Somehow my renku repositories all report errors in the builds, for example here:
I tried updating renku, but that didn’t help. Do you know what goes wrong? It is something general, as I have it in multiple repositories.
1 Like
Hi Remko,
We have encountered this problem over the last few weeks - it is due to an external dependency on rdfjson-lib. There is a quick fix here: Error during Environment creation - #10 by ralf.grubenmann where you can modify the Dockerfile slightly. It should solve the problem for that repository. Hopefully the fix is small enough to propagate to the other repos where it is erroring.
Let us know if that works!
Gavin
hi @rcnijzink ,
we have made a series of updates to our templates (including a fix for that failing external dependency). If you could edit your Dockerfile to match our newest dockerfile for python it would be great.
You can apply the same fix to your other repositories as needed, taking into account the type of project (R, python, bioc).
Best,
Pamela
Thanks! But the Docker image still fails unfortunately, but at a different point now:
Or with the other new Dockerfile:
So this issue was originally introduced by a breaking change in setuptools 58 that broke quite a few old packages. We fixed it in the renku 0.16.1.post1 hotfix and also collaborated with some downstream dependencies so they could fix it, which they did.
Only pyshacl fixed it in version 0.17.0 but then they broke it again in 0.17.0.post2 where they reintroduced the obsolete rdflib-jsonld library. Which in turn unfixed our hotfix release.
There is another issue where the templates have been updates for a new feature that will be included in the next version of renku, but the fallback that we provided for the templating engine didn’t work, that’s why you’re getting the new error.
Your Dockerfile currently looks like
[...]
ARG RENKU_VERSION={{ __renku_version__ | default("0.16.1.post1") }}
########################################################
# Do not edit this section and do not add anything below
# Install renku from pypi or from github if it's a dev version
RUN if [ -n "$RENKU_VERSION" ] ; then \
source .renku/venv/bin/activate ; \
currentversion=$(renku --version) ; \
if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
pip uninstall renku ; \
gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\3/p") ; \
if [ -n "$gitversion" ] ; then \
pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
else \
pip install --force renku==${RENKU_VERSION} ;\
fi \
fi \
fi
The {{ __renku_version__ | default("0.16.1.post1") }} is a mistake, the templating engine should have replace that with 0.16.1.post1 in old versions of renku, but clearly it didn’t. We’ll look into that.
if you change the end of your Dockerfile to
ARG RENKU_VERSION=0.16.1.post1
########################################################
# Do not edit this section and do not add anything below
# Install renku from pypi or from github if it's a dev version
RUN if [ -n "$RENKU_VERSION" ] ; then \
source .renku/venv/bin/activate ; \
currentversion=$(renku --version) ; \
if [ "$RENKU_VERSION" != "$currentversion" ] ; then \
pip uninstall renku ; \
gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\3/p") ; \
if [ -n "$gitversion" ] ; then \
pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ;\
else \
pip install --force renku==${RENKU_VERSION} pyshacl==0.17.0.post1 ;\
fi \
fi \
fi
it should work
I just updated the Dockerfile again with the last correction, but I still get an error, related now to the packages you mentioned:
ERROR: Cannot install pyshacl==0.17.0.post1 and renku==0.16.1.post1 because these package versions have conflicting dependencies. ERROR: ResolutionImpossible: for help visit https://pip.pypa.io/en/latest/user_guide/#fixing-conflicting-dependencies
That’s unfortunate behavior on the part of pip/pipx. When I tried it locally it complained but still installed.
We’re working on a hotfix renku version, 0.16.2 that fixes this (again…), which should be released relatively soon.
We have a 0.16.2 release that should fix it. so you can just change the Dockerfile to read
ARG RENKU_VERSION=0.16.2
Let me know if that works for you.
Yes, that worked indeed! Thanks!
I just used this fix:
ARG RENKU_VERSION=0.16.2
to finally get one of the renku project template dockerfiles to work (the bioconductor one)
It would be nice if you could correct them for future users !
