docker build error ERROR: failed to solve: process "/bin/bash -c apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean" did not complete successfully: exit code: 100

[MilldrewAdvaita]

My aim is to build the image from the source code. I don't see any special instructions for building the image so I tried doing it with the docker build command, and the most recent commit without changing anything. On multiple branches.

When I run:

docker build -t single-cell .
or
docker image build -t single-cell . 

In the project root where the Dockerfile is

.
├── Dockerfile
├── LICENSE
├── R
├── README.md
├── configuration_file_for_integration_analysis.csv
├── docs
├── global.R
├── scripts
├── server.R
├── sh-bin
├── ui.R
└── www

I get the following error

[+] Building 12.7s (9/83)
 => [internal] load .dockerignore                                                                                                                                                                                                                                          0.0s
 => => transferring context: 2B                                                                                                                                                                                                                                            0.0s
 => [internal] load build definition from Dockerfile                                                                                                                                                                                                                       0.0s
 => => transferring dockerfile: 3.93kB                                                                                                                                                                                                                                     0.0s
 => [internal] load metadata for docker.io/kirstlab/asc_seurat:dynverse_v2.2                                                                                                                                                                                               0.6s
 => [internal] load build context                                                                                                                                                                                                                                          0.0s
 => => transferring context: 1.82kB                                                                                                                                                                                                                                        0.0s
 => [ 1/79] FROM docker.io/kirstlab/asc_seurat:dynverse_v2.2@sha256:c927953f47475c8a674eec97d27d5d39627ce3888262b212a62a3279646c39a3                                                                                                                                       0.0s
 => CACHED [ 2/79] WORKDIR /app                                                                                                                                                                                                                                            0.0s
 => CACHED [ 3/79] COPY www /app/www                                                                                                                                                                                                                                       0.0s
 => CACHED [ 4/79] COPY R /app/R                                                                                                                                                                                                                                           0.0s
 => ERROR [ 5/79] RUN apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean                                                                                                                                                                   12.1s
------
 > [ 5/79] RUN apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean:
#0 0.623 Get:2 http://deb.debian.org/debian testing InRelease [167 kB]
#0 0.866 Get:1 http://cdn-fastly.deb.debian.org/debian sid InRelease [199 kB]
#0 3.119 Get:3 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages.diff/Index [63.6 kB]
#0 3.128 Ign:3 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages.diff/Index
#0 3.233 Get:4 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages [9,565 kB]
#0 7.741 Reading package lists...
#0 12.08 E: Repository 'http://deb.debian.org/debian testing InRelease' changed its 'Codename' value from 'bookworm' to 'trixie'
------
Dockerfile:13
--------------------
  11 |     COPY R /app/R
  12 |
  13 | >>> RUN apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean
  14 |     RUN apt-get install -y libcurl4-openssl-dev unixodbc-dev && apt-get clean
  15 |     RUN apt-get install -y gfortran
--------------------
ERROR: failed to solve: process "/bin/bash -c apt-get update && apt-get install -y xml2 libxml2-dev libssl-dev && apt-get clean" did not complete successfully: exit code: 100

I will be working to fix this bug. If someone has encountered the same thing of found a solution we can work together using this thread.

Thanks!

[wendelljpereira]

Hi @MilldrewAdvaita,

Is there a reason you prefer to build the image from scratch to use the already built one? I tested, and access to the last image is still working well.

Regarding the error, it seems like your problem is related to the line "#0 12.08 E: Repository 'http://deb.debian.org/debian testing InRelease' changed its 'Codename' value from 'bookworm' to 'trixie'".

Doing a quick googling, I found this discussion that might help: https://groups.google.com/g/linux.debian.user/c/CBtJSiZDPJQ.

I am not testing this solution since it is not a bug on Asc-Seurat.

Best Regards,
Wendell

[MilldrewAdvaita]

This PR #22 is a proposed solution to this issue , @wendelljpereira

[MilldrewAdvaita]

@wendelljpereira if we build the image from source code we can develop the source code to meet our needs and then create a new image.

we will be iterating and scaling this application.

@wendelljpereira my intention is to keep our fork's main branch aligned with this projects main branch.

if you like I can let you know when we launch our application to production so you can take a look.

Thanks!