I am trying to deploy an app to Shiny.io with a new package via rsconnect::deployApp() that I have developed locally and not hosted on CRAN. My question is similar to this one but I cannot solve using the same recommendation.
My package is installed on a private github repository and my shinyapps.io account settings have access to this private repo. My app depends on packages both on CRAN and now also this new one I have developed.
Could use a bit of direction on how to solve this.
Thanks
Uploading bundle for application: 5447651...Warning:
* May be unable to deploy package dependency 'Mycpp'; could not determine a repository URL for the source 'CRAN'.
* Unable to determine the source location for some packages. Packages should be installed from a package repository like CRAN
or a version control system. Check that options('repos') refers to a package repository containing the needed package
versions.
DONE
Deploying bundle: 6849209 for application: 5447651 ...
Waiting for task: 1273530594
building: Processing bundle: 6849209
building: Parsing manifest
building: Building image: 8100493
building: Fetching packages
building: Building package: Mycpp
################################ Begin Task Log ################################
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 1273530595 failed: Error building image: Error fetching Mycpp (1.0) source. <CRANPackageSource repo='http://cran.rstudio.org'> unable to satisfy package: Mycpp (1.0)
In addition: Warning message:
In FUN(X[[i]], ...) :
Package 'Mycpp 1.0' was installed from sources; Packrat will assume this package is available from a CRAN-like repository during future restores
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.
I was playing with dotnet cli to create f# project. I ran the following command to install NewtonSoft.Json NuGet Package.
$>dotnet add src/Library/Library.fsproj package Newtonsoft.Json
the output is
Writing C:\Users\MyUserName\AppData\Local\Temp\tmp440E.tmp
info : Adding PackageReference for package 'Newtonsoft.Json' into project 'src/Library/Library.fsproj'.
info : Restoring packages for c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\Library.fsproj...
info : GET https://api.nuget.org/v3-flatcontainer/newtonsoft.json/index.json
info : OK https://api.nuget.org/v3-flatcontainer/newtonsoft.json/index.json 288ms
error: Unable to load the service index for source https://MyEmployer.pkgs.visualstudio.com/_packaging/NuGetServerName/nuget/v3/index.json.
error: Response status code does not indicate success: 401 (Unauthorized).
I am wondering why this operation has failed due to 401 response from a irrelevant package source which is a private azure artifacts pointed by user-level scoped Nuget.Config file.
$>dotnet nuget --version
NuGet Command Line
5.2.0.3
Package can be installed successfully to projecy by specifying Source and version explicitly
$> dotnet add src/Library/Library.fsproj package Newtonsoft.Json --source https://api.nuget.org/v3-flatcontainer/newtonsoft.json/index.json --version 12.0.2
Writing C:\Users\MyUserName\AppData\Local\Temp\tmp8A3B.tmp
info : Adding PackageReference for package 'Newtonsoft.Json' into project 'src/Library/Library.fsproj'.
info : Restoring packages for c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\Library.fsproj...
info : Package 'Newtonsoft.Json' is compatible with all the specified frameworks in project 'src/Library/Library.fsproj'.
info : PackageReference for package 'Newtonsoft.Json' version '12.0.2' added to file 'c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\Library.fsproj'.
info : Committing restore...
info : Writing assets file to disk. Path: c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\obj\project.assets.json
log : Restore completed in 193.98 ms for c:\Learning\Projects\FSNetCore\FSNetCore\src\Library\Library.fsproj.
Why dotnet cli tried to load the service index from irrelevant package source ?
When I install hsqml, I get the following error:
cabal install hsqml
Resolving dependencies...
Configuring hsqml-0.3.4.1...
Failed to install hsqml-0.3.4.1
Build log ( C:\Users\wjsgm\AppData\Roaming\cabal\logs\hsqml-0.3.4.1.log ):
cabal: Entering directory 'C:\Users\wjsgm\AppData\Local\Temp\cabal-tmp-16012\hsqml-0.3.4.1'
[1 of 1] Compiling Main ( C:\Users\wjsgm\AppData\Local\Temp\cabal-tmp-16012\hsqml-0.3.4.1\dist\setup\setup.hs, C:\Users\wjsgm\AppData\Local\Temp\cabal-tmp-16012\hsqml-0.3.4.1\dist\setup\Main.o )
Linking C:\Users\wjsgm\AppData\Local\Temp\cabal-tmp-16012\hsqml-0.3.4.1\dist\setup\setup.exe ...
Configuring hsqml-0.3.4.1...
setup.exe: Missing dependencies on foreign libraries:
* Missing C libraries: Qt5Core, Qt5Gui, Qt5Widgets, Qt5Qml, Qt5Quick
This problem can usually be solved by installing the system packages that
provide these libraries (you may need the "-dev" versions). If the libraries
are already installed but in a non-standard location then you can use the
flags --extra-include-dirs= and --extra-lib-dirs= to specify where they are.
cabal: Leaving directory 'C:\Users\wjsgm\AppData\Local\Temp\cabal-tmp-16012\hsqml-0.3.4.1'
cabal: Error: some packages failed to install:
hsqml-0.3.4.1 failed during the configure step. The exception was:
ExitFailure 1
I'm trying to install SparkR
library(devtools)
install_github("amplab-extras/SparkR-pkg", subdir="pkg")
but then I find this error
Launching sbt from sbt/sbt-launch-0.13.6.jar
Invalid or corrupt jarfile sbt/sbt-launch-0.13.6.jar
make: *** [target/scala-2.10/sparkr-assembly-0.1.jar] Error 1
ERROR: compilation failed for package ‘SparkR’
* removing ‘/Users/apple/Library/R/3.2/library/SparkR’
Error: Command failed (1)
Read before proceeding:
amplab-extras/SparkR-pkg is no longer maintained. Current versions of SparkR are shipped with Spark itself. See also Installing of SparkR
Sbt download links in the repository are invalid and what you get is actually a HTML file. You can either correct URL2 in pkg/src/sbt/sbt so it points to:
http://repo.typesafe.com/typesafe/ivy-releases/org.scala-sbt/sbt-launch/0.13.6/sbt-launch.jar
or download and install sbt, clone the repository:
git clone https://github.com/amplab-extras/SparkR-pkg.git
go to src:
cd SparkR-pkg/pkg/src
assembly:
sbt assembly
and install:
R -e "devtools::install('.')"