Thanks !
Hi @bopekno, this is already done in the newest template - or were you having trouble with an older project?
Hi @rrrrrok, for some reasons I don’t fully understand one of my projects (https://sv-renku-git.epfl.ch/pulver/pontis-rna-seq-2021-te-activities/, I could give you access if you need / are interested) started failing to build even though I had not touched the Dockerfile.
I tried several things to get it back, in the end I just copied the Dockerfile from the renku bioconductor image, but the build still failed. I’ve copied the log at the end. What I got from it whas that this line was problematic, and so I changed it in the following commit, and the image build succeeded… not sure what to make of this ^^
Log for the failed build, using the latest renku bioconductor Dockerfile as is:
Running with gitlab-runner 14.2.0 (58ba2b95) on sv-renku-git-run.epfl.ch cMGas78W Preparing the "docker" executor 00:02 Using Docker executor with image docker:stable ... Pulling docker image docker:stable ... Using docker image sha256:b0757c55a1fdbb59c378fd34dde3e12bd25f68094dd69546cf5ca00ddbaa7a33 for docker:stable with digest docker@sha256:fd4d028713fd05a1fb896412805daed82c4a0cc84331d8dad00cb596d7ce3e3a ... Preparing environment 00:00 Running on runner-cmgas78w-project-461-concurrent-0 via e70a719a144d... Getting source from Git repository 00:01 Fetching changes with git depth set to 50... Reinitialized existing Git repository in /builds/pulver/pontis-rna-seq-2021-te-activities/.git/ Checking out caf6812f as master... Skipping Git submodules setup Executing "step_script" stage of the job script 08:19 Using docker image sha256:b0757c55a1fdbb59c378fd34dde3e12bd25f68094dd69546cf5ca00ddbaa7a33 for docker:stable with digest docker@sha256:fd4d028713fd05a1fb896412805daed82c4a0cc84331d8dad00cb596d7ce3e3a ... $ docker login -u gitlab-ci-token -p $CI_JOB_TOKEN http://$CI_REGISTRY WARNING! Using --password via the CLI is insecure. Use --password-stdin. WARNING! Your password will be stored unencrypted in /root/.docker/config.json. Configure a credential helper to remove this warning. See https://docs.docker.com/engine/reference/commandline/login/#credentials-store Login Succeeded $ CI_COMMIT_SHA_7=$(echo $CI_COMMIT_SHA | cut -c1-7) # collapsed multi-line command Step 1/7 : FROM renku/renkulab-bioc:RELEASE_3_12-0.10.1 ---> a6406b98aa62 Step 2/7 : COPY install.R /tmp/ ---> 89548ddca355 Step 3/7 : RUN R -f /tmp/install.R ---> Running in 887b3871f8f5 R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out" Copyright (C) 2020 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > BIOCONDUCTOR_VERSION = '3.12' > > #BiocManager::install(version = BIOCONDUCTOR_VERSION, update = TRUE, ask = FALSE, quiet = TRUE) > > pkgs <- c("plyr", "dplyr", "stringr", "GenomicFeatures", "biomaRt", "RMariaDB") > > ip <- rownames(installed.packages()) > pkgs <- setdiff(pkgs, ip) > print(pkgs) [1] "plyr" "dplyr" "GenomicFeatures" "biomaRt" [5] "RMariaDB" > > BiocManager::install(pkgs, version=BIOCONDUCTOR_VERSION, quiet=TRUE) Bioconductor version '3.12' is out-of-date; the current release version '3.14' is available with R version '4.1'; see https://bioconductor.org/install 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details replacement repositories: CRAN: https://packagemanager.rstudio.com/cran/__linux__/focal/2021-02-17 Bioconductor version 3.12 (BiocManager 1.30.12), R 4.0.3 (2020-10-10) Installing package(s) 'plyr', 'dplyr', 'GenomicFeatures', 'biomaRt', 'RMariaDB' also installing the dependencies ‘formatR’, ‘lambda.r’, ‘futile.options’, ‘matrixStats’, ‘futile.logger’, ‘snow’, ‘MatrixGenerics’, ‘DelayedArray’, ‘BiocParallel’, ‘Rhtslib’, ‘SummarizedExperiment’, ‘GenomeInfoDbData’, ‘blob’, ‘bitops’, ‘zlibbioc’, ‘Rsamtools’, ‘GenomicAlignments’, ‘dbplyr’, ‘bit’, ‘generics’, ‘tidyselect’, ‘BiocGenerics’, ‘S4Vectors’, ‘IRanges’, ‘GenomeInfoDb’, ‘GenomicRanges’, ‘AnnotationDbi’, ‘DBI’, ‘RSQLite’, ‘RCurl’, ‘XVector’, ‘Biostrings’, ‘rtracklayer’, ‘Biobase’, ‘XML’, ‘progress’, ‘BiocFileCache’, ‘bit64’, ‘hms’, ‘lubridate’, ‘plogr’ > Removing intermediate container 887b3871f8f5 ---> c700b7bf107e Step 4/7 : COPY requirements.txt /tmp/ ---> 288b727ecb04 Step 5/7 : RUN pip3 install -r /tmp/requirements.txt ---> Running in 290b5cfaea5f Collecting jupytext Downloading jupytext-1.13.3-py3-none-any.whl (296 kB) Requirement already satisfied: nbformat in /opt/conda/lib/python3.9/site-packages (from jupytext->-r /tmp/requirements.txt (line 1)) (5.1.3) Collecting toml Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) Requirement already satisfied: pyyaml in /opt/conda/lib/python3.9/site-packages (from jupytext->-r /tmp/requirements.txt (line 1)) (5.4.1) Collecting mdit-py-plugins Downloading mdit_py_plugins-0.3.0-py3-none-any.whl (43 kB) Collecting markdown-it-py~=1.0 Downloading markdown_it_py-1.1.0-py3-none-any.whl (83 kB) Requirement already satisfied: attrs<22,>=19 in /opt/conda/lib/python3.9/site-packages (from markdown-it-py~=1.0->jupytext->-r /tmp/requirements.txt (line 1)) (21.2.0) Requirement already satisfied: ipython-genutils in /opt/conda/lib/python3.9/site-packages (from nbformat->jupytext->-r /tmp/requirements.txt (line 1)) (0.2.0) Requirement already satisfied: traitlets>=4.1 in /opt/conda/lib/python3.9/site-packages (from nbformat->jupytext->-r /tmp/requirements.txt (line 1)) (5.0.5) Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /opt/conda/lib/python3.9/site-packages (from nbformat->jupytext->-r /tmp/requirements.txt (line 1)) (3.2.0) Requirement already satisfied: jupyter-core in /opt/conda/lib/python3.9/site-packages (from nbformat->jupytext->-r /tmp/requirements.txt (line 1)) (4.7.1) Requirement already satisfied: setuptools in /opt/conda/lib/python3.9/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->jupytext->-r /tmp/requirements.txt (line 1)) (57.5.0) Requirement already satisfied: six>=1.11.0 in /opt/conda/lib/python3.9/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->jupytext->-r /tmp/requirements.txt (line 1)) (1.16.0) Requirement already satisfied: pyrsistent>=0.14.0 in /opt/conda/lib/python3.9/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->jupytext->-r /tmp/requirements.txt (line 1)) (0.17.3) Installing collected packages: markdown-it-py, toml, mdit-py-plugins, jupytext Successfully installed jupytext-1.13.3 markdown-it-py-1.1.0 mdit-py-plugins-0.3.0 toml-0.10.2 WARNING: You are using pip version 21.2.4; however, version 21.3.1 is available. You should consider upgrading via the '/opt/conda/bin/python3 -m pip install --upgrade pip' command. Removing intermediate container 290b5cfaea5f ---> c267ebfe202b Step 6/7 : ARG RENKU_VERSION={{ __renku_version__ | default("0.16.2") }} ---> Running in c53c9b286d8c Removing intermediate container c53c9b286d8c ---> eedfb4d391fd Step 7/7 : RUN if [ -n "$RENKU_VERSION" ] ; then source .renku/venv/bin/activate ; currentversion=$(renku --version) ; if [ "$RENKU_VERSION" != "$currentversion" ] ; then pip uninstall renku -y ; gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; if [ -n "$gitversion" ] ; then pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ; else pip install --force renku==${RENKU_VERSION} ; fi fi fi ---> Running in 2c72c09e7490 /bin/sh: 1: source: not found /bin/sh: 1: renku: not found WARNING: Skipping renku as it is not installed. ERROR: Could not find a version that satisfies the requirement renku=={{ (from versions: 0.1.0.dev20180405, 0.1.0.dev20180518, 0.1.0.dev20180604, 0.1.0.dev20180614, 0.1.0.dev20180618, 0.1.0.dev20180621, 0.2.0.dev20180823, 0.2.0rc1, 0.2.0rc2.dev20180824, 0.2.0, 0.2.1.dev98, 0.3.0a1, 0.3.0a2.dev1, 0.3.0a2.dev9, 0.3.0a2.dev10, 0.3.0a2.dev11, 0.3.0a2.dev15, 0.3.0, 0.3.0.post1, 0.3.0.post2, 0.3.0.post3.dev1, 0.3.0.post3.dev9, 0.3.0.post3.dev10, 0.3.1, 0.3.2.dev11, 0.3.2, 0.3.2.post1, 0.3.2.post2.dev12, 0.3.3, 0.3.4.dev13, 0.3.4.dev16, 0.3.4.dev18, 0.3.4.dev20, 0.3.4.dev21, 0.3.4.dev28, 0.3.4.dev29, 0.3.4.dev30, 0.3.4.dev31, 0.3.4.dev33, 0.3.4.dev34, 0.3.4.dev35, 0.3.4.dev36, 0.3.4.dev37, 0.3.4.dev39, 0.3.4.dev40, 0.3.4.dev41, 0.3.4.dev44, 0.3.4.dev45, 0.3.4.dev46, 0.3.4.dev47, 0.3.4.dev49, 0.3.4.dev50, 0.3.4.dev51, 0.3.4.dev52, 0.3.4.dev53, 0.3.4.dev54, 0.3.4.dev56, 0.3.4.dev58, 0.3.4.dev61, 0.4.0a1, 0.4.0a2, 0.4.0a3, 0.4.0a4, 0.4.0a5, 0.4.0a6.dev2, 0.4.0, 0.4.1.dev5, 0.4.1.dev7, 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0.9.2.dev25, 0.9.2.dev26, 0.9.2.dev27, 0.9.2.dev28, 0.10.0, 0.10.1.dev5, 0.10.1.dev6, 0.10.1, 0.10.2, 0.10.3.dev1, 0.10.3.dev2, 0.10.3.dev3, 0.10.3.dev4, 0.10.3.dev5, 0.10.3.dev6, 0.10.3.dev7, 0.10.3.dev8, 0.10.3.dev10, 