sneumann
commented
2 years ago Hi, can you provide the Dockerfile ? Yours, Steffen
Open allyite opened 2 years ago
sneumann
commented
2 years ago Hi, can you provide the Dockerfile ? Yours, Steffen
allyite
commented
2 years ago Hi, can you provide the Dockerfile ? Yours, Steffen
Here it is:
FROM r-base:3.6.2
EXPOSE 4200
ENV DEBIAN_FRONTEND=noninteractive
RUN apt-get update \
&& apt-get install -y libcurl4-openssl-dev libudunits2-dev libxml2-dev libgdal-dev \
make build-essential zlib1g-dev \
libbz2-dev libreadline-dev libsqlite3-dev git wget curl llvm libncurses5-dev \
libncursesw5-dev xz-utils tk-dev libffi-dev liblzma-dev python3-openssl\
libmagick++-dev\
libnetcdf-dev
RUN R -e 'install.packages("packrat")'
USER docker
RUN curl https://pyenv.run | bash
ENV PATH="/home/docker/.pyenv/bin:$PATH"
RUN eval "$(pyenv init -)" && eval "$(pyenv virtualenv-init -)"
RUN PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.6.0
USER root
ENV PATH="/home/docker/.pyenv/bin:$PATH"
ENV PATH="/home/docker/.pyenv/versions/3.6/bin:$PATH"File- Packrat.lock :: (mentioning only some of the packages below)
PackratFormat: 1.4
PackratVersion: 0.5.0.310210272
RVersion: 3.6.2
Repos: BioCsoft=https://bioconductor.org/packages/3.10/bioc,
BioCann=https://bioconductor.org/packages/3.10/data/annotation,
BioCexp=https://bioconductor.org/packages/3.10/data/experiment,
BioCworkflows=https://bioconductor.org/packages/3.10/workflows,
CRAN=https://cloud.r-project.org
Package: mzID
Source: Bioconductor
Version: 1.24.0
Hash: 57f4c8208913005696fc40cca83fb411
Requires: ProtGenerics, XML, doParallel, foreach, iterators, plyr
Package: mzR
Source: Bioconductor
Version: 2.20.0
Hash: 07034fc31539dbdea9fb6096e2eae04a
Requires: Biobase, BiocGenerics, ProtGenerics, Rcpp, Rhdf5lib, ncdf4,
zlibbioc
Package: ncdf4
Source: CRAN
Version: 1.17
Hash: 7cf17483666153addae35552ca6debd9
Package: BiocManager
Source: CRAN
Version: 1.30.9
Hash: 0dc0169c4d82275fdf64cdd8dfb27311
Package: BiocParallel
Source: Bioconductor
Version: 1.20.1
Hash: cefc0c2a973eeb14746cf935eec1c99d
Requires: BH, futile.logger, snowHm, I dont even get that far:
Downloading Python-3.6.0.tar.xz...
-> https://www.python.org/ftp/python/3.6.0/Python-3.6.0.tar.xz
Installing Python-3.6.0...
/home/docker/.pyenv/plugins/python-build/bin/python-build: line 1899: 11453 Segmentation fault (core dumped) "$PYTHON_BIN" -s -m ensurepip ${ensurepip_opts} > /dev/null 2>&1
Installing pip from https://bootstrap.pypa.io/pip/3.6/get-pip.py...
/home/docker/.pyenv/plugins/python-build/bin/python-build: line 1880: 11457 Segmentation fault (core dumped) "${PYTHON_BIN}" -s "${get_pip}" ${GET_PIP_OPTS} 1>&4 2>&1
error: failed to install pip via get-pip.py
BUILD FAILED (Debian GNU/Linux using python-build 20180424)
Inspect or clean up the working tree at /tmp/python-build.20220210143325.63
Results logged to /tmp/python-build.20220210143325.63.log
Last 10 log lines:
upgrade) ensurepip="--upgrade" ;; \
install|*) ensurepip="" ;; \
esac; \
LD_LIBRARY_PATH=/tmp/python-build.20220210143325.63/Python-3.6.0 ./python -E -m ensurepip \
$ensurepip --root=/ ; \
fi
Collecting setuptools
Collecting pip
Installing collected packages: setuptools, pip
Successfully installed pip-9.0.1 setuptools-28.8.0
The command '/bin/sh -c PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install 3.6.0' returned a non-zero code: 1=> Can you edit your above error trace as a code block ? I am having a hard time reading it. The GitHub Issue Editor needs three backticks (```) above and below the text to format it as code.
allyite
commented
2 years ago I've put it in a nice code block now :) Sorry about that.
