I'm using Anaconda3 and Miniconda on Windows 11. I don't know what happened but my conda seems not to have file permissions when I execute any subcommands.
Specifically, even if I remove a certain package (whether in a virtual environment or not), it always prompts me that the uninstallation is successful, but when I go to the installation directory, I will find that the file of that package is still there.
Another strange thing is that when I run conda clean --all -y, it always prompts a long list of warnings that the various packages that have been installed cannot be deleted due to file permission issues. The specific logs are as follows:
Will remove 153 (77.9 MB) tarball(s).
Will remove 1 index cache(s).
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\cache
Will remove 28 (62.7 MB) package(s).
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\anyio-3.6.1-py310h5588dad_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\ca-certificates-2022.3.29-haa95532_1
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\certifi-2021.10.8-py39haa95532_2
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\certifi-2022.5.18.1-py310h5588dad_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\certifi-2022.5.18.1-py39hcbf5309_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\certifi-2022.6.15-py310h5588dad_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\conda-4.12.0-py39haa95532_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\conda-content-trust-0.1.1-pyhd3eb1b0_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\cryptography-36.0.0-py39h21b164f_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\cython-0.29.28-py310hd77b12b_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\dnspython-1.16.0-py310haa95532_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\eth-hash-0.2.0-py_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\h2-4.1.0-pyhd8ed1ab_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\importlib_metadata-4.11.4-hd8ed1ab_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\openssl-1.1.1n-h2bbff1b_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\pip-21.2.4-py310haa95532_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\python-snappy-0.6.0-py310hd77b12b_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\python_abi-3.10-2_cp310
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\python_abi-3.9-2_cp39
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\six-1.16.0-pyhd3eb1b0_1
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\snappy-1.1.9-h6c2663c_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\sqlite-3.38.2-h2bbff1b_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\tqdm-4.63.0-pyhd3eb1b0_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\trio-0.19.0-py310haa95532_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\typing-extensions-4.2.0-hd8ed1ab_1
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\ujson-5.1.0-py310hd77b12b_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\urllib3-1.26.8-pyhd3eb1b0_0
WARNING: cannot remove, file permissions: D:\miniconda3\pkgs\vc-14.2-h21ff451_1
There are no tempfile(s) to remove.
There are no logfile(s) to remove.
I've always thought it was a file permissions issue, but I'm sure I haven't tweaked these things, they worked fine before (perhaps a win11 issue?). What's more, I tried to set full permissions to all user groups, the problem still exists. So it could be a deeper problem?
At the moment I'm completely clueless as to how to fix this, what tests should I do next to further identify the problem? Or is there any solution to try?
Related
Following the suggestion of #liberforce, I am running Mingw-w64 64bit shell.
I got less warnings than with msys2 shell.
Here are the warnings I got.
warning: could not get file information for clang32/
warning: could not get file information for clang32/bin/
warning: could not get file information for clang32/etc/
warning: could not get file information for clang32/etc/config.site
warning: could not get file information for clang32/include/
warning: could not get file information for clang32/lib/
warning: could not get file information for clang32/share/
warning: could not get file information for clang64/
warning: could not get file information for clang64/bin/
warning: could not get file information for clang64/etc/
warning: could not get file information for clang64/etc/config.site
warning: could not get file information for clang64/include/
warning: could not get file information for clang64/lib/
warning: could not get file information for clang64/share/
warning: could not get file information for opt/
warning given when extracting /usr/bin/cygpath.exe (Can't create '/usr/bin/cygpath.exe')
warning given when extracting /usr/bin/cygwin-console-helper.exe (Can't create '/usr/bin/cygwin-console-helper.exe')
warning given when extracting /usr/bin/locale.exe (Can't create '/usr/bin/locale.exe')
warning given when extracting /usr/bin/tzset.exe (Can't create '/usr/bin/tzset.exe')
warning: terminate MSYS2 without returning to shell and check for updates again
warning: for example close your terminal window instead of calling exit
Normally when I follow the last instruction, when I run the shell again, it just opens the terminal window, quickly shows an error, I can't read quick enough, and quickly closes.
So, I reinstall, and don't use pacman -Syu, to update, but install each module with pacman -S.
However, at this point, I want to know, will the above warnings prove problematic going forward?
Password:
The directory '/Users/allin/Library/Caches/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/Users/allin/Library/Caches/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
Invalid requirement: '–upgrade'
Traceback (most recent call last):
File "/Library/Python/2.7/site-packages/pip/_internal/req/req_install.py", line 252, in from_line
req = Requirement(req)
File "/Library/Python/2.7/site-packages/pip/_vendor/packaging/requirements.py", line 97, in __init__
requirement_string[e.loc:e.loc + 8]))
InvalidRequirement: Invalid requirement, parse error at "'\xe2\x80\x93upgra'"
The correct command is
sudo pip install frida --upgrade --ignore-installed six
i.e. use double minuses, not em/en-dashes. Do not blindly copy commands from web pages without understanding them.
While I am trying to install any package from homebrew, it returns me this weird error.
