Building container image failes due to missing files #51
Description
There are at least 2 files missing.
I just did a clean checkout of the repository and wanted to build the image (yes, I'm on Windows -- not all of us have a choice here).
PS C:\Users\marcherm\src\single-cell-tutorial> git status
On branch master
Your branch is up to date with 'origin/master'.
nothing to commit, working tree clean
PS C:\Users\marcherm\src\single-cell-tutorial> git rev-parse --short HEAD
8168bcb
It fails with the following message:
> docker build -t single-cell-tutorial .
[+] Building 9.8s (40/41)
=> [internal] load .dockerignore 0.1s
=> => transferring context: 2B 0.0s
=> [internal] load build definition from Dockerfile 0.3s
=> => transferring dockerfile: 3.23kB 0.0s
=> [internal] load metadata for docker.io/library/debian:10 9.2s
=> [internal] load build context 0.1s
=> => transferring context: 2B 0.0s
=> CANCELED [1/37] FROM docker.io/library/debian:10@sha256:e2cc6fb403be437ef8af68bdc3a89fd58e80b4e390c58f14c77c466002391193 0.1s
=> => resolve docker.io/library/debian:10@sha256:e2cc6fb403be437ef8af68bdc3a89fd58e80b4e390c58f14c77c466002391193 0.0s
=> CACHED [2/37] RUN apt-get update && apt-get install -y --no-install-recommends build-essential apt-utils ca-certificates zlib1g-dev gfortran locales libxml2-dev libcurl4-openssl-dev libssl-dev libzmq3-dev lib 0.0s
=> CACHED [3/37] RUN apt-get update && apt-get install -y --no-install-recommends wget curl htop less nano vim emacs git 0.0s
=> CACHED [4/37] RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && locale-gen en_US.utf8 && /usr/sbin/update-locale LANG=en_US.UTF-8 0.0s
=> CACHED [5/37] WORKDIR /opt/R 0.0s
=> CACHED [6/37] RUN wget https://cran.rstudio.com/src/base/R-3/R-3.6.3.tar.gz 0.0s
=> CACHED [7/37] RUN tar xvfz R-3.6.3.tar.gz && rm R-3.6.3.tar.gz 0.0s
=> CACHED [8/37] WORKDIR /opt/R/R-3.6.3 0.0s
=> CACHED [9/37] RUN ./configure --enable-R-shlib --with-cairo --with-libpng --prefix=/opt/R/ 0.0s
=> CACHED [10/37] RUN make && make install 0.0s
=> CACHED [11/37] WORKDIR /opt/R 0.0s
=> CACHED [12/37] RUN rm -rf /opt/R/R-3.6.3 0.0s
=> CACHED [13/37] RUN Rscript -e "update.packages(ask=FALSE, repos='https://ftp.gwdg.de/pub/misc/cran/')" 0.0s
=> CACHED [14/37] RUN Rscript -e "install.packages(c('devtools', 'gam', 'RColorBrewer', 'BiocManager', 'IRkernel'), repos='https://ftp.gwdg.de/pub/misc/cran/')" 0.0s
=> CACHED [15/37] RUN Rscript -e "devtools::install_github(c('patzaw/neo2R', 'patzaw/BED'))" 0.0s
=> CACHED [16/37] RUN Rscript -e "BiocManager::install(c('scran','MAST','monocle','ComplexHeatmap','limma','slingshot','clusterExperiment','DropletUtils'), version = '3.10')" 0.0s
=> CACHED [17/37] RUN Rscript -e 'writeLines(capture.output(sessionInfo()), "../package_versions_r.txt")' --default-packages=scran,RColorBrewer,slingshot,monocle,gam,clusterExperiment,ggplot2,plyr,MAST,DropletUt 0.0s
=> CACHED [18/37] WORKDIR /opt/python 0.0s
=> CACHED [19/37] RUN wget https://www.python.org/ftp/python/3.7.7/Python-3.7.7.tgz 0.0s
=> CACHED [20/37] RUN tar zxfv Python-3.7.7.tgz && rm Python-3.7.7.tgz 0.0s
=> CACHED [21/37] WORKDIR /opt/python/Python-3.7.7 0.0s
=> CACHED [22/37] RUN ./configure --enable-optimizations --with-lto --prefix=/opt/python/ 0.0s
=> CACHED [23/37] RUN make && make install 0.0s
=> CACHED [24/37] WORKDIR /opt/python 0.0s
=> CACHED [25/37] RUN rm -rf /opt/python/Python-3.7.7 0.0s
=> CACHED [26/37] RUN ln -s /opt/python/bin/python3 /opt/python/bin/python 0.0s
=> CACHED [27/37] RUN ln -s /opt/python/bin/pip3 /opt/python/bin/pip 0.0s
=> CACHED [28/37] RUN pip install --no-cache-dir -U pip wheel setuptools cmake 0.0s
=> CACHED [29/37] RUN pip install --no-cache-dir -U scanpy==1.4.6 python-igraph==0.8.0 louvain==0.6.1 jupyterlab=2.1.0 cellxgene==0.15.0 rpy2==3.2.7 anndata2ri==1.0.2 leidenalg==0.7.0 fa2==0.3.5 MulticoreTSNE==0 0.0s
=> CACHED [30/37] RUN pip install --no-cache-dir git+https://github.com/le-ander/epiScanpy.git 0.0s
=> CACHED [31/37] RUN jupyter contrib nbextension install --system 0.0s
=> CACHED [32/37] RUN jupyter nbextension enable --py widgetsnbextension 0.0s
=> CACHED [33/37] RUN pip freeze > ../package_versions_py.txt 0.0s
=> CACHED [34/37] RUN Rscript -e "IRkernel::installspec(user = FALSE)" 0.0s
=> ERROR [35/37] COPY .bashrc_docker /root/.bashrc 0.0s
=> ERROR [36/37] COPY .profile_docker /root/.profile 0.0s
------
> [35/37] COPY .bashrc_docker /root/.bashrc:
------
------
> [36/37] COPY .profile_docker /root/.profile:
------
failed to solve with frontend dockerfile.v0: failed to build LLB: failed to compute cache key: "/.profile_docker" not found: not found