refer to this paragraph:
installed(pkg) → Void | VersionNumber
If pkg is installed, return the installed version number, otherwise return nothing.
from JuliaDoc
Pkg.installed("anInvalidPackage") function should return nothing but it throws an error:
julia> VERSION
v"0.5.0"
julia> Pkg.installed("anInvalidPackage")
ERROR: anInvalidPackage is not a package (not registered or installed)
in installed(::String) at .\pkg\entry.jl:123
in (::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#installed,Tuple{String}})
() at .\pkg\dir.jl:31
in cd(::Base.Pkg.Dir.##2#3{Array{Any,1},Base.Pkg.Entry.#installed,Tuple{String}
}, ::String) at .\file.jl:48
in #cd#1 at .\pkg\dir.jl:31
in installed(::String) at .\pkg\pkg.jl:129
EDIT : issue
If we tale a look at the source code for the Pkg module in base it should give use some clues:
function installed(pkg::AbstractString)
avail = Read.available(pkg)
if Read.isinstalled(pkg)
res = typemin(VersionNumber)
### some libgit2 stuff ###
end
isempty(avail) && throw(PkgError("$pkg is not a package (not registered or installed)"))
return nothing # registered but not installed
end
From the last two lines we can see that Julia is going to throw an error if the package is not registered or installed. However if the package is registered but not installed then no error will be thrown and nothing is returned.
So
var = Pkg.installed("AMD") # returns nothing for me as I don't have AMD installed
# but it is a registered package
But:
altvar = Pkg.installed("this_is_not_the_name_of_any_package")
# will throw an error
I agree the docs should probably make this more clear...
Related
I want to use https://github.com/bazelbuild/rules_webtesting. I am using Bazel 5.2.0.
The whole project can be found here.
My WORKSPACE.bazel file looks like this:
load("#bazel_tools//tools/build_defs/repo:http.bzl", "http_archive")
http_archive(
name = "io_bazel_rules_webtesting",
sha256 = "3ef3bb22852546693c94e9b0b02c2570e74abab6f800fd58e0cbe79492e49c1b",
urls = [
"https://github.com/bazelbuild/rules_webtesting/archive/581b1557e382f93419da6a03b91a45c2ac9a9ec8/rules_webtesting.tar.gz",
],
)
load("#io_bazel_rules_webtesting//web:repositories.bzl", "web_test_repositories")
web_test_repositories()
My BUILD.bazel file looks like this:
load("#io_bazel_rules_webtesting//web:py.bzl", "py_web_test_suite")
py_web_test_suite(
name = "browser_test",
srcs = ["browser_test.py"],
browsers = [
"#io_bazel_rules_webtesting//browsers:chromium-local",
],
local = True,
deps = ["#io_bazel_rules_webtesting//testing/web"],
)
browser_test.py looks like this:
import unittest
from testing.web import webtest
class BrowserTest(unittest.TestCase):
def setUp(self):
self.driver = webtest.new_webdriver_session()
def tearDown(self):
try:
self.driver.quit()
finally:
self.driver = None
# Your tests here
if __name__ == "__main__":
unittest.main()
When I try to do a bazel build //... I get (under Ubuntu 20.04 and macOS):
INFO: Invocation ID: 74c03efd-9caa-4174-9fda-42f7ff37e38b
ERROR: error loading package '': Every .bzl file must have a corresponding package, but '#io_bazel_rules_webtesting//web:repositories.bzl' does not have one. Please create a BUILD file in the same or any parent directory. Note that this BUILD file does not need to do anything except exist.
INFO: Elapsed time: 0.038s
INFO: 0 processes.
FAILED: Build did NOT complete successfully (0 packages loaded)
The error message does not make sense to me, since there is a BUILD file in
https://github.com/bazelbuild/rules_webtesting/blob/581b1557e382f93419da6a03b91a45c2ac9a9ec8/BUILD.bazel
and https://github.com/bazelbuild/rules_webtesting/blob/581b1557e382f93419da6a03b91a45c2ac9a9ec8/web/BUILD.bazel.
