xz-utils required for installation

[bart1]

I noticed installation failed in the docker container rocker/tidyverse see below. This is resolved when xz-utils are installed. It might be good to add this to the system requirements or atleast improve the error message

(base) ...@...:~$ docker run rocker/tidyverse /bin/bash -c 'apt-get update; apt-get install -yy  cargo; R -e "remotes::install_cran(\"gifski\")"'
Get:1 http://security.ubuntu.com/ubuntu noble-security InRelease [126 kB]
Get:2 http://security.ubuntu.com/ubuntu noble-security/multiverse amd64 Packages [15.3 kB]
Get:3 http://archive.ubuntu.com/ubuntu noble InRelease [256 kB]
Get:4 http://security.ubuntu.com/ubuntu noble-security/main amd64 Packages [586 kB]
Get:5 http://security.ubuntu.com/ubuntu noble-security/restricted amd64 Packages [548 kB]
Get:6 http://security.ubuntu.com/ubuntu noble-security/universe amd64 Packages [725 kB]
Get:7 http://archive.ubuntu.com/ubuntu noble-updates InRelease [126 kB]
Get:8 http://archive.ubuntu.com/ubuntu noble-backports InRelease [126 kB]
Get:9 http://archive.ubuntu.com/ubuntu noble/multiverse amd64 Packages [331 kB]
Get:10 http://archive.ubuntu.com/ubuntu noble/main amd64 Packages [1,808 kB]
Get:11 http://archive.ubuntu.com/ubuntu noble/restricted amd64 Packages [117 kB]
Get:12 http://archive.ubuntu.com/ubuntu noble/universe amd64 Packages [19.3 MB]
Get:13 http://archive.ubuntu.com/ubuntu noble-updates/restricted amd64 Packages [548 kB]
Get:14 http://archive.ubuntu.com/ubuntu noble-updates/multiverse amd64 Packages [18.4 kB]
Get:15 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 Packages [812 kB]
Get:16 http://archive.ubuntu.com/ubuntu noble-updates/universe amd64 Packages [932 kB]
Get:17 http://archive.ubuntu.com/ubuntu noble-backports/universe amd64 Packages [11.8 kB]
Fetched 26.4 MB in 4s (7,360 kB/s)
Reading package lists...
Reading package lists...
Building dependency tree...
Reading state information...
The following additional packages will be installed:
  libstd-rust-1.75 libstd-rust-dev rustc
Suggested packages:
  cargo-doc llvm-17 lld-17 clang-17
The following NEW packages will be installed:
  cargo libstd-rust-1.75 libstd-rust-dev rustc
0 upgraded, 4 newly installed, 0 to remove and 8 not upgraded.
Need to get 69.9 MB of archives.
After this operation, 296 MB of additional disk space will be used.
Get:1 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 libstd-rust-1.75 amd64 1.75.0+dfsg0ubuntu1-0ubuntu7.1 [20.0 MB]
Get:2 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 libstd-rust-dev amd64 1.75.0+dfsg0ubuntu1-0ubuntu7.1 [40.6 MB]
Get:3 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 rustc amd64 1.75.0+dfsg0ubuntu1-0ubuntu7.1 [3,183 kB]
Get:4 http://archive.ubuntu.com/ubuntu noble-updates/main amd64 cargo amd64 1.75.0+dfsg0ubuntu1-0ubuntu7.1 [6,053 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 69.9 MB in 5s (12.8 MB/s)
Selecting previously unselected package libstd-rust-1.75:amd64.
(Reading database ... 26884 files and directories currently installed.)
Preparing to unpack .../libstd-rust-1.75_1.75.0+dfsg0ubuntu1-0ubuntu7.1_amd64.deb ...
Unpacking libstd-rust-1.75:amd64 (1.75.0+dfsg0ubuntu1-0ubuntu7.1) ...
Selecting previously unselected package libstd-rust-dev:amd64.
Preparing to unpack .../libstd-rust-dev_1.75.0+dfsg0ubuntu1-0ubuntu7.1_amd64.deb ...
Unpacking libstd-rust-dev:amd64 (1.75.0+dfsg0ubuntu1-0ubuntu7.1) ...
Selecting previously unselected package rustc.
Preparing to unpack .../rustc_1.75.0+dfsg0ubuntu1-0ubuntu7.1_amd64.deb ...
Unpacking rustc (1.75.0+dfsg0ubuntu1-0ubuntu7.1) ...
Selecting previously unselected package cargo.
Preparing to unpack .../cargo_1.75.0+dfsg0ubuntu1-0ubuntu7.1_amd64.deb ...
Unpacking cargo (1.75.0+dfsg0ubuntu1-0ubuntu7.1) ...
Setting up libstd-rust-1.75:amd64 (1.75.0+dfsg0ubuntu1-0ubuntu7.1) ...
Setting up libstd-rust-dev:amd64 (1.75.0+dfsg0ubuntu1-0ubuntu7.1) ...
Setting up rustc (1.75.0+dfsg0ubuntu1-0ubuntu7.1) ...
Setting up cargo (1.75.0+dfsg0ubuntu1-0ubuntu7.1) ...
Processing triggers for libc-bin (2.39-0ubuntu8.3) ...

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> remotes::install_cran("gifski")
Installing 1 packages: gifski
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://p3m.dev/cran/__linux__/noble/latest/src/contrib/gifski_1.32.0-1.tar.gz'
Content type 'binary/octet-stream' length 7178057 bytes (6.8 MB)
==================================================
downloaded 6.8 MB

* installing *source* package ‘gifski’ ...
** package ‘gifski’ successfully unpacked and MD5 sums checked
** using staged installation
Using /usr/bin/cargo
Rustc version: rustc 1.75.0 (82e1608df 2023-12-21) (built from a source tarball)
** libs
using C compiler: ‘gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include   -pthread -fvisibility=hidden -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wrapper.c -o wrapper.o
if [ -f myrustlib/vendor.tar.xz ]; then tar xf myrustlib/vendor.tar.xz && mkdir -p /tmp/RtmpEo5LiX/R.INSTALLd76999c2e3/gifski/src/.cargo && cp myrustlib/vendor-config.toml /tmp/RtmpEo5LiX/R.INSTALLd76999c2e3/gifski/src/.cargo/config.toml; fi
tar (child): xz: Cannot exec: No such file or directory
tar (child): Error is not recoverable: exiting now
tar: Child returned status 2
tar: Error is not recoverable: exiting now
make: *** [Makevars:14: myrustlib/target/release/libmyrustlib.a] Error 2
ERROR: compilation failed for package ‘gifski’
* removing ‘/usr/local/lib/R/site-library/gifski’

The downloaded source packages are in
	‘/tmp/RtmpyRrnWl/downloaded_packages’
> 
> 
Warning message:
In i.p(...) : installation of package ‘gifski’ had non-zero exit status

[jeroen]

Thanks. Using xz is the official R policy on Rust packages, so I think it should be part of the default R installation and we may assume it in packages. But maybe the rocker folks think different. https://cran.r-project.org/web/packages/using_rust.html

[bart1]

Do you think this should then be brought up in the rocker repository for a general solution?

[jeroen]

Yes I think so. I don't think it makes sense for R packages to test for the presence of standard tooling that is assumed by R.