The export_png() function in the R ggvis package requires us to have the program vg2png installed, from the node.js module vega.
(source: R Documentation )
I have node and npm installed on windows, and I ran npm install vega.
This is the output that I got on running npm install vega:
C:\Users\username>npm install -g trifacta/vega
\
> canvas#1.1.6 install C:\Users\username\AppData\Roaming\npm\node_modules\vega\node_modules\canvas
> node-gyp rebuild
|
C:\Users\username\AppData\Roaming\npm\node_modules\vega\node_modules\canvas>node "C:\Program Files\nodejs\node_modules\npm\bin\node-gyp-bi
n\\..\..\node_modules\node-gyp\bin\node-gyp.js" rebuild
Node Commands
Syntax:
node {operator} [options] [arguments]
Parameters:
/? or /help - Display this help message.
list - List nodes or node history or the cluster
listcores - List cores on the cluster
view - View properties of a node
online - Set nodes or node to online state
offline - Set nodes or node to offline state
pause - Pause node [deprecated]
resume - Resume node [deprecated]
For more information about HPC command-line tools,
see http://go.microsoft.com/fwlink/?LinkId=120724.
C:\Users\username\AppData\Roaming\npm\vg2svg -> C:\Users\username\AppData\Roaming\npm\node_modules\vega\bin\vg2svg
C:\Users\username\AppData\Roaming\npm\vg2png -> C:\Users\username\AppData\Roaming\npm\node_modules\vega\bin\vg2png
vega#1.5.0 C:\Users\username\AppData\Roaming\npm\node_modules\vega
├── yargs#2.3.0 (wordwrap#0.0.2)
├── canvas#1.1.6 (nan#1.2.0)
├── d3#3.5.5
├── request#2.53.0 (caseless#0.9.0, json-stringify-safe#5.0.0, forever-agent#0.5.2, aws-sign2#0.5.0, stringstream#0.0.4, oauth-sign#0.6.0, tunnel-agen
t#0.4.0, isstream#0.1.2, node-uuid#1.4.3, qs#2.3.3, combined-stream#0.0.7, form-data#0.2.0, tough-cookie#0.12.1, mime-types#2.0.10, http-signature#0.1
0.1, hawk#2.3.1, bl#0.9.4)
├── topojson#1.6.18 (queue-async#1.0.7, rw#0.1.4, optimist#0.3.7, shapefile#0.3.0)
└── d3-geo-projection#0.2.14 (brfs#1.4.0)
I'm not sure if it has installed correctly. Now, when I run:
mtcars %>%
ggvis(x = ~wt) %>%
export_png()
I get the following error:
Writing to file plot.png
Error in vega_file(vis, file = file, type = "png") :
Conversion program vg2pngnot found.
Is there a specific way in which vega has to be installed on Windows, which would resolve this error?
Related
Here's what I'm doing:
I have a blog that uses blogdown to render .Rmd files.
Some of the code snippets in the blog are in Python. I'm using reticulate for that.
I'm using a GitHub workflow to build and publish the blog as part of a larger website. This workflow sets up the environment and package dependencies in miniconda.
The last time this ran was six months ago. At that time, it worked. Now, it does not. I can't seem to replicate the behavior locally for more detailed debugging.
It seems to be trying to put a mamba command into normalizePath instead of a filesystem path (www-main is the name of the repository):
conda activate www-main
Rscript -e 'blogdown::build_site(local=FALSE, run_hugo=FALSE, build_rmd="content/blog/2020-08-28-api.Rmd")'
shell: /usr/bin/bash -l {0}
env:
CONDA_PKGS_DIR: /home/runner/conda_pkgs_dir
Rendering content/blog/2020-08-28-api.Rmd...
[...]
