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Why are un-requested packages removed (docker build)?
How is Docker different from a virtual machine?Should I use Vagrant or Docker for creating an isolated environment?How to list containers in DockerHow to get a Docker container's IP address from the host?How to remove old Docker containersHow does one remove an image in Docker?How to deal with persistent storage (e.g. databases) in DockerCopying files from Docker container to hostCopying files from host to Docker containerHow to remove old and unused Docker images
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So, I'm building my docker with the following Dockerfile
# dummy base, which contains R
ARG MY_BASE_IMAGE=r-base
FROM $MY_BASE_IMAGE
ARG KING_URL="http://people.virginia.edu/~wc9c/KING/executables/Linux-king215.tar.gz"
ARG PLINK2_URL="https://github.com/chrchang/plink-ng/releases/download/2019/plink2_linux_x86_64_20190107.zip"
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get -qqy update --fix-missing &&
apt-get -qqy dist-upgrade &&
apt-get -qqy install --no-install-recommends
wget unzip &&
cd /tmp &&
wget -q $KING_URL &&
tar -xzf Linux-king215.tar.gz -C /usr/local/bin &&
wget -q $PLINK2_URL &&
unzip plink2_linux_x86_64_20190107.zip -d /usr/local/bin &&
cd -- &&
apt-get -qqy remove wget unzip &&
rm -rf /tmp/*
/var/tmp/*
/var/cache/apt/*
/var/lib/apt/lists/*
/usr/share/man/??
/usr/share/man/??_*
However, this seems to remove R, unless I explicitly remove the line apt-get -qqy remove wget unzip.
I'm having difficulty understanding why. Help much appreciated!
UPDATE
I've dug deeper, and fount that if I run apt-get -qqy remove wget, things go OK.
BUT! If I apt-get -qqy remove unzip, back to the old weird behavior of the following:
Removing littler (0.3.7-2) ...
Removing r-base (3.5.3-1) ...
Removing r-recommended (3.5.3-1) ...
Removing r-cran-mgcv (1.8-28-1) ...
Removing r-base-dev (3.5.3-1) ...
Removing r-cran-littler (0.3.7-2) ...
Removing r-cran-boot (1.3-20-2) ...
Removing r-cran-class (7.3-15-1) ...
Removing r-cran-cluster (2.0.7-1-1+b3) ...
Removing r-cran-codetools (0.2-16-1) ...
Removing r-cran-foreign (0.8.71-1) ...
Removing r-cran-kernsmooth (2.23-15-3+b4) ...
Removing r-cran-nlme (3.1.137-1+b3) ...
Removing r-cran-mass (7.3-51.1-1) ...
Removing r-cran-nnet (7.3-12-2+b2) ...
Removing r-cran-rpart (4.1-13-1+b1) ...
Removing r-cran-spatial (7.3-11-2+b2) ...
Removing r-cran-survival (2.43-3-1) ...
Removing r-cran-matrix (1.2-17-1) ...
Removing r-cran-lattice (0.20-38-1) ...
Removing r-base-core (3.5.3-1) ...
Removing unzip (6.0-22) ...
docker
asked Mar 27 at 21:24
CloudyTreesCloudyTrees
1991 gold badge5 silver badges15 bronze badges
add a comment |
So, I'm building my docker with the following Dockerfile
# dummy base, which contains R
ARG MY_BASE_IMAGE=r-base
FROM $MY_BASE_IMAGE
ARG KING_URL="http://people.virginia.edu/~wc9c/KING/executables/Linux-king215.tar.gz"
ARG PLINK2_URL="https://github.com/chrchang/plink-ng/releases/download/2019/plink2_linux_x86_64_20190107.zip"
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get -qqy update --fix-missing &&
apt-get -qqy dist-upgrade &&
apt-get -qqy install --no-install-recommends
wget unzip &&
cd /tmp &&
wget -q $KING_URL &&
tar -xzf Linux-king215.tar.gz -C /usr/local/bin &&
wget -q $PLINK2_URL &&
unzip plink2_linux_x86_64_20190107.zip -d /usr/local/bin &&
cd -- &&
apt-get -qqy remove wget unzip &&
rm -rf /tmp/*
/var/tmp/*
/var/cache/apt/*
/var/lib/apt/lists/*
/usr/share/man/??
/usr/share/man/??_*
However, this seems to remove R, unless I explicitly remove the line apt-get -qqy remove wget unzip.
I'm having difficulty understanding why. Help much appreciated!
UPDATE
I've dug deeper, and fount that if I run apt-get -qqy remove wget, things go OK.
BUT! If I apt-get -qqy remove unzip, back to the old weird behavior of the following:
Removing littler (0.3.7-2) ...
Removing r-base (3.5.3-1) ...
