I am trying to use the library libspatialite to extend sqlite on a NetBSD platform. I've taken the first step of creating a package for libspatialite in pkgsrc (libspatialite-4.1.1). The package appears to work; pkg_info says it's installed and I've verified that the files from PLIST (in code chunk below) have been installed in /usr/pkg/. However, when I try to install the package I built for spatialite-tools, configure says that libspatialite isn't installed. Also I can't figure out how to load the library in sqlite3 with load_extenstion(X,Y); what is the library file referred to in the documentation?
pkgsrc/databases/libsqlite/PLIST:
#comment $NetBSD$
include/spatialite.h
include/spatialite/debug.h
include/spatialite/gaiaaux.h
include/spatialite/gaiaexif.h
include/spatialite/gaiageo.h
include/spatialite/geopackage.h
include/spatialite/gg_advanced.h
include/spatialite/gg_const.h
include/spatialite/gg_core.h
include/spatialite/gg_dxf.h
include/spatialite/gg_dynamic.h
include/spatialite/gg_formats.h
include/spatialite/gg_mbr.h
include/spatialite/gg_structs.h
include/spatialite/gg_wfs.h
include/spatialite/gg_xml.h
include/spatialite/spatialite.h
include/spatialite/sqlite.h
lib/libspatialite.la
lib/pkgconfig/spatialite.pc
Do you have a buildlink3.mk file in the libspatialite package?
If not:
In order to avoid a package building against implicit dependencies pkgsrc only makes libraries which have been explicitly listed visible to the building package.
This stop the issue of a package picking up an optional dependency which just happens to be installed, then building a binary package which uses that library but does not have it listed in the package metadata. The resultant binary package will work fine on that system... until the optional dependency is removed, and will fail on any other system without that hidden dependency.
Anyway... buildlink3.mk files are used in pkgsrc to make the necessary files visible during a build. A libspatialite buildlink3.mk might look like the below (adjust 1.0 to the current lib version)
# $NetBSD$
BUILDLINK_TREE+= libspatialite
.if !defined(LIBSPATIALITE_BUILDLINK3_MK)
LIBSPATIALITE_BUILDLINK3_MK:=
BUILDLINK_API_DEPENDS.libspatialite+=libspatialite>=1.0
BUILDLINK_PKGSRCDIR.libspatialite?= ../../devel/libspatialite
BUILDLINK_LIBDIRS.libspatialite+= lib/spatialite
BUILDLINK_RPATHDIRS.libspatialite+= lib/spatialite
BUILDLINK_INCDIRS.libspatialite+= include/spatialite
.endif # LIBSPATIALITE_BUILDLINK3_MK
BUILDLINK_TREE+= -libspatialite
Then in the depending package add something like:
.include "../../devel/libspatialite/buildlink3.mk"
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antonio wants to draw more attention to this question:
Explain what is the proper workflow when you are building two packages, where one depends on the other. What is the correct way to run devtools::check() on the depending-on package?
I want to add a local package dependency using R devtools.
The suggested way to add packages to the package DESCRIPTION file is one of the two functions use_package() and use_dev_package(), from the usethis package. The latter adds a dependency on an in-development package. The function help shows the following prototype:
use_dev_package(package, type = "Imports", remote = NULL)
where remote is
a character string to specify the remote, e.g. ‘"gitlab::jimhester/covr"’, using any syntax supported by the remotes package.
The remotes vignette shows the following
# Local
Remotes: local::/pkgs/testthat
So the command should be along these lines:
use_dev_package(foopack, type = "Imports", remote = "local::<foopack>")
However, what should be the path to the foopack. An absolute one or relative to project dir? The root package directory or the R directory with the code, or perhaps the foopack.tar.gz build?
All attempts failed for me.
Needless to say that, beyond having the local dependency properly listed in the DESCRIPTION file, I need it to be seen by the devtools build & check functions.
Edit
As regards use_dev_package(), I found a solution:
if I use devtools::check(), then the dependency appears in the search path, and use_dev_package() does not complain any more (see answer below).
However, it is still unclear to me what arguments should I use to make a development check() for the main package, in particular when the package has a vignette.
Ideally, I should be able to pass the check with local dependencies by passing cran = FALSE, but this still gives
"Package required but not available".
It seems that I have to check the local dependencies before adding them to the description file.
devtools::check("path/to/foopack")
usethis::use_dev_package("foopack", remote ="local::path/to/foopack")
The paths can be relative or absolute, and even a single colon works.
It might be worth noting that, when I build the main package, I can use the ordinary:
devtools::build()
but, for a successful check, I need to use the remote argument:
devtools::check(remote = TRUE)
I can't see a rationale for restating what is in the DESCRIPTION file, but I do not have enough expertise to say it's a bug.
