Newbie trying to get going with IJulia on Debian Jessie, and am stuck with an error. Don't know how to interpret the message, and not actually sure on what to do next.
The beginning is all ok :
julia> Pkg.init()
INFO: Initializing package repository /home/sybs/.julia/v0.3
INFO: Cloning METADATA from git://github.com/JuliaLang/METADATA.jl
julia> Pkg.add("IJulia")
INFO: Cloning cache of BinDeps from git://github.com/JuliaLang/BinDeps.jl.git
INFO: Cloning cache of Compat from git://github.com/JuliaLang/Compat.jl.git
INFO: Cloning cache of Conda from git://github.com/Luthaf/Conda.jl.git
INFO: Cloning cache of Dates from git://github.com/quinnj/Dates.jl.git
INFO: Cloning cache of HttpCommon from git://github.com/JuliaWeb/HttpCommon.jl.git
INFO: Cloning cache of IJulia from git://github.com/JuliaLang/IJulia.jl.git
INFO: Cloning cache of JSON from git://github.com/JuliaLang/JSON.jl.git
INFO: Cloning cache of Nettle from git://github.com/staticfloat/Nettle.jl.git
INFO: Cloning cache of SHA from git://github.com/staticfloat/SHA.jl.git
INFO: Cloning cache of URIParser from git://github.com/JuliaWeb/URIParser.jl.git
INFO: Cloning cache of ZMQ from git://github.com/JuliaLang/ZMQ.jl.git
INFO: Installing BinDeps v0.3.21
INFO: Installing Compat v0.7.11
INFO: Installing Conda v0.1.9
INFO: Installing Dates v0.3.2
INFO: Installing HttpCommon v0.1.2
INFO: Installing IJulia v1.1.8
INFO: Installing JSON v0.5.0
INFO: Installing Nettle v0.2.2
INFO: Installing SHA v0.1.2
INFO: Installing URIParser v0.0.7
INFO: Installing ZMQ v0.3.1
INFO: Building Nettle
INFO: Building ZMQ
INFO: Building IJulia
INFO: Installing Jupyter via the Conda package.
INFO: Downloading miniconda installer ...
--2016-02-23 14:43:46-- http://repo.continuum.io/miniconda/Miniconda-3.9.1-Linux-x86_64.sh
Résolution de repo.continuum.io (repo.continuum.io)… 23.21.205.0, 174.129.25.1
Connexion à repo.continuum.io (repo.continuum.io)|23.21.205.0|:80… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 23531867 (22M) [application/octet-stream]
Sauvegarde en : « /home/sybs/.julia/v0.3/Conda/deps/usr/installer.sh »
home/sybs/.julia/v0. 48%[=========> ] 10,86M 16,4KB/s eta 14m 14s/home/sybs/.julia/v 100%[=====================>] 22,44M 13,8KB/s ds 29m 43ss
Then I get a "chmod not defined" error :
INFO: Installing miniconda ...
===============================[ ERROR: IJulia ]================================
chmod not defined
while loading /home/sybs/.julia/v0.3/IJulia/deps/build.jl, in expression starting on line 35
================================================================================
================================[ BUILD ERRORS ]================================
WARNING: IJulia had build errors.
- packages with build errors remain installed in /home/sybs/.julia/v0.3
- build a package and all its dependencies with `Pkg.build(pkg)`
- build a single package by running its `deps/build.jl` script
================================================================================
INFO: Package database updated
I opened up the build.jl file and scroll before and after line35 and got this :
if jupyter_vers < v"3.0" || dirname(jupyter) == abspath(Conda.SCRIPTDIR)
info("Installing Jupyter via the Conda package.")
Conda.add("jupyter")
jupyter = abspath(Conda.SCRIPTDIR,"jupyter")
jupyter_vers = prog_version(jupyter)
jupyter_vers < v"3.0" && error("failed to find $jupyter 3.0 or later")
end
info("Found Jupyter version $jupyter_vers: $jupyter")
#######################################################################
# Warn people upgrading from older IJulia versions:
try
juliaprof = chomp(readall(pipeline(`$ipython locate profile julia`,
stderr=DevNull)))
warn("""You should now run IJulia just via `$jupyter notebook`, without
the `--profile julia` flag. IJulia no longer maintains the profile.
Consider deleting $juliaprof""")
end
#######################################################################
# Install Jupyter kernel-spec file.
So, what shall I do next ? chmod a+x build.jl ? then Pkg.build("IJulia") ?
Conda.jl author here. I do not have enough reputation to comment, so here is an answer.
Conda is tested on the latest julia 0.3, which is 0.3.12, and works there. So a possible fix would be to update your Julia version to either that or 0.4.
You can also try to install it manually, by making it executable and then running ./installer.sh -b -f -p $HOME/.julia/v0.3/Conda/deps/usr/.
Related
I'm having trouble installing R from a homebrew formula on our Intel garbage can mac pro at work. I was having trouble installing tidyverse from source code so I removed and have been attempting to reinstalling R, as I thought it might have been a version mismatch somewhere.