I also tried a different version of Bazel - but with the same result.
Any ideas on how to get this working?
You need to add a strip_prefix = "rules_webtesting-581b1557e382f93419da6a03b91a45c2ac9a9ec8" in your http_archive call.
For debugging, you can look in the folder where Bazel extracts it: bazel-out/../../../external/io_bazel_rules_webtesting. #io_bazel_rules_webtesting//web translates to bazel-out/../../../external/io_bazel_rules_webtesting/web, so if that folder doesn't exist things won't work.
Two related questions:
1. How does one install R and selected packages in the configuration.nix?
2. How does one add packages not only from CRAN but also from Gitub or at least locally stored?
In the wiki you will find instructions like these to install R packages. https://github.com/NixOS/nixpkgs/blob/master/doc/languages-frameworks/r.section.md . Have it working when using nix-shell but I'm stuck while trying to do the installation from configuration.nix.
Regarding building R packages and I have found this example regarding building packages:
let
pkgs = import <nixpkgs> {};
buildRPackage = import <nixpkgs/pkgs/development/r-modules/generic-builder.nix> pkgs.R;
in
with pkgs.rPackages;
{
foobar = buildRPackage {
name = "your-package-name-1.0";
src = ./.;
propagatedBuildInputs = [/* required dependencies go here */];
};
}
The command "nix-build . -A foobar" would then compile it.
But would like to run all from configuration.nix in order to the machine configuration in one place.
Ok, with the help of Bulats pointer above I managed to find a solution. A complete example was found here: https://github.com/NixOS/nixpkgs/issues/44290
For future reference here is one way of adding r packages both from CRAN and Github inline in configuration.nix:
environment.systemPackages = with pkgs;
[(pkgs.rWrapper.override {
packages = with pkgs.rPackages; let
llr = buildRPackage {
name = "llr";
src = pkgs.fetchFromGitHub {
owner = "dirkschumacher";
repo = "llr";
rev = "0a654d469af231e9017e1100f00df47bae212b2c";
sha256 = "0ks96m35z73nf2sb1cb8d7dv8hq8dcmxxhc61dnllrwxqq9m36lr";};
propagatedBuildInputs = [ rlang knitr];
nativeBuildInputs = [ rlang knitr ];};
in [knitr
rlang
llr
tidyverse
## the rest of your R packages here
devtools];})
pkgs.postgresql
pkgs.isync
pkgs.msmtp
pkgs.notmuch
gnupg
## the rest of your Nixos packages (derivations) here
];
I am trying to use the selenium webdriver API directly from R using rJava. I am subject to a fairly restrictive IT environment, so I can't access a remote driver currently (hence why I'm not currently using the Rselenium package), and I don't have either Chrome or Firefox availaible--just phantomjs. I am able to get this working okay from the Scala REPL. I used sbt to get all the dependenices--build.sbt contains, for example:
retrieveManaged := true
libraryDependencies ++= Seq (
"org.seleniumhq.selenium" % "selenium-java" % "3.9.1",
"com.codeborne" % "phantomjsdriver" % "1.4.4"
)
(Note that I have phantomjs installed as /usr/local/bin/phantomjs, and it is
version 2.1.1).