0.10.3.dev11, 0.10.3.dev14, 0.10.3.dev15, 0.10.3.dev17, 0.10.3.dev18, 0.10.3.dev19, 0.10.3.dev21, 0.10.3.dev22, 0.10.3.dev23, 0.10.3.dev24, 0.10.3.dev25, 0.10.3.dev26, 0.10.3.dev27, 0.10.3, 0.10.4.dev2, 0.10.4.dev3, 0.10.4.dev7, 0.10.4.dev10, 0.10.4.dev12, 0.10.4.dev13, 0.10.4.dev14, 0.10.4.dev16, 0.10.4.dev17, 0.10.4.dev18, 0.10.4.dev19, 0.10.4.dev25, 0.10.4.dev26, 0.10.4.dev27, 0.10.4.dev28, 0.10.4.dev29, 0.10.4.dev30, 0.10.4.dev31, 0.10.4.dev33, 0.10.4.dev35, 0.10.4, 0.10.5.dev1, 0.10.5.dev3, 0.10.5.dev4, 0.10.5.dev5, 0.10.5.dev6, 0.10.5.dev7, 0.10.5.dev9, 0.10.5.dev10, 0.10.5.dev11, 0.10.5.dev13, 0.10.5.dev14, 0.10.5.dev15, 0.10.5.dev16, 0.10.5.dev17, 0.10.5.dev18, 0.10.5.dev19, 0.10.5.dev20, 0.10.5.dev21, 0.10.5.dev30, 0.10.5.dev31, 0.10.5.dev62, 0.10.5.dev63, 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0.12.3.dev20, 0.12.3.dev21, 0.12.3.dev23, 0.12.3, 0.13.0, 0.13.1.dev3, 0.13.1.dev4, 0.13.1.dev5, 0.13.1.dev6, 0.13.1.dev7, 0.13.1.dev8, 0.13.1.dev9, 0.13.1.dev13, 0.13.1.dev14, 0.13.1.dev15, 0.13.1.dev17, 0.13.1.dev20, 0.13.1.dev21, 0.13.1.dev22, 0.13.1.dev23, 0.13.1.dev27, 0.13.1.dev28, 0.13.1.dev29, 0.13.1.dev31, 0.13.1.dev32, 0.13.1.dev33, 0.14.0, 0.14.1.dev3, 0.14.1.dev5, 0.14.1.dev6, 0.14.1.dev7, 0.14.1, 0.14.2.dev2, 0.14.2.dev3, 0.14.2.dev6, 0.14.2.dev8, 0.14.2, 0.14.3.dev1, 0.14.3.dev3, 0.14.3.dev5, 0.14.3.dev6, 0.14.3.dev7, 0.14.3.dev9, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.16.1.post1, 0.16.2, 0.17.0rc1, 1.0.0rc1, 1.0.0, 1.0.1) ERROR: No matching distribution found for renku=={{ WARNING: You are using pip version 21.2.4; however, version 21.3.1 is available. You should consider upgrading via the '/opt/conda/bin/python3 -m pip install --upgrade pip' command. The command '/bin/sh -c if [ -n "$RENKU_VERSION" ] ; then source .renku/venv/bin/activate ; currentversion=$(renku --version) ; if [ "$RENKU_VERSION" != "$currentversion" ] ; then pip uninstall renku -y ; gitversion=$(echo "$RENKU_VERSION" | sed -n "s/^[[:digit:]]\+\.[[:digit:]]\+\.[[:digit:]]\+\(rc[[:digit:]]\+\)*\(\.dev[[:digit:]]\+\)*\(+g\([a-f0-9]\+\)\)*\(+dirty\)*$/\4/p") ; if [ -n "$gitversion" ] ; then pip install --force "git+https://github.com/SwissDataScienceCenter/renku-python.git@$gitversion" ; else pip install --force renku==${RENKU_VERSION} ; fi fi fi' returned a non-zero code: 1 Cleaning up file based variables 00:01 ERROR: Job failed: exit code 1
Hi @bopekno I see what’s happening here - I believe you copied over the whole Dockerfile from the template - this is using Jinja templating for certain parts, in this case the renku version. The template is rendered by renku when the project is created and is not meant to be used verbatim. That’s why you have a line like
ARG RENKU_VERSION={{ __renku_version__ | default("0.16.2") }}
You should replace it with
ARG RENKU_VERSION=0.16.2
and the image should build again.