I used
brew install R
and after a bunch of output where it's downloading other packages, I get back the following
==> Installing dependencies for r: libpng, freetype, fontconfig, gettext, libffi, pcre, glib, pkg-config, libpthread-stubs, xorgproto, libxau, libxdmcp, libxcb, libx11, libxext, libxrender, lzo, pixman, cairo, gmp, isl, mpfr, libmpc, lz4, xz, zstd, gcc, jpeg-turbo, openblas, pcre2, readline, ca-certificates, openssl#1.1 and tcl-tk
==> Installing r dependency: libpng
Unknown option: -C
usage: git [--version] [--help] [-c name=value]
[--exec-path[=<path>]] [--html-path] [--man-path] [--info-path]
[-p|--paginate|--no-pager] [--no-replace-objects] [--bare]
[--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>]
<command> [<args>]
Error: Command failed with exit 129: git
Is this in fact a git error? What is the -C command?
Things I've tried:
removing and reinstalling command line tools
removing and reinstalling Homebrew
My machine:
Mac Pro (Late 2013)
2.7 GHz 12-Core Xeon E5
Thanks!
Sam
I think it tries to use an old version of git at /usr/bin/git, but you need to run brew install git to install a newer version of git to /usr/local/bin/git.
If /usr/local/bin/ isn't on your PATH before /usr/bin/, then you can add a line like this to ~/.bash_profile:
export PATH=/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
However /usr/local/bin is included in /etc/paths by default, so it should be added to PATH by programs that run path_helper (like Terminal and iTerm 2 but not Script Editor or Emacs.app).
pip install apache-airflow
pip3.9 install apache-airflow
The Err by Collecting urllib3<1.27,>=1.21.1
Using cached urllib3-1.26.8-py2.py3-none-any.whl (138 kB)
Using legacy 'setup.py install' for flask-login, since package 'wheel' is not installed.
Using legacy 'setup.py install' for python-nvd3, since package 'wheel' is not installed.
Using legacy 'setup.py install' for python-slugify, since package 'wheel' is not installed.
Using legacy 'setup.py install' for termcolor, since package 'wheel' is not installed.
Using legacy 'setup.py install' for unicodecsv, since package 'wheel' is not installed.
Using legacy 'setup.py install' for blinker, since package 'wheel' is not installed.
Using legacy 'setup.py install' for Flask-JWT-Extended, since package 'wheel' is not installed.
Building wheels for collected packages: setproctitle
Building wheel for setproctitle (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for setproctitle (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [6 lines of output]
running bdist_wheel
running build
running build_ext
building 'setproctitle' extension
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun
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 setproctitle
Failed to build setproctitle
ERROR: Could not build wheels for setproctitle, which is required to install pyproject.toml-based projects
actually already tried to downgrade the pip version from pip 22.0.3 to 20.2.4
pip install --upgrade pip==20.2.4
like solution in the thread "Could not build wheels for setproctitle..."
still the same error
Im trying to set up a CI for a R package. In that regard I`m considering circleCI, which has worked out with previous R projects. However this time, I get the following error:
Downloading renv 0.14.0 ... OK (downloaded source)
Installing renv 0.14.0 ... Done!
Successfully installed and loaded renv 0.14.0.
Project '~/main' loaded. [renv 0.14.0]
devtools::install_deps(dependencies = TRUE)
Error in loadNamespace(x) : there is no package called ‘devtools’
Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
My .circleci/config.yml looks similar to that one
version: 2
jobs:
build:
docker:
- image: my_random_image
steps:
- checkout
- run:
name: Install package dependencies
command: R -e "devtools::install_deps(dep = TRUE)"
- run:
name: Build package
command: R CMD build .
- run:
name: Check package
command: R CMD check *tar.gz
and my_random_image looks as follows:
FROM r-base:4.1.2
RUN apt-get update \
&& apt-get install git libssl-dev ssh texlive-latex-base texlive-fonts-recommended
libcurl4-openssl-dev libxml2-dev -y \
&& rm -rf /var/lib/apt/lists/*
RUN R -e "install.packages(c('devtools', 'roxygen2'), repos='http://cran.us.r- project.org')"
So its pretty standard stuff, as far as I can see. The error only occurs if renv is part if my R package. Otherwise circleCI does not complain and runs as expected without any errors.
I would like to keep renv in my R project and therefore struggle to understand the issue and the solution to that.
appreciate any help!!
The issue here is most likely that your run stage, here:
- run:
name: Install package dependencies
command: R -e "devtools::install_deps(dep = TRUE)"
installs packages into the default user / site libraries, but when R is launched in your project's working directory:
Downloading renv 0.14.0 ... OK (downloaded source)
Installing renv 0.14.0 ... Done!
Successfully installed and loaded renv 0.14.0.
Project '~/main' loaded. [renv 0.14.0]
the renv autoloader is automatically downloading renv, and activating the renv project library.
By default, renv isolates projects from the user / site library, so the packages installed in your earlier steps are not visible within the project. This behavior is intentional, and ensures that different project libraries are isolated both from changes in the user / site libraries, as well as in other project libraries.