I'm using the exact same docker-file as shared above, with docker desktop and Visual studio code (with Remote containers extension). You can avoid the python-related stuff from docker-file. I guess its not related to the mzR-issue.
sneumann
commented
2 years ago Hm, can't reproduce. (Docker and Packrat renamed to *.txt to please GitHub Dockerfile.txt Packrat.lock.txt )
[Dockerfile.txt](https://github.com/sneumann/mzR/files/8047143/Dockerfile.txt)
[Packrat.lock.txt](https://github.com/sneumann/mzR/files/8047144/Packrat.lock.txt)
Sending build context to Docker daemon 5.632kB
Step 1/5 : FROM r-base:3.6.2
---> 46edce0e80af
Step 2/5 : EXPOSE 4200
---> Using cache
---> 7633db18650d
Step 3/5 : ENV DEBIAN_FRONTEND=noninteractive
---> Using cache
---> 96f407fdd5ee
Step 4/5 : RUN apt-get update && apt-get install -y libcurl4-openssl-dev libudunits2-dev libxml2-dev libgdal-dev make build-essential zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev git wget curl llvm libncurses5-dev libncursesw5-dev xz-utils tk-dev libffi-dev liblzma-dev python3-openssl libmagick++-dev libnetcdf-dev
---> Using cache
---> b9b6cf285517
Step 5/5 : RUN R -e 'install.packages("packrat")'
---> Using cache
---> 95c1c4aa7914
Successfully built 95c1c4aa7914Hi.. I'm also able to build the container. But after that, have you been able to install mzR package (along with its dependencies) as mentioned in packrat.lock? If yes, can you please share your project folder/repo with me?
Commands after container built:
R -e "packrat::init()"
R -e "packrat::restore()"If no, you can try installing it using below packrat.lock file (I've included mzr and its needed dependencies).
PackratFormat: 1.4
PackratVersion: 0.5.0.310210272
RVersion: 3.6.2
Repos: BioCsoft=https://bioconductor.org/packages/3.10/bioc,
BioCann=https://bioconductor.org/packages/3.10/data/annotation,
BioCexp=https://bioconductor.org/packages/3.10/data/experiment,
BioCworkflows=https://bioconductor.org/packages/3.10/workflows,
CRAN=https://cloud.r-project.org/
Package: mzR
Source: Bioconductor
Version: 2.20.0
Hash: 07034fc31539dbdea9fb6096e2eae04a
Requires: Biobase, BiocGenerics, ProtGenerics, Rcpp, Rhdf5lib, ncdf4, zlibbioc
Package: Biobase
Source: Bioconductor
Version: 2.46.0
Hash: 8cafc212f9d20d470843c13c4988771c
Requires: BiocGenerics
Package: BiocGenerics
Source: Bioconductor
Version: 0.32.0
Hash: b64f82cc8788075b3d2b3c85d879fbf4
Package: ProtGenerics
Source: Bioconductor
Version: 1.18.0
Hash: 48c92173f285349bdbd5408c683551fd
Package: Rcpp
Source: CRAN
Version: 1.0.6
Hash: d891b607ea796cf30abfe4795380423f
Package: Rhdf5lib
Source: Bioconductor
Version: 1.8.0
Hash: d745e0bfadca3d7ebc4bc246eadcc8b2
Package: ncdf4
Source: CRAN
Version: 1.17
Hash: 7cf17483666153addae35552ca6debd9
Package: zlibbioc
Source: Bioconductor
Version: 1.32.0
Hash: 5fadfb71ee7cd5fe6b00762e79b56cf8Sorry, I need much more handholding to reproduce, I have zero experience with packrat.
I have done the R -e "packrat::init()" and copied the packrat.lock into the container, but restore() wont do anything. What am I missing ? Yours, Steffen
root@fc34c03f997c:/tmp# ls -l
total 8
drwxr-xr-x 6 root root 4096 Feb 12 13:00 packrat
-rw-r--r-- 1 root root 984 Feb 12 13:06 packrat.lock
root@fc34c03f997c:/tmp# head packrat.lock
PackratFormat: 1.4
PackratVersion: 0.5.0.310210272
RVersion: 3.6.2
Repos: BioCsoft=https://bioconductor.org/packages/3.10/bioc,
BioCann=https://bioconductor.org/packages/3.10/data/annotation,
BioCexp=https://bioconductor.org/packages/3.10/data/experiment,
BioCworkflows=https://bioconductor.org/packages/3.10/workflows,
CRAN=https://cloud.r-project.org
Package: mzID
[...]
root@fc34c03f997c:/tmp# R -e "packrat::restore()"
R version 3.6.3 RC (2020-02-21 r77847) -- "Holding the Windsock"
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.
Natural language support but running in an English locale
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.
> packrat::restore()
Already up to date.
> You cloud provide a container on github or quay for testing, and dump it after we fixed things. Yours, Steffen
Wh1isper
commented
1 year ago Same problem, maybe related to https://github.com/easybuilders/easybuild-easyconfigs/issues/11393#issuecomment-701675656
Due to the privacy agreement, I can't provide a complete Dockerfile at present, sorry
Wh1isper
commented
1 year ago Just tried to build with the latest code and succeed
Known it from https://github.com/sneumann/mzR/issues/235#issuecomment-1066926826
git clone https://github.com/sneumann/mzR.git
R CMD INSTALL mzR/cc @allyite
Thank you!
Hi, I'm trying to install mzr on docker with:- R version: 3.6 Bioconductor version: 3.10
I apologise in advance, if this question has been asked earlier. I'm not an expert but I've tried everything I could find & understand on google. Any help would be really appreciated.
Note: I can't upgrade my R version, because I'm trying to run an app as-is & with tonnes of other packages.
Error msg (till the end)::