Let's see what the others say in this regard.
Edit
Unfortunately, it seems that the remote argument above does not apply to vignettes. So, if I add a vignette to the package, checks fail with local packages
Until an actual solution is found, all I can do is (sadly) to ignore vignette checks:
devtools::check(remote = TRUE, vignettes = FALSE)
In Python, if I install mambaforge or conda then I can make a file with extension .yml and then inside it list the name of packages I want to install alongside their specific versions. How can I do a similar way of installing packages in Julia?
I understand that if I have already installed Julia packages by addcommand in package manager, then I have a file named Project.toml which I can use to install the same packages later. However, this still does not look as good as Python's way of installing packages.
Upon further investigation I realized that to install Julia packages from an empty Prokect.tomlfile, I should add [deps]in the file followed by the name of packages I want and then give each package a uuidwhich can be found here. For example:
[deps]
Images = "916415d5-f1e6-5110-898d-aaa5f9f070e0"
After all , this is still tedious as it needs to find all those uuids.
How can I install packages in Julia the same way I described for Python?
Is there a particular reason that you want to write package names to a .yml file and then read the packages from there? After all, you can generate the Project file and add multiple dependencies automatically:
(#v1.8) pkg> generate MyProject # or whatever name you like
(#v1.8) pkg> activate MyProject
(MyProject) pkg> add Countries Crayons CSV # some example packages
(In recent versions of Julia, an installation prompt will appear if a package isn't already installed).
Speaking from experience, learning to use environments in Julia can be challenging to a new user, but rewarding! The documentation for Pkg.jl are helpful here.
If you are just assembling an environment for your own code, there is probably no need for you to manually edit Project.toml. On the other hand, if you are maintaining a package, you might wish to edit the file directly (e.g., for specifying compatability).
Maybe you can use this:
using TOML
using HTTP
using DataStructures
## Get the Registry.toml file if it already doesn't exist in the current directory
function raed_reg()
if !isfile("Registry.toml")
HTTP.download(
"https://raw.githubusercontent.com/JuliaRegistries/General/master/Registry.toml",
"Registry.toml"
)
end
reg = TOML.parsefile("Registry.toml")["packages"]
return reg
end
## Find the UUID of a specific package from the Registry.toml file
function get_uuid(pkg_name)
reg = raed_reg()
for (uuid, pkg) in reg
if pkg["name"] == pkg_name
return uuid
end
end
end
## Create a dictionary for the gotten UUIDs, by setting the name = UUID and convert it to a project.toml file
function create_project_toml(Pkgs::Vector{String})
reg = raed_reg()
pkgs_names_uuid = OrderedDict{AbstractString, AbstractString}()
pkgs_names_uuid["[deps]"] = ""
for pkg in Pkgs
_uuid = get_uuid(pkg)
pkgs_names_uuid[pkg] = _uuid
end
open("project.toml", "w") do io
TOML.print(io, pkgs_names_uuid)
end
end
## Test on the packages "ClusterAnalysis" and "EvoTrees"
create_project_toml(["ClusterAnalysis", "EvoTrees"])
I've just pushed a package on Github, which I regularly document, test and install on my machine with the following R commands:
library(devtools)
library(testthat)
setwd("bimark")
document() # cheers to roxygen2!
use_testthat() # cheers to testthat!
setwd("..")
install("bimark", build_vignettes=TRUE) # cheers to R-markdown!
library(bimark)
test_package("bimark")
run_examples("bimark")
However, installing it from github with:
install_github("iago-lito/bimark")
does not work since
ERROR: a 'NAMESPACE' file is required
The reason why I do not version my NAMESPACE file is that it is automatically generated by devtools::document().
How can I make the full doc-test-installation easy for my users without versionning non-source files such as NAMESPACE?
NAMESPACE is autogenerated only if devtools::document() and roxygen2 is used. Otherwise, you create it by hand. Therefore, I think they consider it as a source file which needs to be versioned.
I want to use packrat on a Windows 7 machine with no internet connection.
I have downloaded all binary packages from http://cran.r-project.org/bin/windows/contrib/3.1/ into the local folder C:/xyz/CRAN_3_1.
The problem is now that
packrat::init(options=list(local.repos="C:/xyz/CRAN_3_1"))
throws a bunch of warnings and errors like
Warning: unable to access index for repository http://cran.rstudio/bin/...
Warning: unable to access index for repository http://cran.rstudio/src/...
Fetching sources for Rcpp (0.11.4) ... Failed
Package Rcpp not available in repository or locally
As it seems packrat tries to find
the binary version of Rcpp on CRAN (fails since there is no internet connection)
the source of Rcpp on CRAN (fails since there is no internet connection)
the local source of the package (fails since I only have the binaries)
What I don't understand is why packrat does not also search for the local binary package...