Quitting from lines 401-410 (2020-08-28-api.Rmd)
Error in normalizePath(conda, winslash = "/", mustWork = TRUE) :
path[1]="# cmd: /usr/share/miniconda/condabin/mamba update --name www-main --file /home/runner/work/www-main/www-main/conda": No such file or directory
Calls: local ... python_munge_path -> get_python_conda_info -> normalizePath
Execution halted
Error: Failed to render content/blog/2020-08-28-api.Rmd
Execution halted
Lines 401-410 of 2020-08-28-api.Rmd are a Python code block:
400 ```{python python-data, dev='svg'}
401 import covidcast
402 from datetime import date
403 import matplotlib.pyplot as plt
404
405 data = covidcast.signal("fb-survey", "smoothed_hh_cmnty_cli",
406 date(2020, 9, 8), date(2020, 9, 8),
407 geo_type="state")
408 covidcast.plot_choropleth(data, figsize=(7, 5))
409 plt.title("% who know someone who is sick, Sept 8, 2020")
410 ```
The useful bits of the output of conda info, in case it helps:
active environment : www-main
active env location : /usr/share/miniconda/envs/www-main
shell level : 1
user config file : /home/runner/.condarc
populated config files : /home/runner/.condarc
conda version : 4.12.0
conda-build version : not installed
python version : 3.9.12.final.0
virtual packages : __linux=5.15.0=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /usr/share/miniconda (writable)
conda av data dir : /usr/share/miniconda/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/runner/conda_pkgs_dir
envs directories : /usr/share/miniconda/envs
/home/runner/.conda/envs
platform : linux-64
user-agent : conda/4.12.0 requests/2.27.1 CPython/3.9.12 Linux/5.15.0-1020-azure ubuntu/20.04.5 glibc/2.31
UID:GID : 1001:121
netrc file : None
offline mode : False
I found this, but their workaround doesn't make sense for me since I'm not using papermill: https://github.com/rstudio/reticulate/issues/1184
I found this, but my paths don't have spaces: https://github.com/rstudio/reticulate/issues/1149
I found this, but their problem includes an entirely reasonable value for path[1], unlike mine: How can I tell R where the conda environment is via a docker image?
The build environment for this is a bit of a bear but I can probably put together a minimum working (/nonworking) example if needed, lmk
I tracked this down to at least two bits of weird/buggy behavior in reticulate and found a workaround: switch from vanilla miniconda to Mambaforge.
The TL;DR seems to be that whatever wacky ubuntu-latest setup-miniconda#v2 environment started putting into meta/history doesn't include a create line, which is what reticulate needs in order to figure out which conda goes with which python, because (1) it ignores the reticulate.conda_binary setting for some reason, and (2) it uses a more restrictive regex to parse the lines of the history file than the regex it uses to select them. Mambaforge does include the create line, so reticulate is happy.
- uses: conda-incubator/setup-miniconda#v2
with:
python-version: 3.9
activate-environment: www-main
miniforge-variant: Mambaforge
miniforge-version: latest
use-mamba: true
use-only-tar-bz2: true # (for caching support)
- name: Update environment
run: mamba env update -n www-main -f environment.yml
Operating system
nbgrader --version: 0.6.1
jupyterhub --version (if used with JupyterHub): 1.0.0 (Using littlest Jupterhub)
jupyter notebook --version
jupyter core : 4.6.3
jupyter-notebook : 6.0.3
qtconsole : 4.7.2
ipython : 7.13.0
ipykernel : 5.2.0
jupyter client : 6.1.2
jupyter lab : 1.2.8
nbconvert : 5.6.1
ipywidgets : 7.5.1
nbformat : 5.0.4
traitlets : 4.3.3
Expected behavior: When used
nbgrader release_assignment ps1 --force --debug
It should release the assignment in /srv/nbgrader/exchange shared folder.
Actual behavior
I am facing an issue when I try to release the assignment:
nbgrader release_assignment ps1 --force --debug
It releases the assignment without errors but to the location (/home/jupyter-tljh-admin/course_id/outbound/ps1) but not to the shared location /srv/nbgrader/exchange:
[ReleaseAssignmentApp | INFO] Overwriting files: /home/jupyter-tljh-admin/course_id ps1
[ReleaseAssignmentApp | INFO] Source: /home/jupyter-tljh-admin/course_id/release/./ps1
[ReleaseAssignmentApp | INFO] Destination: /home/jupyter-tljh-admin/course_id/outbound/ps1
[ReleaseAssignmentApp | INFO] Released as: /home/jupyter-tljh-admin/course_id ps1
The folder /srv/nbgrader/exchange has write permissions.
Please suggest, what could be the issue?