Removing r-recommended (3.5.3-1) ...
Removing r-cran-mgcv (1.8-28-1) ...
Removing r-base-dev (3.5.3-1) ...
Removing r-cran-littler (0.3.7-2) ...
Removing r-cran-boot (1.3-20-2) ...
Removing r-cran-class (7.3-15-1) ...
Removing r-cran-cluster (2.0.7-1-1+b3) ...
Removing r-cran-codetools (0.2-16-1) ...
Removing r-cran-foreign (0.8.71-1) ...
Removing r-cran-kernsmooth (2.23-15-3+b4) ...
Removing r-cran-nlme (3.1.137-1+b3) ...
Removing r-cran-mass (7.3-51.1-1) ...
Removing r-cran-nnet (7.3-12-2+b2) ...
Removing r-cran-rpart (4.1-13-1+b1) ...
Removing r-cran-spatial (7.3-11-2+b2) ...
Removing r-cran-survival (2.43-3-1) ...
Removing r-cran-matrix (1.2-17-1) ...
Removing r-cran-lattice (0.20-38-1) ...
Removing r-base-core (3.5.3-1) ...
Removing unzip (6.0-22) ...
docker
asked Mar 27 at 21:24
CloudyTreesCloudyTrees
1991 gold badge5 silver badges15 bronze badges
What do you mean by remove R ?
– Corey
Mar 28 at 1:03
1
Sorry for the confusion. I meant R seems to be uninstalled by the ‘remove’ command, even though I did not ask for that.
– CloudyTrees
Mar 28 at 4:08
1
It sounds as ifunzipis a dependency of theRpackage. Since you are asking apt to removeunzip, it will also need to remove anything that depends onunzip. That is how package managers usually work.
– larsks
Mar 28 at 15:09
That's right @larsks! I was just about to report back on this. Do you mind writing a formal answer? Honestly I was surprised R depends on unzip.
– CloudyTrees
Mar 28 at 16:57
add a comment |
So, I'm building my docker with the following Dockerfile
# dummy base, which contains R
ARG MY_BASE_IMAGE=r-base
FROM $MY_BASE_IMAGE
ARG KING_URL="http://people.virginia.edu/~wc9c/KING/executables/Linux-king215.tar.gz"
ARG PLINK2_URL="https://github.com/chrchang/plink-ng/releases/download/2019/plink2_linux_x86_64_20190107.zip"
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get -qqy update --fix-missing &&
apt-get -qqy dist-upgrade &&
apt-get -qqy install --no-install-recommends
wget unzip &&
cd /tmp &&
wget -q $KING_URL &&
tar -xzf Linux-king215.tar.gz -C /usr/local/bin &&
wget -q $PLINK2_URL &&
unzip plink2_linux_x86_64_20190107.zip -d /usr/local/bin &&
cd -- &&
apt-get -qqy remove wget unzip &&
rm -rf /tmp/*
/var/tmp/*
/var/cache/apt/*
/var/lib/apt/lists/*
/usr/share/man/??
/usr/share/man/??_*
However, this seems to remove R, unless I explicitly remove the line apt-get -qqy remove wget unzip.
I'm having difficulty understanding why. Help much appreciated!
UPDATE
I've dug deeper, and fount that if I run apt-get -qqy remove wget, things go OK.
BUT! If I apt-get -qqy remove unzip, back to the old weird behavior of the following:
Removing littler (0.3.7-2) ...
Removing r-base (3.5.3-1) ...
Removing r-recommended (3.5.3-1) ...
Removing r-cran-mgcv (1.8-28-1) ...
Removing r-base-dev (3.5.3-1) ...
Removing r-cran-littler (0.3.7-2) ...
Removing r-cran-boot (1.3-20-2) ...
Removing r-cran-class (7.3-15-1) ...
Removing r-cran-cluster (2.0.7-1-1+b3) ...
Removing r-cran-codetools (0.2-16-1) ...
Removing r-cran-foreign (0.8.71-1) ...
Removing r-cran-kernsmooth (2.23-15-3+b4) ...
Removing r-cran-nlme (3.1.137-1+b3) ...
Removing r-cran-mass (7.3-51.1-1) ...
Removing r-cran-nnet (7.3-12-2+b2) ...
Removing r-cran-rpart (4.1-13-1+b1) ...
Removing r-cran-spatial (7.3-11-2+b2) ...
Removing r-cran-survival (2.43-3-1) ...
Removing r-cran-matrix (1.2-17-1) ...
Removing r-cran-lattice (0.20-38-1) ...
Removing r-base-core (3.5.3-1) ...