$ brew install postgres
Error: No such file or directory # rb_sysopen - /tmp/github_api_headers20171005-1039-1blysiu
$ brew doctor
\Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!
Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.
Unexpected header files:
/usr/local/include/node/ares.h
/usr/local/include/node/ares_build.h
/usr/local/include/node/ares_rules.h
/usr/local/include/node/ares_version.h
/usr/local/include/node/nameser.h
/usr/local/include/node/pthread-fixes.h
/usr/local/include/node/v8-experimental.h
Error: No such file or directory # rb_file_s_stat - /tmp
I'm trying to install the trader extension.
I successfully installed pear/pecl.
When first running the command "pecl install trader" I had some issues on folders that were not writable, so I manually give those read/write permissions.
Now I'm at the point I get "ERROR: `phpize' failed"
Please how to get this solved?
I run mamp server on a mac 10.6.8
computer-van-gebruiker:~ Gebruiker$ sudo pecl install trader
Password:
WARNING: channel "pecl.php.net" has updated its protocols, use "pecl channel-update pecl.php.net" to update
Warning: Invalid argument supplied for foreach() in PEAR/Downloader.php on line 593
Warning: Invalid argument supplied for foreach() in /usr/local/pear/share/pear/PEAR/Downloader.php on line 593
downloading trader-0.4.0.tgz ...
Starting to download trader-0.4.0.tgz (298,434 bytes)
...........................done: 298,434 bytes
Warning: Invalid argument supplied for foreach() in PEAR/PackageFile/v2/Validator.php on line 870
Warning: Invalid argument supplied for foreach() in /usr/local/pear/share/pear/PEAR/PackageFile/v2/Validator.php on line 870
332 source files, building
running: phpize
grep: /usr/include/php/main/php.h: No such file or directory
grep: /usr/include/php/Zend/zend_modules.h: No such file or directory
grep: /usr/include/php/Zend/zend_extensions.h: No such file or directory
Configuring for:
PHP Api Version:
Zend Module Api No:
Zend Extension Api No:
Cannot find autoconf. Please check your autoconf installation and the
$PHP_AUTOCONF environment variable. Then, rerun this script.
ERROR: `phpize' failed
You should be more specific about PEAR/PECL and PHP version.
Your problem's source is that you're missing the development package for PHP that contains the C header files.
I'm getting a number of strange error messages while trying to cabal install data-default. The same basic phenomenon happens for that package even in a fresh sandbox. I can install other packages with no problem.
The error messages are of the following form, but occur for each of the 4 data-default-instances- packages:
[1 of 1] Compiling Data.Default.Instances.OldLocale ( Data\Default\Instances\OldLocale.hs, dist\dist-sandbox-6a114df1\build\Data\Default\Instances\OldLocale.o )
C:\Program Files (x86)\MinGHC-7.10.1\ghc-7.10.1\mingw\bin\ar.exe: dist/dist-sandbox-6a114df1\build\libHSdata-default-instances-old-locale-0.0.1-6jcjjaR25tK4x3nJhHHjFM.a-8696\libHSdata-default-instances-old-locale-0.0.1-6jcjjaR25tK4x3nJhHHjFM.a: No such file or directory
Any idea what's going on?
Output from ghc-pkg check
C:\Users\Doug\Documents\GitHub\bird-brain [estimator]> ghc-pkg check
WARNING: cache is out of date: C:/Program Files (x86)/MinGHC-7.10.1/ghc-7.10.1\lib\package.conf.d\pa
ckage.cache
ghc will see an old view of this package db. Use 'ghc-pkg recache' to fix.
Warning: haddock-interfaces: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\QuickCh
eck-2.8\html\QuickCheck.haddock doesn't exist or isn't a file
Warning: haddock-html: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\QuickCheck-2.
8\html doesn't exist or isn't a directory
Warning: haddock-interfaces: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\tf-rand
om-0.5\html\tf-random.haddock doesn't exist or isn't a file
Warning: haddock-html: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\tf-random-0.5
\html doesn't exist or isn't a directory
Warning: haddock-interfaces: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\random-
1.1\html\random.haddock doesn't exist or isn't a file
Warning: haddock-html: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\random-1.1\ht
ml doesn't exist or isn't a directory
Warning: haddock-interfaces: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\primiti
ve-0.5.4.0\html\primitive.haddock doesn't exist or isn't a file
Warning: haddock-html: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\primitive-0.5
.4.0\html doesn't exist or isn't a directory
Warning: haddock-interfaces: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\mtl-2.2
.1\html\mtl.haddock doesn't exist or isn't a file
Warning: haddock-html: C:\Users\Doug\AppData\Roaming\cabal\doc\i386-windows-ghc-7.10.1\mtl-2.2.1\htm
l doesn't exist or isn't a directory
Using the strategy at https://github.com/haskell/cabal/issues/2502 it is possible to fix this problem, which ultimately has to do with the Windows limit on overall path length.
Using stack is another solution, probably one to try first, because it internally uses a folder that is likely to be close enough to the root for the path to work.