One of the following should help:
If your renv.lock is up to date, call renv::restore() before trying to use devtools or other packages;
Allow renv to see the user library, with e.g. the environment variable RENV_CONFIG_USER_LIBRARY = TRUE.
I'd recommend reading https://rstudio.github.io/renv/articles/renv.html and https://rstudio.github.io/renv/articles/ci.html if you haven't already.
I'm facing a problem with Poetry and GitHub actions in the last days. Maybe because Poetry has an updated version.
Information
Poetry version 1.1.9
I'm using the following .yml file for the CICD
jobs:
execute-linters:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout#v2
- name: Pyton 3.9
uses: actions/setup-python#v2
with:
python-version: 3.9
- name: Poetry
uses: Gr1N/setup-poetry#v7
- name: Dependencies
run: poetry install
...
Whenever it runs, during the Dependencies job, it fails and I've got the following error
• Installing py (1.10.0)
EnvCommandError
Command ['/home/runner/work/ds-gdem-pvso/ds-gdem-pvso/.venv/bin/pip', 'install', '--no-deps', '/home/runner/.cache/pypoetry/artifacts/c8/3a/b1/6d8182aff6a688801f32ca473f2ba55ecb83446a84cf3d1afad18800e0/ibm_db-3.0.4.tar.gz'] errored with the following return code 1, and output:
Processing /home/runner/.cache/pypoetry/artifacts/c8/3a/b1/6d8182aff6a688801f32ca473f2ba55ecb83446a84cf3d1afad18800e0/ibm_db-3.0.4.tar.gz
ERROR: Command errored out with exit status 1:
command: /home/runner/work/ds-gdem-pvso/ds-gdem-pvso/.venv/bin/python -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-c_nfk704/setup.py'"'"'; __file__='"'"'/tmp/pip-req-build-c_nfk704/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-9hi5cw5y
cwd: /tmp/pip-req-build-c_nfk704/
Complete output (3 lines):
Detected 64-bit Python
Downloading https://public.dhe.ibm.com/ibmdl/export/pub/software/data/db2/drivers/odbc_cli/linuxx64_odbc_cli.tar.gz
error in ibm_db setup command: use_2to3 is invalid.
----------------------------------------
WARNING: Discarding file:///home/runner/.cache/pypoetry/artifacts/c8/3a/b1/6d8182aff6a688801f32ca473f2ba55ecb83446a84cf3d1afad18800e0/ibm_db-3.0.4.tar.gz. Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
at ~/.local/share/pypoetry/venv/lib/python3.9/site-packages/poetry/utils/env.py:1180 in _run
1176│ output = subprocess.check_output(
1177│ cmd, stderr=subprocess.STDOUT, **kwargs
1178│ )
1179│ except CalledProcessError as e:
→ 1180│ raise EnvCommandError(e, input=input_)
1181│
1182│ return decode(output)
1183│
1184│ def execute(self, bin, *args, **kwargs):
• Installing pyarrow (4.0.1)
• Installing regex (2021.8.28)
• Installing scikit-learn (0.24.2)
• Installing toml (0.10.2)
• Installing tomli (1.2.1)
• Installing tqdm (4.62.3)
• Installing typing-inspect (0.7.1)
• Installing wrapt (1.12.1)
Error: Process completed with exit code 1.
Attempts
At first I was using the Gr1N/setup-poetry#v4 and I notice that it was outdated. I've tried to update it to Gr1N/setup-poetry#v7, but didn't work.
I also received this Warning: The lock file is not up to date with the latest changes in pyproject.toml. You may be getting outdated dependencies. Run update to update them.. I've tried to delete poetry.lock and run poetry update to generate a new one, no success at all.
Could anyone try to help me?
I think you can pin the poetry version link to what you have in your local environment (use poetry --version) to fix that.
- uses: Gr1N/setup-poetry#v7
with:
poetry-version: 1.1.7
It is always a good practice to pin down your libraries and make sure your local environment is as similar as possible to the deployment environment.
I need to use the RequestsLibrary library and when I import it:
*** Settings ***
Library SeleniumLibrary
Library RequestsLibrary
I get an error module not found. When I run pipenv graph I can clearly see it's installed:
(marek) bash-3.2$ pipenv graph
robotframework-requests==0.5.0
- requests [required: Any, installed: 2.22.0]
- certifi [required: >=2017.4.17, installed: 2019.6.16]
- chardet [required: >=3.0.2,<3.1.0, installed: 3.0.4]
- idna [required: >=2.5,<2.9, installed: 2.8]
- urllib3 [required: >=1.21.1,<1.26,!=1.25.1,!=1.25.0, installed: 1.25.3]
- robotframework [required: Any, installed: 3.1.2]
What am I doing wrong ?
As turned out the issue was the fact that I installed the library using pipenv install xyz and that creates brand new virtual environment prior to library installation. So I basically ended up with a virtual environment within virtual environment and Robot couldn't access it. As soon as I got rid off the extra virtual environment, exited out and ran pipenv install robotframework-requests outside of any venv, it ran.