I am getting the below error when running "pre-commit run --all-files" and when trying to make a commit, it is some python error, python version in use is "Python 2.7.16".
[INFO] Installing environment for https://github.com/pre-commit/mirrors-mypy.
[INFO] Once installed this environment will be reused.
[INFO] This may take a few minutes...
An unexpected error has occurred: CalledProcessError: command: ('/Users/user/.cache/pre-commit/repoq_mv31g8/py_env-default/bin/python', '-mpip', 'install', '.', 'tokenize-rt==3.2.0', 'pydantic')
return code: 1
expected return code: 0
stdout:
Processing /Users/user/.cache/pre-commit/repoq_mv31g8
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Collecting tokenize-rt==3.2.0
Using cached tokenize_rt-3.2.0-py2.py3-none-any.whl (6.1 kB)
Collecting pydantic
Using cached pydantic-1.9.0-cp310-cp310-macosx_11_0_arm64.whl (2.4 MB)
Collecting mypy==0.782
Using cached mypy-0.782-py3-none-any.whl (2.4 MB)
Collecting mypy-extensions<0.5.0,>=0.4.3
Using cached mypy_extensions-0.4.3-py2.py3-none-any.whl (4.5 kB)
Collecting typing-extensions>=3.7.4
Using cached typing_extensions-4.1.1-py3-none-any.whl (26 kB)
Collecting typed-ast<1.5.0,>=1.4.0
Using cached typed_ast-1.4.3.tar.gz (210 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'done'
Building wheels for collected packages: pre-commit-dummy-package, typed-ast
Building wheel for pre-commit-dummy-package (setup.py): started
Building wheel for pre-commit-dummy-package (setup.py): finished with status 'done'
Created wheel for pre-commit-dummy-package: filename=pre_commit_dummy_package-0.0.0-py3-none-any.whl size=1154 sha256=ea7d756fd19dee0f5f03851e3e343db4194f4b306f21fecb796b4d6d89d266fb
Stored in directory: /private/var/folders/v4/nlc505k12rn9pf4c9kntz8qm0000gn/T/pip-ephem-wheel-cache-4jcph5rz/wheels/80/78/0d/746d1697141e342b257e21c980fc51ac134e6b6400568c3646
Building wheel for typed-ast (setup.py): started
Building wheel for typed-ast (setup.py): finished with status 'error'
Running setup.py clean for typed-ast
Successfully built pre-commit-dummy-package
Failed to build typed-ast
Installing collected packages: typed-ast, mypy-extensions, typing-extensions, tokenize-rt, pydantic, mypy, pre-commit-dummy-package
Running setup.py install for typed-ast: started
Running setup.py install for typed-ast: finished with status 'error'
stderr:
error: subprocess-exited-with-error
× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [22 lines of output]
running bdist_wheel
running build
running build_py
package init file 'ast3/tests/__init__.py' not found (or not a regular file)
running build_ext
building '_ast27' extension
building '_ast3' extension
ast3/Python/ast.c:844:5: warning: code will never be executed [-Wunreachable-code]
abort();
^~~~~
ast3/Python/ast.c:4514:9: error: implicit declaration of function '_PyUnicode_DecodeUnicodeEscape' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
v = _PyUnicode_DecodeUnicodeEscape(s, len, NULL, &first_invalid_escape);
^
ast3/Python/ast.c:4514:9: note: did you mean 'PyUnicode_DecodeUnicodeEscape'?
/opt/homebrew/opt/python#3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10/unicodeobject.h:608:23: note: 'PyUnicode_DecodeUnicodeEscape' declared here
PyAPI_FUNC(PyObject*) PyUnicode_DecodeUnicodeEscape(
^
ast3/Python/ast.c:4514:7: warning: incompatible integer to pointer conversion assigning to 'PyObject *' (aka 'struct _object *') from 'int' [-Wint-conversion]
v = _PyUnicode_DecodeUnicodeEscape(s, len, NULL, &first_invalid_escape);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2 warnings and 1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for typed-ast
error: subprocess-exited-with-error
× Running setup.py install for typed-ast did not run successfully.
│ exit code: 1
╰─> [24 lines of output]
running install
/Users/user/.cache/pre-commit/repoq_mv31g8/py_env-default/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
warnings.warn(
running build
running build_py
package init file 'ast3/tests/__init__.py' not found (or not a regular file)
running build_ext
building '_ast27' extension
building '_ast3' extension
ast3/Python/ast.c:844:5: warning: code will never be executed [-Wunreachable-code]
abort();
^~~~~
ast3/Python/ast.c:4514:9: error: implicit declaration of function '_PyUnicode_DecodeUnicodeEscape' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
v = _PyUnicode_DecodeUnicodeEscape(s, len, NULL, &first_invalid_escape);
^
ast3/Python/ast.c:4514:9: note: did you mean 'PyUnicode_DecodeUnicodeEscape'?