I faced a similar problem. When I opened the Formgrader there was a notification saying that the directory /srv/nbgrader/exchange does not exist or could not be created. I simply created the directory on my own, but not directly. First I created the directory /srv/nbgrader with sudo. Then I cd into that directory and created the subdirectory exchange, also with sudo. I also added a nbgrader_config.py in /etc/jupyter with the following content:
from nbgrader.auth import JupyterHubAuthPlugin
c = get_config()
c.Exchange.path_includes_course = True
c.Authenticator.plugin_class = JupyterHubAuthPlugin
This solved the issue for me.
Create the /srv/nbgrader/exchange directory and add the permissions like this: chmod ugo+rw /srv/nbgrader/exchange
Open the nbgrader_config.py that was created after running nbgrader quickstart <course-id>
Make sure these two lines are present and uncommented:
c.CourseDirectory.course_id = "<course-id>"
c.IncludeHeaderFooter.header = "source/header.ipynb"
Search for the specific line that says: c.CourseDirectory.root = '', uncomment it, and set it to c.CourseDirectory.root = /full/path/to/your/course-id/
Search for the specific line that says: c.Exchange.assignment_dir = '.' and actually set it to c.Exchange.assignment_dir = '/srv/nbgrader/exchange'
Copy this exact nbgrader_config.py into .jupyter or any other directory that apprear in jupyter --paths
Stop and restart your server
I am unable to setup & run a simple darkflow program. Infact can't even configure darkflow library:
from darkflow.net.build import TFNet
==> ModuleNotFoundError: No module named 'darkflow'
My Target is to run the following program:
from darkflow.net.build import TFNet
import cv2
options = {"model": "cfg/yolo.cfg", "load": "bin/yolo.weights", "threshold": 0.1}
tfnet = TFNet(options)
imgcv = cv2.imread("./test/dog.jpg")
result = tfnet.return_predict(imgcv)
print(result
Please suggest steps so that I could configure darkflow on Jupyter Notebook (with no GPU) and run the above code
Fixed by creating the file in ipynb file in darkflow directory (downloaded from github) and executing the following from the notebook:
!python3 setup.py build_ext --inplace
!pip install -e .
!pip install .
I'm trying to use llvm binding in ocaml, in my file test.ml, I have one line of code:
open Llvm
When I run the command
ocamlbuild -use-ocamlfind test.byte -package llvm
I get this result:
+ ocamlfind ocamldep -package llvm -modules test.ml > test.ml.depends
ocamlfind: Package `llvm' not found
Command exited with code 2.
Compilation unsuccessful after building 1 target (0 cached) in 00:00:00.
What did I do wrong in this? Thanks.
BTW, the _tag file contains:
"src": traverse
<src/{lexer,parser}.ml>: use_camlp4, pp(camlp4of)
<*.{byte,native}>: g++, use_llvm, use_llvm_analysis
myocamlbuild.ml contains:
open Ocamlbuild_plugin;;
ocaml_lib ~extern:true "llvm";;
ocaml_lib ~extern:true "llvm_analysis";;
flag ["link"; "ocaml"; "g++"] (S[A"-cc"; A"g++"]);;
I don't know why the instructions that you're using are so complex. You don't have to do anything like this to use llvm bindings in OCaml, provided you have installed them via opam.
Here is the recipe:
Install llvm bindings via opam.
it could be as simple as
opam install llvm
However, opam may try to install the latest version that is not available on your system, so pick a particular version, that you have and do the following (suppose you have llvm-3.8):
opam install conf-llvm.3.8
opam install llvm --criteria=-changed
(The -criteria flag will prevent opam from upgrading conf-llvm to the newest version)
Once it succeeds, you can easily compile your programs without any additional scaffolding.
Create and build your project
create a fresh new folder, e.g.,
mkdir llvm-project
cd llvm-project
create a sample application (borrowed from some tutorial, that I've found online):
cat >test.ml<<EOF
open Llvm
let _ =
let llctx = Llvm.global_context () in
let llmem = Llvm.MemoryBuffer.of_file Sys.argv.(1) in
let llm = Llvm_bitreader.parse_bitcode llctx llmem in
Llvm.dump_module llm ;
()
EOF
compile it for bytecode
ocamlbuild -pkgs llvm,llvm.bitreader test.byte
or to the native code
ocamlbuild -pkgs llvm,llvm.bitreader test.native
run it
./test.native mycode.bc
I have installed a fresh copy of arcanist on to Mac OS X El Capitan (10.11.4) into /usr/local/phabricator/arcanist.