I then copied all the jar files to a single-level folder via cp jars/*/*/*.jar alljars/ containing the following:
animal-sniffer-annotations-1.14.jar httpcore-4.4.6.jar selenium-api-3.9.1.jar
byte-buddy-1.7.9.jar j2objc-annotations-1.1.jar selenium-chrome-driver-3.9.1.jar
checker-compat-qual-2.0.0.jar jline-2.14.5.jar selenium-edge-driver-3.9.1.jar
commons-codec-1.10.jar jsr305-1.3.9.jar selenium-firefox-driver-3.9.1.jar
commons-exec-1.3.jar okhttp-3.9.1.jar selenium-ie-driver-3.9.1.jar
commons-logging-1.2.jar okio-1.13.0.jar selenium-java-3.9.1.jar
error_prone_annotations-2.1.3.jar phantomjsdriver-1.4.4.jar selenium-opera-driver-3.9.1.jar
gson-2.8.2.jar scala-compiler-2.12.4.jar selenium-remote-driver-3.9.1.jar
guava-23.6-jre.jar scala-library-2.12.4.jar selenium-safari-driver-3.9.1.jar
httpclient-4.5.3.jar scala-reflect-2.12.4.jar selenium-support-3.9.1.jar
I start Scala via scala -cp "alljars/*" and can the do following:
val drv = new org.openqa.selenium.phantomjs.PhantomJSDriver
drv.get("https://www.google.com")
val q = drv.findElementByName("q")
q.sendKeys("rJava selenium")
q.submit
drv.getTitle
I think the following is roughly the same thing in R using rJava:
library(rJava)
.jinit()
jars <- dir("alljars", pattern = "*.jar", full.names = TRUE)
.jaddClassPath(jars)
drv <- .jnew('org/openqa/selenium/phantomjs/PhantomJSDriver')
drv$get("https://www.google.com")
q <- drv$findElementByName("q")
q$sendKeys("rJava selenium")
q$submit()
drv$getTitle()
This fails at the point q$sendKeys("rJava selenium") with the following error:
Error in .jcall("RJavaTools", "Ljava/lang/Object;", "invokeMethod", cl, :
java.lang.NoSuchMethodException: No suitable method for the given parameters
In RStudio, if I type q$ and press TAB, sendKeys is definitely in the list of available methods. I tried to be explicit about this, and tried:
keys <- .jnew("java/lang/String", "rJava selenium")
keys <- .jcast(keys, "java/lang/CharSequence", check = TRUE)
q <- .jcast(q, "org/openqa/selenium/WebElement", check = TRUE)
.jcall(q, "V", "sendKeys", keys)
which resulted in the following error:
Error in .jcall(q, "V", "sendKeys", keys) :
method sendKeys with signature (Ljava/lang/CharSequence;)V not found
q has class org/openqa/selenium/remote/RemoteWebElement in R, and org/openqa/selenium/WebElement in Scala; but in both cases the return is void and the required argument is CharSequence according to the javadocs. I tried a few variations of this--java.lang.String instead of CharSequence, RemoteWebElement instead of WebElement, etc., but no joy.
I doubt this is a problem with rJava, but I'm stumped nonetheless and need help!
Oh good grief. I didn't know about .jmethods. Running this:
> .jmethods(q, "sendKeys")
[1] "public void org.openqa.selenium.remote.RemoteWebElement.sendKeys(java.lang.CharSequence[])"
So, basically, my problem was that I was passing String instead of String[]. That is, instead of:
q$sendKeys("rJava selenium")
I can use:
q$sendKeys(.jarray("rJava selenium"))
The more you know...
I managed to compile the mruby code adding the mrubygem - mruby-require from https://github.com/mattn/mruby-require
However when I try to call the require './' I get an error. Below is my code:
inc.rb
def test(a, b)
print "Inside the include->test(..)"
return a+b
end
test1.rb
require 'inc.rb'
def helloworld(var1)
print 'hello world ' + var1 + ". Test number = " + test(4, 5)
end
helloworld('test')
When I execute test1.rb I get this error from mruby:
NoMethodError: undefined method 'puts' for main
After some analysis I found out the 'puts' is not working with mruby. Infact after adding mruby-require gem, no ruby code gets execute. Do I need to add any dependency with mruby-require?
Can someone help me please?
