu VM, or installing into said VM from its BASH command line. I'm getting the errors on two separate machines running Windows 8.1 and 10, and not getting it on another machine that still runs Windows 7 (when using the same Vagrant file for provisioning).
In contrast to the original error posted, the ERROR conda.core.link:_execute(507) is accompanied by OSError(26, 'Text file busy'). Like Nathan wrote above on January 5th, the error is generated when uninstalling openssl (in my case as part of an installation of Jupyter Notebook, with openssl being updated from version 1.1.1a-h7b6447c_0 to version 1.1.1b-h7b6447c_1). Output from lsof shows that the python executable is being written to, which is probably why I'm seeing the 'Text file busy' error. Please advise if I need to open a new issue because of different behavior, I can imagine this is not as easily solved by running as admin (for completeness' sake, I'm running cmd as admin under Windows).
marabout2015
commented
5 years ago @fpetruccelli , no running as admin does not allow this to work. Sorry.
manouzi
commented
5 years ago same problem
marabout2015
commented
5 years ago @manouzi I worked around this by reinstalling Anaconda 3 version 4.4.10 from an old installer I had from last year. I use it without updating conda. I don't know whether that solution is possible for you.
harisbal
commented
5 years ago Cloning the environment worked for me
dkruijs
commented
5 years ago Similar error today. It occurs when provisioning a Vagrant Ubuntu VM, or installing into said VM from its BASH command line. I'm getting the errors on two separate machines running Windows 8.1 and 10, and not getting it on another machine that still runs Windows 7 (when using the same Vagrant file for provisioning).
In contrast to the original error posted, the ERROR conda.core.link:_execute(507) is accompanied by OSError(26, 'Text file busy'). Like Nathan wrote above on January 5th, the error is generated when uninstalling openssl (in my case as part of an installation of Jupyter Notebook, with openssl being updated from version 1.1.1a-h7b6447c_0 to version 1.1.1b-h7b6447c_1). Output from lsof shows that the python executable is being written to, which is probably why I'm seeing the 'Text file busy' error. Please advise if I need to open a new issue because of different behavior, I can imagine this is not as easily solved by running as admin (for completeness' sake, I'm running cmd as admin under Windows).
I've found a workaround for this by simply electing to install Anaconda (actually Miniconda, in our case) 'one folder up', so that it is not included in the synced folder which is also accessible in Windows. I read a post somewhere (unfortunately cannot find it anymore) by mr. Hashimoto himself in response to a similar issue, saying that Windows is quite aggressive with file locking. So I tried to remove windows (Windows 10) from the equation by not placing Anaconda into the synced folder. This made any openssl errors go away!
It's not technically proper, since Anaconda expects itself to be installed in the user's folder (which should be /home/vagrant), but I do not expect it to cause any problems.
I am curious to hear if this works for anyone else.
EDIT: I've found the original comment that inspired this workaround: https://github.com/hashicorp/vagrant/issues/2282#issuecomment-25475134
Can not find anything in the forum on this error report. Maybe you can help me with this:
Environment Information