Removing unzip (6.0-22) ...
docker
asked Mar 27 at 21:24
CloudyTreesCloudyTrees
1991 gold badge5 silver badges15 bronze badges
So, I'm building my docker with the following Dockerfile
# dummy base, which contains R
ARG MY_BASE_IMAGE=r-base
FROM $MY_BASE_IMAGE
ARG KING_URL="http://people.virginia.edu/~wc9c/KING/executables/Linux-king215.tar.gz"
ARG PLINK2_URL="https://github.com/chrchang/plink-ng/releases/download/2019/plink2_linux_x86_64_20190107.zip"
ARG DEBIAN_FRONTEND=noninteractive
RUN apt-get -qqy update --fix-missing &&
apt-get -qqy dist-upgrade &&
apt-get -qqy install --no-install-recommends
wget unzip &&
cd /tmp &&
wget -q $KING_URL &&
tar -xzf Linux-king215.tar.gz -C /usr/local/bin &&
wget -q $PLINK2_URL &&
unzip plink2_linux_x86_64_20190107.zip -d /usr/local/bin &&
cd -- &&
apt-get -qqy remove wget unzip &&
rm -rf /tmp/*
/var/tmp/*
/var/cache/apt/*
/var/lib/apt/lists/*
/usr/share/man/??
/usr/share/man/??_*
However, this seems to remove R, unless I explicitly remove the line apt-get -qqy remove wget unzip.
I'm having difficulty understanding why. Help much appreciated!
UPDATE
I've dug deeper, and fount that if I run apt-get -qqy remove wget, things go OK.
BUT! If I apt-get -qqy remove unzip, back to the old weird behavior of the following:
Removing littler (0.3.7-2) ...
Removing r-base (3.5.3-1) ...
Removing r-recommended (3.5.3-1) ...
Removing r-cran-mgcv (1.8-28-1) ...
Removing r-base-dev (3.5.3-1) ...
Removing r-cran-littler (0.3.7-2) ...
Removing r-cran-boot (1.3-20-2) ...
Removing r-cran-class (7.3-15-1) ...
Removing r-cran-cluster (2.0.7-1-1+b3) ...
Removing r-cran-codetools (0.2-16-1) ...
Removing r-cran-foreign (0.8.71-1) ...
Removing r-cran-kernsmooth (2.23-15-3+b4) ...
Removing r-cran-nlme (3.1.137-1+b3) ...
Removing r-cran-mass (7.3-51.1-1) ...
Removing r-cran-nnet (7.3-12-2+b2) ...
Removing r-cran-rpart (4.1-13-1+b1) ...
Removing r-cran-spatial (7.3-11-2+b2) ...
Removing r-cran-survival (2.43-3-1) ...
Removing r-cran-matrix (1.2-17-1) ...
Removing r-cran-lattice (0.20-38-1) ...
Removing r-base-core (3.5.3-1) ...
Removing unzip (6.0-22) ...
docker
docker
asked Mar 27 at 21:24
CloudyTreesCloudyTrees
1991 gold badge5 silver badges15 bronze badges
asked Mar 27 at 21:24
CloudyTreesCloudyTrees
1991 gold badge5 silver badges15 bronze badges
edited Mar 28 at 14:30
CloudyTrees
asked Mar 27 at 21:24
CloudyTreesCloudyTrees
1991 gold badge5 silver badges15 bronze badges
asked Mar 27 at 21:24
CloudyTreesCloudyTrees
1991 gold badge5 silver badges15 bronze badges
asked Mar 27 at 21:24
CloudyTreesCloudyTrees
1991 gold badge5 silver badges15 bronze badges
1991 gold badge5 silver badges15 bronze badges
What do you mean by remove R ?
– Corey
Mar 28 at 1:03
1
Sorry for the confusion. I meant R seems to be uninstalled by the ‘remove’ command, even though I did not ask for that.
– CloudyTrees
Mar 28 at 4:08
1
It sounds as ifunzipis a dependency of theRpackage. Since you are asking apt to removeunzip, it will also need to remove anything that depends onunzip. That is how package managers usually work.
– larsks
Mar 28 at 15:09
That's right @larsks! I was just about to report back on this. Do you mind writing a formal answer? Honestly I was surprised R depends on unzip.
– CloudyTrees
Mar 28 at 16:57
add a comment |
What do you mean by remove R ?
– Corey
Mar 28 at 1:03
1
Sorry for the confusion. I meant R seems to be uninstalled by the ‘remove’ command, even though I did not ask for that.
– CloudyTrees
Mar 28 at 4:08
1
It sounds as ifunzipis a dependency of theRpackage. Since you are asking apt to removeunzip, it will also need to remove anything that depends onunzip. That is how package managers usually work.
– larsks
Mar 28 at 15:09
That's right @larsks! I was just about to report back on this. Do you mind writing a formal answer? Honestly I was surprised R depends on unzip.
