SBRG / cobrame

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)
Other
34 stars 17 forks source link

Cannot build docker image #39

Open mheydasch opened 3 months ago

mheydasch commented 3 months ago
docker build -t cobrame .
[+] Building 6.2s (12/15)                                                                                                                            docker:default
 => [internal] load build definition from Dockerfile                                                                                                           0.0s
 => => transferring dockerfile: 2.45kB                                                                                                                         0.0s
 => WARN: NoEmptyContinuation: Empty continuation line (line 78)                                                                                               0.0s
 => [internal] load metadata for docker.io/sbrg/cobrame:dependencies                                                                                           0.8s
 => [internal] load metadata for docker.io/sbrg/cobrame:qminos                                                                                                 0.8s
 => [internal] load .dockerignore                                                                                                                              0.0s
 => => transferring context: 2B                                                                                                                                0.0s
 => [stage-1 1/9] FROM docker.io/sbrg/cobrame:dependencies@sha256:4670c2c461b99e4e7a45598cf24702754ac055eedbf79ecb7a6b42ecbdefebd8                             0.0s
 => [internal] load build context                                                                                                                              0.0s
 => => transferring context: 30B                                                                                                                               0.0s
 => [qminos 1/1] FROM docker.io/sbrg/cobrame:qminos@sha256:a0b7a30c68cf70de339d8edc906d33adb66e24212f44a3fee817fd68225bb50c                                    0.0s
 => CACHED [stage-1 2/9] COPY --from=qminos /source/libminos.a .                                                                                               0.0s
 => CACHED [stage-1 3/9] COPY --from=qminos /source/libquadminos.a .                                                                                           0.0s
 => CACHED [stage-1 4/9] RUN echo "@community http://dl-cdn.alpinelinux.org/alpine/edge/community" >> /etc/apk/repositories                                    0.0s
 => CACHED [stage-1 5/9] COPY nothing.txt soplex-3.1.1.tg* /source/                                                                                            0.0s
 => ERROR [stage-1 6/9] RUN apk add --no-cache  shadow                                                                                                         5.2s
------
 > [stage-1 6/9] RUN apk add --no-cache         shadow :
4.745 fetch http://dl-cdn.alpinelinux.org/alpine/v3.6/main/x86_64/APKINDEX.tar.gz
5.045 fetch http://dl-cdn.alpinelinux.org/alpine/v3.6/community/x86_64/APKINDEX.tar.gz
5.132 fetch http://dl-cdn.alpinelinux.org/alpine/edge/community/x86_64/APKINDEX.tar.gz
5.170 WARNING: Ignoring http://dl-cdn.alpinelinux.org/alpine/edge/community/x86_64/APKINDEX.tar.gz: UNTRUSTED signature
5.194 WARNING: The repository tag for world dependency 'openblas-dev@community' does not exist
5.194 ERROR: Not committing changes due to missing repository tags. Use --force to override.
------

 2 warnings found (use docker --debug to expand):
 - NoEmptyContinuation: Empty continuation line (line 78)
 - UndefinedVar: Usage of undefined variable '$NB_USER' (line 27)
Dockerfile:25
--------------------
  23 |          shadow \
  24 |     "
  25 | >>> RUN apk add --no-cache $PACKAGES
  26 |
  27 |     ENV NB_USER=meuser \
--------------------
ERROR: failed to solve: process "/bin/sh -c apk add --no-cache $PACKAGES" did not complete successfully: exit code: 255
(etfl9) mheydasch: ~/workspace/cobrame/docker$ ls
Dockerfile  README.rst  ZscalerRootCertificate-2048-SHA256.crt  nothing.txt  soplex-release-311.tar.gz
(etfl9) mheydasch:~/workspace/cobrame/docker$ sudo docker build -t cobrame .
[+] Building 10.1s (12/15)                                                                                                                           docker:default
 => [internal] load build definition from Dockerfile                                                                                                           0.0s
 => => transferring dockerfile: 2.45kB                                                                                                                         0.0s
 => WARN: NoEmptyContinuation: Empty continuation line (line 78)                                                                                               0.0s
 => [internal] load metadata for docker.io/sbrg/cobrame:dependencies                                                                                           0.4s
 => [internal] load metadata for docker.io/sbrg/cobrame:qminos                                                                                                 0.5s
 => [internal] load .dockerignore                                                                                                                              0.0s
 => => transferring context: 2B                                                                                                                                0.0s
 => [stage-1 1/9] FROM docker.io/sbrg/cobrame:dependencies@sha256:4670c2c461b99e4e7a45598cf24702754ac055eedbf79ecb7a6b42ecbdefebd8                             0.0s
 => [internal] load build context                                                                                                                              1.8s
 => => transferring context: 5.05MB                                                                                                                            1.8s
 => [qminos 1/1] FROM docker.io/sbrg/cobrame:qminos@sha256:a0b7a30c68cf70de339d8edc906d33adb66e24212f44a3fee817fd68225bb50c                                    0.0s
 => CACHED [stage-1 2/9] COPY --from=qminos /source/libminos.a .                                                                                               0.0s
 => CACHED [stage-1 3/9] COPY --from=qminos /source/libquadminos.a .                                                                                           0.0s
 => CACHED [stage-1 4/9] RUN echo "@community http://dl-cdn.alpinelinux.org/alpine/edge/community" >> /etc/apk/repositories                                    0.0s
 => [stage-1 5/9] COPY nothing.txt soplex-3.1.1.tg* /source/                                                                                                   0.1s
 => ERROR [stage-1 6/9] RUN apk add --no-cache  shadow                                                                                                         6.7s
------
 > [stage-1 6/9] RUN apk add --no-cache         shadow :
6.242 fetch http://dl-cdn.alpinelinux.org/alpine/v3.6/main/x86_64/APKINDEX.tar.gz
6.496 fetch http://dl-cdn.alpinelinux.org/alpine/v3.6/community/x86_64/APKINDEX.tar.gz
6.582 fetch http://dl-cdn.alpinelinux.org/alpine/edge/community/x86_64/APKINDEX.tar.gz
6.621 WARNING: Ignoring http://dl-cdn.alpinelinux.org/alpine/edge/community/x86_64/APKINDEX.tar.gz: UNTRUSTED signature
6.640 WARNING: The repository tag for world dependency 'openblas-dev@community' does not exist
6.640 ERROR: Not committing changes due to missing repository tags. Use --force to override.
------

 2 warnings found (use docker --debug to expand):
 - NoEmptyContinuation: Empty continuation line (line 78)
 - UndefinedVar: Usage of undefined variable '$NB_USER' (line 27)
Dockerfile:25
--------------------
  23 |          shadow \
  24 |     "
  25 | >>> RUN apk add --no-cache $PACKAGES
  26 |
  27 |     ENV NB_USER=meuser \
--------------------
ERROR: failed to solve: process "/bin/sh -c apk add --no-cache $PACKAGES" did not complete successfully: exit code: 255

using --allow-untrusted -force for RUN apk update will also just result in a segmentation error.