/opt/homebrew/opt/python#3.10/Frameworks/Python.framework/Versions/3.10/include/python3.10/unicodeobject.h:608:23: note: 'PyUnicode_DecodeUnicodeEscape' declared here
PyAPI_FUNC(PyObject*) PyUnicode_DecodeUnicodeEscape(
^
ast3/Python/ast.c:4514:7: warning: incompatible integer to pointer conversion assigning to 'PyObject *' (aka 'struct _object *') from 'int' [-Wint-conversion]
v = _PyUnicode_DecodeUnicodeEscape(s, len, NULL, &first_invalid_escape);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2 warnings and 1 error generated.
error: command '/usr/bin/clang' failed with exit code 1
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure
× Encountered error while trying to install package.
╰─> typed-ast
note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
Check the log at /Users/user/.cache/pre-commit/pre-commit.log
I am running it on Apple M1 Air (macOS Big Sur), what am I missing or is it a known M1 issue ?
I have tried installing pydantic manually, pre-commit is installed by brew.
Thanks in Advance
pre-commit config:
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.0.1
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
- id: check-yaml
- id: check-added-large-files
- repo: https://github.com/psf/black
rev: 21.7b0
hooks:
- id: black
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v0.782
hooks:
- id: mypy
additional_dependencies: [pydantic]
you're installing a very old version of mypy (0.782) which depends on an old version of typed-ast (<1.5.0) which does not support M1
you can ~usually get to the latest version by running pre-commit autoupdate -- or pick a version newer than 0.900 (where mypy started support for M1)
disclaimer: I created pre-commit
I am using Ubuntu 22.04.
In short, when I try git commit, it will report an error because I have installed pre-commit:
An unexpected error has occurred: CalledProcessError: command: ('python', '-mpip', 'install', '.')
return code: 1
expected return code: 0
stdout:
Executable `python` not found
First, we usually have python3 installed, so the python command is invalid.
Do it:
sudo apt install python-is-python3
Then, you usually encounter this problem in Ubuntu 22.04:
An unexpected error has occurred: AssertionError: BUG: expected environment for python to be healthy immediately after install, please open an issue describing your environment
more info:
virtualenv python version did not match created version:
- actual version: <<error retrieving version from /home/wind/.cache/pre-commit/reposyb8net0/py_env-python3/bin/python>>
- expected version: 3.10.4.final.0
To fix this, add this line to your .bashrc file:
export SETUPTOOLS_USE_DISTUTILS=stdlib
Refresh the configuration file by restarting a terminal window or running source ~/.bashrc.
Summary
TravisCI build suddenly fails, possibly due to some rJava shenanigans. Local checks (Linux) are squeaky-clean.
Preamble
My package was building fine on Travis up until 2 months ago, this is the last successful build.
The next build only changed some minor things on README.md (which is even on .Rbuildignore), but TravisCI started failing anyway. This makes me think that all I need to do is adjust .travis.yml accordingly. I've tried every tweak I could find (here's the commit history of the file).
How far I got
The best I could manage so far is to narrow down the error to either this:
The command "sudo R CMD javareconf" failed and exited with 1 during .
or this:
checking whether JNI programs run... configure: error: Unable to run a simple JNI program. Make sure you have configured R with Java support (see R documentation) and check config.log for failure reason.
Error in system(cmd) : (converted from warning) error in running command
removing ‘/usr/local/lib/R/site-library/rJava’
Error in i.p(...) :
(converted from warning) installation of package ‘rJava’ had non-zero exit status
Calls: ... with_rprofile_user -> with_envvar -> force -> force -> i.p
Execution halted
The command "Rscript -e 'deps <- remotes::dev_package_deps(dependencies = >NA);remotes::install_deps(dependencies = TRUE);if (!all(deps$package %in% >installed.packages())) { message("missing: ", paste(setdiff(deps$package, >installed.packages()), collapse=", ")); q(status = 1, save = "no")}'" failed and exited with 1 >during .
The full log of both errors can be found here and here, respectively.
So here is the error i am getting from the console. I understand that hydromad package is not on cran but I have added it as secondary repos in packages(Tools options in R studio) and in .R profile file. Still I am getting this error
****Preparing to deploy application...DONE
Uploading bundle for application: 2120925...DONE
Deploying bundle: 3058356 for application: 2120925 ...