Question 1: I could download the source CRAN repository to get around this problem. But I would like to know from you guys whether there is an easier solution to this, i.e., whether it is possible to make packrat accept a local binary repo.
Question 2: When I create my own package myPackage with packrat enabled, will the myPackage-specific local packrat library also be included in the package? That is, assume that I give the binary myPackage zip File to one of my colleagues who does not have one of the packages that myPackage depends on (let's say Rcpp). Will Rcpp be included in myPackage when I use packrat? Or does my colleague have to install Rcpp himself?
I managed to hack around this problem. Please bear in mind that I have never used packrat before and that I do not know its "proper" behaviour. But my impression is that the hack works.
Here is how I did it:
Open your project, load packrat via library(packrat)
type fixInNamespace("snapshotImpl",ns="packrat") - a window opens - copy its content into the clipboard
Go to /yourProjDir/ and create a file snapshotImplFix.R
Copy the clipboard's content into this file ...
... but change the first line to
snapshotImplFix=function (project, available = NULL, lib.loc = libDir(project),
dry.run = FALSE, ignore.stale = FALSE, prompt = interactive(),
auto.snapshot = FALSE, verbose = TRUE, fallback.ok = FALSE,
snapshot.sources = FALSE)
Note snapshot.sources = FALSE! Save and close the file.
Create /yourProjDir/.Rprofile and add
setHook(packageEvent("packrat","onLoad"),function(...) {
source("./snapshotImplFix.R");
tmpfun=get("snapshotImpl",envir=asNamespace("packrat"));
environment(snapshotImplFix)=environment(tmpfun);
utils::assignInNamespace(x="snapshotImpl",value=snapshotImplFix,ns="packrat");})
Points 2-6 fix the problem with the snapshot.sources argument being TRUE by default (I did not find a better way to change that...)
Finally, we have to tell packrat to take our local repository. It's important that you have the right folder structure. Therefore I moved the repo from C:/xyz/CRAN_3_1 to C:/xyz/CRAN_3_1/bin/windows/contrib/3.1. Do not forget to run library(tools);write_PACKAGES("C:/xyz/CRAN_3_1/bin/windows/contrib/3.1"); if you also have to move your files.
Open yourProjDir/.Rprofile again and add at the end
local({r=getOption("repos");r["CRAN"]="file:///C:/xyz/CRAN_3_1";r["CRANextra"]=r["CRAN"];options(repos=r)})
Note the 3 / right after file! Save and exit file.
Close the project and re-open.
Now you can execute packrat::init() and it should run without errors.
It would be great if someone with more experience regarding packrat could give his/her input so that I can be sure that this hack works. Any pointers to proper solutions are highly appreciated, of course.
Mac64 R> install.packages("quantmod")
Yields a discouraging message. Namely,
Warning: unable to access index for repository http://www.ibiblio.org/pub/languages /R/CRAN/bin/macosx/leopard/contrib/2.12
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘quantmod’ is not available
No big deal, just pass in a different repo, like this:
Mac64 R> install.packages("quantmod", repo="http://R.research.att.com")
And all is well. But how do you set the default repo so you don't need to pass it in every time? In Ubuntu, there is a file that manages this but the documentation for Mac OS X is a bit sparse.
Can't tell if you are using the R64.app GUI but guessing that you may not be. You can set the default repository in the r/Preferences/ panels if you are using R64.app. Personally I use the repository at the same facility that hosts StatLib which shows up on some dialogs something like USA (PA 1) but on my Preferences pane is http://lib.stat.cmu.edu/R/CRAN . Here is a bit of ?options that may be of interest:
repos:
URLs of the repositories for use by update.packages. Defaults to
c(CRAN="#CRAN#"), a value that causes some utilities to prompt for
a CRAN mirror. To avoid this do set the CRAN mirror, by something
like local({r <- getOption("repos"); r["CRAN"] <- "http://my.local.cran";
options(repos=r)}).
Note that you can add more repositories (Bioconductor and Omegahat, notably)
using setRepositories().
At the moment my "other repository" setting in the the R64.app is http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.12/ , because I was doing something to get a package that was only at Ripley's site but it is usually set to R--Forge: http://r-forge.r-project.org/
See the help for function setRepositories; you can manage your list of repositories in a GUI or by editing the file R_HOME/etc/repositories.
You can know what is your R_HOME directly in R:
> R.home()
[1] "/usr/lib/R"
http://cran.r-project.org/doc/manuals/R-admin.html#Managing-libraries
Try creating the folders and files as suggested for UNIX-like systems; chances are that R will check for them on OS X as well when looking for repo settings.