– CloudyTrees
Mar 28 at 16:57
What do you mean by remove R ?
– Corey
Mar 28 at 1:03
What do you mean by remove R ?
– Corey
Mar 28 at 1:03
1
1
Sorry for the confusion. I meant R seems to be uninstalled by the ‘remove’ command, even though I did not ask for that.
– CloudyTrees
Mar 28 at 4:08
Sorry for the confusion. I meant R seems to be uninstalled by the ‘remove’ command, even though I did not ask for that.
– CloudyTrees
Mar 28 at 4:08
1
1
It sounds as if
unzip is a dependency of the R package. Since you are asking apt to remove unzip, it will also need to remove anything that depends on unzip. That is how package managers usually work.– larsks
Mar 28 at 15:09
It sounds as if
unzip is a dependency of the R package. Since you are asking apt to remove unzip, it will also need to remove anything that depends on unzip. That is how package managers usually work.– larsks
Mar 28 at 15:09
That's right @larsks! I was just about to report back on this. Do you mind writing a formal answer? Honestly I was surprised R depends on unzip.
– CloudyTrees
Mar 28 at 16:57
That's right @larsks! I was just about to report back on this. Do you mind writing a formal answer? Honestly I was surprised R depends on unzip.
– CloudyTrees
Mar 28 at 16:57
add a comment |
1 Answer
1
active
oldest
votes
It sounds as if unzip is a dependency of the R package. Since you are asking apt to remove unzip, it will also need to remove anything that depends on unzip. This is typical behavior for a package manager.
You can see the dependency tree for a package with the apt-cache dotty command, which will output the dependencies in dot format. Running apt-cache dotty r-base shows:
r-base -> r-base-core
r-base-core -> unzip
answered Mar 28 at 18:03
larskslarsks
134k23 gold badges220 silver badges221 bronze badges
add a comment |
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It sounds as if unzip is a dependency of the R package. Since you are asking apt to remove unzip, it will also need to remove anything that depends on unzip. This is typical behavior for a package manager.
You can see the dependency tree for a package with the apt-cache dotty command, which will output the dependencies in dot format. Running apt-cache dotty r-base shows:
r-base -> r-base-core
r-base-core -> unzip
answered Mar 28 at 18:03
larskslarsks
134k23 gold badges220 silver badges221 bronze badges
add a comment |
It sounds as if unzip is a dependency of the R package. Since you are asking apt to remove unzip, it will also need to remove anything that depends on unzip. This is typical behavior for a package manager.
You can see the dependency tree for a package with the apt-cache dotty command, which will output the dependencies in dot format. Running apt-cache dotty r-base shows:
r-base -> r-base-core
r-base-core -> unzip
answered Mar 28 at 18:03
larskslarsks
134k23 gold badges220 silver badges221 bronze badges
add a comment |
It sounds as if unzip is a dependency of the R package. Since you are asking apt to remove unzip, it will also need to remove anything that depends on unzip. This is typical behavior for a package manager.
You can see the dependency tree for a package with the apt-cache dotty command, which will output the dependencies in dot format. Running apt-cache dotty r-base shows:
r-base -> r-base-core
r-base-core -> unzip
answered Mar 28 at 18:03
larskslarsks
134k23 gold badges220 silver badges221 bronze badges
It sounds as if unzip is a dependency of the R package. Since you are asking apt to remove unzip, it will also need to remove anything that depends on unzip. This is typical behavior for a package manager.
You can see the dependency tree for a package with the apt-cache dotty command, which will output the dependencies in dot format. Running apt-cache dotty r-base shows:
r-base -> r-base-core
r-base-core -> unzip
answered Mar 28 at 18:03
larskslarsks
134k23 gold badges220 silver badges221 bronze badges
answered Mar 28 at 18:03
larskslarsks
134k23 gold badges220 silver badges221 bronze badges
answered Mar 28 at 18:03
larskslarsks
134k23 gold badges220 silver badges221 bronze badges
answered Mar 28 at 18:03
larskslarsks
134k23 gold badges220 silver badges221 bronze badges
134k23 gold badges220 silver badges221 bronze badges
add a comment |
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What do you mean by remove R ?
– Corey
Mar 28 at 1:03
1
Sorry for the confusion. I meant R seems to be uninstalled by the ‘remove’ command, even though I did not ask for that.
– CloudyTrees
Mar 28 at 4:08
1
It sounds as if
unzipis a dependency of theRpackage. Since you are asking apt to removeunzip, it will also need to remove anything that depends onunzip. That is how package managers usually work.– larsks
Mar 28 at 15:09
That's right @larsks! I was just about to report back on this. Do you mind writing a formal answer? Honestly I was surprised R depends on unzip.
– CloudyTrees
Mar 28 at 16:57