Update: Pasting the content of build_config.rb as requested. I have removed the lines which are commented.
build_config.rb
MRuby::Build.new do |conf|
if ENV['VisualStudioVersion'] || ENV['VSINSTALLDIR']
toolchain :visualcpp
else
toolchain :gcc
end
enable_debug
# adding the mruby-require library
conf.gem 'mrbgems/mruby-require'
conf.gembox 'default'
end
MRuby::Build.new('host-debug') do |conf|
if ENV['VisualStudioVersion'] || ENV['VSINSTALLDIR']
toolchain :visualcpp
else
toolchain :gcc
end
enable_debug
conf.gembox 'default'
conf.cc.defines = %w(ENABLE_DEBUG)
conf.gem :core => "mruby-bin-debugger"
end
The following quote is from its README.md:
When mruby-require is being used, additional mrbgems that appear after mruby-require in build_config.rb must be required to be used.
This is from your build_config.rb:
conf.gem 'mrbgems/mruby-require'
conf.gembox 'default'
The default gembox contains mruby-print. So either require mruby-print or preferably swap the lines to make it a built-in gem (the default behavior without mruby-require).
I recently rewrote a package to use the new(er) R reference class objects. I've exported the three classes using export() in the NAMESPACE file so as far as I'm aware that should work. However when I test build the package I get an error at lazy loading stage:
** preparing package for lazy loading
Error in file(con, "rb") : invalid 'description' argument
ERROR: lazy loading failed for package ‘PACKAGE_NAME_HERE’
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/PACKAGE_NAME_HERE’
I'm not sure what the problem is here. I don't know if it's relevant but the reference classes do store data on files in the tmp directory by having some fields set as accessor functions - I don't know if that's what s being complained about here when it says (con, "rb") which I guess is some connection thing. Does anybody have any ideas or advice for making sure reference classes get exported properly? My namespace is currently simple -
export(Main)
export(Mainseq)
export(Maintriplet)
Which are the three reference classes I exported by using #export tags in roxygen2.
What is it I'm doing (or not doing) that is throwing the lazy load error?
(ASIDE - I have no compiled code - all R, although the reference class methods do call some internal functions that are not exported, but these are supposed to be internal so I don't think I need to export them.
Thanks,
Ben.
EDIT:
My description file is as follows:
Package: HybRIDS
Type: Package
Title: Quick detection and dating of Recombinant Regions in DNA sequence data.
Version: 1.0
Date: 2013-03-13
Author: Ben J. Ward
Maintainer: Ben J. Ward <b.ward#uea.ac.uk>
Description: A simple R package for the quick detection and dating of Recombinant Regions in DNA sequence data.
License: GPL-2
Depends: ggplot2,grid,gridExtra,png,ape
I can't see what is wrong with this - the Depends are correct.
EDIT:
I've eliminated the first error with the description but I'm still getting the con error.
I think it's because the Mainseq class (which is nested in class Main) has some fields:
FullSequenceFile = "character",
FullSequence = function( value ) {
if( missing( value ) ){
as.character( read.dna( file = FullSequenceFile, format = "fasta", as.matrix = TRUE ) )
} else {
write.dna( value, file = FullSequenceFile, format = "fasta" )
}
},
InformativeSequenceFile = "character",
InformativeSequence = function( value ) {
if( missing( value ) ){
as.character( read.dna( file = InformativeSequenceFile, format = "fasta", as.matrix = TRUE ) )
} else {
write.dna( value, file = InformativeSequenceFile, format = "fasta" )
}
}
The idea being upon initialisation, the two character fields are filled with a path to a temp file in tmpdir, and when the variables are called or edited the files containing the variable data are read or written to. However it seems the variables are being accessed before this path is available because up package build the following happens:
** preparing package for lazy loading
Warning in file(con, "rb") :
cannot open file '/var/folders/kp/clkqvqn9739ffw2755zjwy74_skf_z/T//RtmpLB8ESC/FullSequenceaba52ac591f3': No such file or directory
Error in file(con, "rb") : cannot open the connection