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dgomezpere / msm_tfm

Development of an application to visualize, annotate and prioritize somatic variants in cancer
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[docker%dockerfile] Error while installing R base #6

Closed segarmond closed 2 years ago

segarmond commented 2 years ago

Traceback error

 => ERROR [14/21] RUN apt install -y dirmngr gnupg apt-transport-https ca-certificates     && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys  6.9s
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 > [14/21] RUN apt install -y dirmngr gnupg apt-transport-https ca-certificates     && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9     && add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'     && add-apt-repository ppa:c2d4u.team/c2d4u4.0+     && apt update && apt install -y r-base r-base-dev:                                                                                          
#18 0.344                                                                                                                                                    
#18 0.344 WARNING: apt does not have a stable CLI interface. Use with caution in scripts.                                                                    
#18 0.344 
#18 0.378 Reading package lists...
#18 0.780 Building dependency tree...
#18 0.861 Reading state information...
#18 0.953 ca-certificates is already the newest version (20210119~20.04.2).
#18 0.953 ca-certificates set to manually installed.
#18 0.953 dirmngr is already the newest version (2.2.19-3ubuntu2.1).
#18 0.953 dirmngr set to manually installed.
#18 0.953 gnupg is already the newest version (2.2.19-3ubuntu2.1).
#18 0.953 gnupg set to manually installed.
#18 0.953 The following NEW packages will be installed:
#18 0.954   apt-transport-https
#18 1.235 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
#18 1.235 Need to get 4,680 B of archives.
#18 1.235 After this operation, 162 kB of additional disk space will be used.
#18 1.235 Get:1 http://ports.ubuntu.com/ubuntu-ports focal-updates/universe arm64 apt-transport-https all 2.0.6 [4,680 B]
#18 1.400 debconf: delaying package configuration, since apt-utils is not installed
#18 1.425 Fetched 4,680 B in 0s (16.8 kB/s)
#18 1.440 Selecting previously unselected package apt-transport-https.
(Reading database ... 49530 files and directories currently installed.)
#18 1.512 Preparing to unpack .../apt-transport-https_2.0.6_all.deb ...
#18 1.514 Unpacking apt-transport-https (2.0.6) ...
#18 1.540 Setting up apt-transport-https (2.0.6) ...
#18 1.597 Warning: apt-key output should not be parsed (stdout is not a terminal)
#18 1.612 Executing: /tmp/apt-key-gpghome.VqgXIDiwbJ/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
#18 1.722 gpg: key 51716619E084DAB9: public key "Michael Rutter <marutter@gmail.com>" imported
#18 1.731 gpg: Total number processed: 1
#18 1.731 gpg:               imported: 1
#18 2.357 Hit:1 http://ports.ubuntu.com/ubuntu-ports focal InRelease
#18 2.424 Hit:2 https://deb.nodesource.com/node_14.x focal InRelease
#18 2.456 Get:3 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ InRelease [3,622 B]
#18 2.468 Hit:4 http://ports.ubuntu.com/ubuntu-ports focal-updates InRelease
#18 2.585 Hit:5 http://ports.ubuntu.com/ubuntu-ports focal-backports InRelease
#18 2.712 Hit:6 http://ports.ubuntu.com/ubuntu-ports focal-security InRelease
#18 2.722 Get:7 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ Packages [47.2 kB]
#18 2.777 Fetched 50.8 kB in 1s (72.9 kB/s)
#18 2.777 Reading package lists...
#18 3.512  A PPA for R packages from CRAN's Task Views built against R 4.0 (and subsequent releases).  Only building packages for LTS releases.
#18 3.512  More info: https://launchpad.net/~c2d4u.team/+archive/ubuntu/c2d4u4.0+
#18 4.042 Get:1 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease [18.1 kB]
#18 4.049 Hit:2 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ InRelease
#18 4.059 Hit:3 https://deb.nodesource.com/node_14.x focal InRelease
#18 4.173 Hit:4 http://ports.ubuntu.com/ubuntu-ports focal InRelease
#18 4.256 Get:5 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal/main arm64 Packages [583 kB]
#18 4.307 Hit:6 http://ports.ubuntu.com/ubuntu-ports focal-updates InRelease
#18 4.458 Hit:7 http://ports.ubuntu.com/ubuntu-ports focal-backports InRelease
#18 4.639 Hit:8 http://ports.ubuntu.com/ubuntu-ports focal-security InRelease
#18 4.706 Fetched 601 kB in 1s (752 kB/s)
#18 4.706 Reading package lists...
#18 5.115 
#18 5.115 WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
#18 5.115 
#18 5.249 Hit:1 http://ppa.launchpad.net/c2d4u.team/c2d4u4.0+/ubuntu focal InRelease
#18 5.288 Hit:2 https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/ InRelease
#18 5.303 Hit:3 https://deb.nodesource.com/node_14.x focal InRelease
#18 5.388 Hit:4 http://ports.ubuntu.com/ubuntu-ports focal InRelease
#18 5.495 Hit:5 http://ports.ubuntu.com/ubuntu-ports focal-updates InRelease
#18 5.602 Hit:6 http://ports.ubuntu.com/ubuntu-ports focal-backports InRelease
#18 5.727 Hit:7 http://ports.ubuntu.com/ubuntu-ports focal-security InRelease
#18 5.791 Reading package lists...
#18 6.180 Building dependency tree...
#18 6.265 Reading state information...
#18 6.272 All packages are up to date.
#18 6.279 
#18 6.279 WARNING: apt does not have a stable CLI interface. Use with caution in scripts.
#18 6.279 
#18 6.301 Reading package lists...
#18 6.687 Building dependency tree...
#18 6.770 Reading state information...
#18 6.810 Some packages could not be installed. This may mean that you have
#18 6.810 requested an impossible situation or if you are using the unstable
#18 6.810 distribution that some required packages have not yet been created
#18 6.810 or been moved out of Incoming.
#18 6.810 The following information may help to resolve the situation:
#18 6.810 
#18 6.810 The following packages have unmet dependencies:
#18 6.850  r-base : Depends: r-base-core (>= 4.1.1-1.2004.0) but it is not going to be installed
#18 6.850           Depends: r-recommended (= 4.1.1-1.2004.0) but it is not going to be installed
#18 6.850           Recommends: r-base-html but it is not going to be installed
#18 6.850           Recommends: r-doc-html but it is not going to be installed
#18 6.850  r-base-dev : Depends: r-base-core (>= 4.1.1-1.2004.0) but it is not going to be installed
#18 6.859 E: Unable to correct problems, you have held broken packages.
------
executor failed running [/bin/sh -c apt install -y dirmngr gnupg apt-transport-https ca-certificates     && apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9     && add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/'     && add-apt-repository ppa:c2d4u.team/c2d4u4.0+     && apt update && apt install -y r-base r-base-dev]: exit code: 100
dgomezpere commented 2 years ago

The tracebak error reports (attention in lines with ->):

#18 6.810 The following packages have unmet dependencies:
-> #18 6.850  r-base : Depends: r-base-core (>= 4.1.1-1.2004.0) but it is not going to be installed
-> #18 6.850           Depends: r-recommended (= 4.1.1-1.2004.0) but it is not going to be installed
#18 6.850           Recommends: r-base-html but it is not going to be installed
#18 6.850           Recommends: r-doc-html but it is not going to be installed
-> #18 6.850  r-base-dev : Depends: r-base-core (>= 4.1.1-1.2004.0) but it is not going to be installed

It seems that apt is not correctly building the dependecies tree of r-base and r-base-dev.

Maybe forcing to install these dependencies solve the problem.