If I first cd into /usr/local/phabricator/arcanist and run either bin/arc or just arc (as I added /usr/local/phabricator/arcanist/bin to my PATH) then all is fine. However if I try and run arc lint from my rocksdb directory on my system then I always get a fatal error, the output looks like this:
$ arc lint --trace
ARGV '/usr/local/phabricator/arcanist/bin/../scripts/arcanist.php' 'lint' '--trace'
LOAD Loaded "phutil" from "/usr/local/phabricator/libphutil/src".
LOAD Loaded "arcanist" from "/usr/local/phabricator/arcanist/src".
Config: Did not find user configuration at "/Users/aretter/.arcrc".
Config: Did not find system configuration at "/etc/arcconfig".
Working Copy: Reading .arcconfig from "/Users/aretter/code/rocksdb/.arcconfig".
Working Copy: Path "/Users/aretter/code/rocksdb" is part of `git` working copy "/Users/aretter/code/rocksdb".
Working Copy: Project root is at "/Users/aretter/code/rocksdb".
Config: Did not find local configuration at "/Users/aretter/code/rocksdb/.git/arc/config".
Loading phutil library from '/Users/aretter/code/rocksdb/arcanist_util'...
[2016-06-14 09:31:17] EXCEPTION: (PhutilMissingSymbolException) Failed to load class or interface 'ArcanistBaseWorkflow': the class or interface 'ArcanistBaseWorkflow' is not defined in the library map for any loaded phutil library.
If you are not a developer, this almost always means that a library is out of date. For example, you may have upgraded `phabricator` without upgrading `libphutil`, or vice versa. It might also mean that you need to restart Apache or PHP-FPM. Make sure all libraries are up to date and all services have been restarted.
If you are a developer and this symbol was recently added or moved, your library map may need to be rebuilt. You can rebuild the map by running 'arc liberate'. For more information, see:
https://secure.phabricator.com/book/phabcontrib/article/adding_new_classes/ at [<phutil>/src/__phutil_library_init__.php:25]
arcanist(head=master, ref.master=c13e5a629535), arcanist_util(head=java-wb-save-restore-points, ref.master=fda098461b3f, ref.java-wb-save-restore-points=dd6d2e75d836), phutil(head=master, ref.master=fb1e159d3640)
#0 __phutil_autoload(string)
#1 spl_autoload_call(string) called at [<arcanist_util>/config/FacebookArcanistConfiguration.php:7]
#2 include_once(string) called at [<phutil>/src/moduleutils/PhutilBootloader.php:226]
#3 PhutilBootloader::executeInclude(string) called at [<phutil>/src/moduleutils/PhutilBootloader.php:216]
#4 PhutilBootloader::loadLibrarySource(string, string) called at [<phutil>/src/symbols/PhutilSymbolLoader.php:381]
#5 PhutilSymbolLoader::loadSymbol(array) called at [<phutil>/src/symbols/PhutilSymbolLoader.php:256]
#6 PhutilSymbolLoader::selectAndLoadSymbols() called at [<phutil>/src/__phutil_library_init__.php:22]
#7 __phutil_autoload(string)
#8 spl_autoload_call(string) called at [<arcanist>/scripts/arcanist.php:186]
Please note that I have tried reinstalling it and also running arc liberate, but neither has fixed the issue.
Can someone tell me what is wrong on my system?
I have also checked with Git that my arcanist is indeed correct and up-to-date:
$ cd /usr/local/phabricator/arcanist
$ git remote -v
origin github.com/phacility/arcanist.git (fetch)
origin github.com/phacility/arcanist.git (push)
$ git status
On branch master Your branch is up-to-date with 'origin/master'. nothing to commit, working directory clean
$ git pull
Already up-to-date.
I also tried reinstalling via this mechanism:
$ cd /usr/local/phabricator
$ rm -rf arcanist libphutil
$ git clone https://github.com/phacility/libphutil.git
$ git clone https://github.com/phacility/arcanist.git
arcanist_util(head=java-wb-save-restore-points, ref.master=fda098461b3f, ref.java-wb-save-restore-points=dd6d2e75d836)
This doesn't look like a fresh copy of arcanist to me from source, at least the upstream isn't responsible for "arcanist_util". Where did you get it from? I would delete it, and pull directly from GitHub. http://github.com/phacility/arcanist