Installing on a Raspberry pi 4 (64 bits)

[marinmarcillat]

Hello ! I've been trying to install a local instance of Biigle on a rpi4 for testing purposes. But I'm stuck during the build step of the core.
Here are first every commands that I ran, if somebody want to reproduce.

What I've done yet

• Burning a pi os 64 lite to a sd card
• Installing docker

# Install some required packages first
sudo apt update
sudo apt install -y \
     apt-transport-https \
     ca-certificates \
     curl \
     gnupg2 \
     software-properties-common


# Get the Docker signing key for packages
curl -fsSL https://download.docker.com/linux/$(. /etc/os-release; echo "$ID")/gpg | sudo apt-key add -

# Add the Docker official repos
echo "deb [arch=$(dpkg --print-architecture)] https://download.docker.com/linux/$(. /etc/os-release; echo "$ID") \
     $(lsb_release -cs) stable" | \
    sudo tee /etc/apt/sources.list.d/docker.list

# Install Docker
sudo apt update
sudo apt install -y --no-install-recommends \
    docker-ce \
    cgroupfs-mount

sudo systemctl enable --now docker

sudo usermod -aG docker pi

• Install docker compose

DOCKER_CONFIG=${DOCKER_CONFIG:-$HOME/.docker}
mkdir -p $DOCKER_CONFIG/cli-plugins

curl -SL https://github.com/docker/compose/releases/download/v2.3.3/docker-compose-linux-aarch64 -o $DOCKER_CONFIG/cli-plugins/docker-compose
chmod +x $DOCKER_CONFIG/cli-plugins/docker-compose

• Install php 8.1

echo "deb https://packages.sury.org/php/ $(lsb_release -sc) main"\
 | sudo tee /etc/apt/sources.list.d/sury-php.list
 
 wget -qO - https://packages.sury.org/php/apt.gpg | sudo apt-key add -
 
 sudo apt update
 
 sudo apt install -y php8.1-common php8.1-cli

• Install composer (not sure if this is necessary, but just in case)

wget -O composer-setup.php https://getcomposer.org/installer
sudo php composer-setup.php --install-dir=/usr/local/bin --filename=composer
rm -rf composer-setup.php

• Clone Biigle core, branch arm64v8
• Copy .env.example to .env and edit parameters
• ./build.sh

What is going wrong

pi@raspberrypi:~/biigle/core $ ./build.sh
Sending build context to Docker daemon  13.07MB
Step 1/24 : FROM arm64v8/php:8.0-fpm-alpine
 ---> 5a9452dc4996
Step 2/24 : MAINTAINER Martin Zurowietz <martin@cebitec.uni-bielefeld.de>
 ---> Using cache
 ---> 84b6a47c8b21
Step 3/24 : LABEL org.opencontainers.image.source https://github.com/biigle/core
 ---> Using cache
 ---> 7f56f9f86412
Step 4/24 : RUN ln -s "$PHP_INI_DIR/php.ini-production" "$PHP_INI_DIR/php.ini"
 ---> Using cache
 ---> 0007aa6b6493
Step 5/24 : ADD ".docker/all-php.ini" "$PHP_INI_DIR/conf.d/all.ini"
 ---> Using cache
 ---> a454984c0a25
Step 6/24 : ADD ".docker/app-php.ini" "$PHP_INI_DIR/conf.d/app.ini"
 ---> Using cache
 ---> c889a2cd3f87
Step 7/24 : RUN apk add --no-cache         openssl         postgresql         libxml2         libzip     && apk add --no-cache --virtual .build-deps         postgresql-dev         libxml2-dev         libzip-dev     && docker-php-ext-configure pgsql -with-pgsql=/usr/local/pgsql     && docker-php-ext-install -j$(nproc)         pdo         pdo_pgsql         pgsql         zip         exif         soap     && apk del --purge .build-deps
 ---> Using cache
 ---> 92be0073f975
Step 8/24 : RUN [ -z "$HTTP_PROXY" ] || pear config-set http_proxy $HTTP_PROXY
 ---> Using cache
 ---> f21d16eaab52
Step 9/24 : RUN apk add --no-cache yaml     && apk add --no-cache --virtual .build-deps g++ make autoconf yaml-dev     && pecl install yaml     && docker-php-ext-enable yaml     && apk del --purge .build-deps
 ---> Running in 58d145d8b65f
fetch https://dl-cdn.alpinelinux.org/alpine/v3.16/main/aarch64/APKINDEX.tar.gz
fetch https://dl-cdn.alpinelinux.org/alpine/v3.16/community/aarch64/APKINDEX.tar.gz
(1/1) Installing yaml (0.2.5-r0)
OK: 44 MiB in 49 packages
fetch https://dl-cdn.alpinelinux.org/alpine/v3.16/main/aarch64/APKINDEX.tar.gz
fetch https://dl-cdn.alpinelinux.org/alpine/v3.16/community/aarch64/APKINDEX.tar.gz
(1/18) Installing binutils (2.38-r3)
(2/18) Installing libgomp (11.2.1_git20220219-r2)
(3/18) Installing libatomic (11.2.1_git20220219-r2)
(4/18) Installing gmp (6.2.1-r2)
(5/18) Installing isl22 (0.22-r0)
(6/18) Installing mpfr4 (4.1.0-r0)
(7/18) Installing mpc1 (1.2.1-r0)
(8/18) Installing gcc (11.2.1_git20220219-r2)
(9/18) Installing musl-dev (1.2.3-r0)
(10/18) Installing libc-dev (0.7.2-r3)
(11/18) Installing g++ (11.2.1_git20220219-r2)
(12/18) Installing make (4.3-r0)
(13/18) Installing m4 (1.4.19-r1)
(14/18) Installing perl (5.34.1-r0)
(15/18) Installing autoconf (2.71-r0)
(16/18) Installing pkgconf (1.8.0-r1)
(17/18) Installing yaml-dev (0.2.5-r0)
(18/18) Installing .build-deps (20221011.073403)
Executing busybox-1.35.0-r17.trigger
OK: 266 MiB in 67 packages
No releases available for package "pecl.php.net/yaml"
install failed
Sending build context to Docker daemon  13.07MB
Step 1/26 : FROM ghcr.io/biigle/app:arm64v8 as intermediate
Sending build context to Docker daemon  13.07MB
Step 1/13 : FROM ghcr.io/biigle/app:arm64v8 as intermediate
3 errors occurred:
        * Status: The command '/bin/sh -c apk add --no-cache yaml     && apk add --no-cache --virtual .build-deps g++ make autoconf yaml-dev     && pecl install yaml     && docker-php-ext-enable yaml     && apk del --purge .build-deps' returned a non-zero code: 1, Code: 1
        * Status: manifest unknown, Code: 1
        * Status: manifest unknown, Code: 1

My different versions:

• Docker version 20.10.18
• Docker Compose version v2.3.3
• php v8.1

I've tried to understand the underlying of this issue, but I can't find anything. Any ideas ?

[mzur]

The relevant error is this:

No releases available for package "pecl.php.net/yaml"
install failed

So it fails to install the PHP YAML extension through PECL. Maybe it has something to do with the system architecture. Unfortunately, I don't have an ARM machine available to test this. Maybe you can learn more if you execute these steps manually in a new Docker container (docker run --rm -it arm64v8/php:8.0-fpm-alpine sh).