Waiting for task: 720810692
building: Parsing manifest
building: Building image: 3408182
building: Installing system dependencies
building: Fetching packages
error: Building package: hydromad
########################## Begin Task Log ################################
[2020-04-24T06:51:09.225825780+0000] Execute script: packages/build/sys.sh
+ set -e
+ apt-get update -qq
+ apt-get install -y libapparmor-dev
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
libapparmor-dev
0 upgraded, 1 newly installed, 0 to remove and 114 not upgraded.
Need to get 67.8 kB of archives.
After this operation, 229 kB of additional disk space will be used.
Get:1 http://us-east-1.ec2.archive.ubuntu.com/ubuntu xenial-updates/main amd64 libapparmor-dev amd64 2.10.95-0ubuntu2.11 [67.8 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 67.8 kB in 0s (0 B/s)
Selecting previously unselected package libapparmor-dev:amd64.
(Reading database ... 119718 files and directories currently installed.)
Preparing to unpack .../libapparmor-dev_2.10.95-0ubuntu2.11_amd64.deb ...
Unpacking libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
Processing triggers for man-db (2.7.5-1) ...
Setting up libapparmor-dev:amd64 (2.10.95-0ubuntu2.11) ...
########################### End Task Log #################################
Error: Unhandled Exception: Child Task 720810693 failed: Error building image: Error fetching hydromad (0.9-26) source. <CRANPackageSource repo='http://cran.rstudio.org'> unable to satisfy package: hydromad (0.9-26)
In addition: Warning message:
In FUN(X[[i]], ...) :
Package 'hydromad 0.9-26' was installed from sources; Packrat will assume this package is available from a CRAN-like repository during future restores
Execution halted****
Can anyone help me resolve this error? Will be grateful
Welcome to StackOverflow! Your question is quite specific, so I would recommend to use a more specialized resource. The good news is that package hydromad has its own forum
While installing "car" package in Rstudio in Ubuntu, I faced an error saying that dependencies "nloptr","lme4" and one more, are not installed.
So I started installing "nloptr" but I faced this error-
configure: Need to download and build NLopt
trying URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
Error in download.file(url = "http://ab-initio.mit.edu/nlopt/nlopt-
2.4.2.tar.gz", :
cannot open URL 'http://ab-initio.mit.edu/nlopt/nlopt-2.4.2.tar.gz'
Execution halted
/bin/tar: This does not look like a tar archive
gzip: stdin: unexpected end of file
/bin/tar: Child returned status 1
/bin/tar: Error is not recoverable: exiting now
Warning message:
In untar(tarfile = "nlopt-2.4.2.tar.gz") :
'/bin/tar -xf 'nlopt-2.4.2.tar.gz'' returned error code 2
configure: Starting to install library to
/tmp/RtmpSeLv7g/R.INSTALL18a67910d582/nloptr/nlopt-2.4.2
./configure: line 3325: cd: nlopt-2.4.2: No such file or directory
System hangs after last line and when I restart after some time, "nloptr" is not installed and hence I am unable to install "car" package.
Please help me. Thanks in advance.
I was encountering the same problem under R (pure R 3.2.3 on Linux Debian). I was first blocked by another issue during the same installation : the installation process failed to lock directory ~/.../R/x86_64.../3.2 and suggested to remove ~/.../R/x86_64.../3.2/00LOCK-nloptr . I did it, restart the car package installation, and then it blocked at the same point: it needs nlopt.h.
So, I installed libnlopt-dev (sudo apt-get install libnlopt-dev) and re-restart the car installation ... and then it worked.
Ok, this is under linux, but perhaps should you try to focus on installing something about NLOPT under windows.
Good luck.
I am getting the following error when I try to run
sudo apt-get upgrade
I am not sure what is the issue. Please guide me. Thanks
Preparing to unpack .../nginx_1.8.0-1~jessie_amd64.deb ...
Unpacking nginx (1.8.0-1~jessie) over (1.6.2-5) ...
dpkg: error processing archive /var/cache/apt/archives/nginx_1.8.0-1~jessie_amd64.deb (--unpack):
trying to overwrite '/usr/sbin/nginx', which is also in package nginx-full 1.6.2-5
dpkg-deb: error: subprocess paste was killed by signal (Broken pipe)
Errors were encountered while processing:
/var/cache/apt/archives/nginx_1.8.0-1~jessie_amd64.deb
E: Sub-process /usr/bin/dpkg returned an error code (1)