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Murali-group / Beeline

BEELINE: evaluation of algorithms for gene regulatory network inference
GNU General Public License v3.0
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SCODE Docker container failing to build #40

Closed ibebio closed 3 years ago

ibebio commented 4 years ago

Hello,

I encountered the following error when building the SCODE docker container:

Some packages could not be installed. This may mean that you have                                                                  
requested an impossible situation or if you are using the unstable                                                                 
distribution that some required packages have not yet been created                                                                 
or been moved out of Incoming.                                                                                                     
The following information may help to resolve the situation:                                                                       

The following packages have unmet dependencies:                                                                                    
 libc6-dev : Breaks: libgcc-8-dev (< 8.4.0-2~) but 8.3.0-3 is to be installed                                                      
E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages.

To resolve it, I had to modify Dockerfile to install gcc-8-base after running apt-get update

Hsu-Che-Wei commented 3 years ago

Hello,

Same problem when trying to build SCNS Docker container. But this time, installing gcc-8-base after running apt-get update does not solve the problem. Do you have any idea?

tmmurali commented 3 years ago

@Hsu-Che-Wei can you share the error you get?

Hsu-Che-Wei commented 3 years ago

@tmmurali

(base) raphael830102@beeline-cwh:~/Beeline$ . ./initialize.sh This may take a while... sha256:4344a80c7f38d8da9cec73a03c372272f5e6d32a904ba7383ea1a396092e656a Docker container for ARBORETO is built and tagged as arboreto:base sha256:367feaae8ca9b603a43d65922960d0c39455517d96e799530d3154b2dcf584d4 Docker container for GRISLI is built and tagged as grisli:base sha256:55f529fe30035e67a2d82584faa2db62015bc4269a277ec635fab965722a62c2 Docker container for GRNVBEM is built and tagged as grnvbem:base sha256:ec0faad4537412325b41c3aba32bca97f63b8b39fba70d5587a7c20deebcbca6 Docker container for JUMP3 is built and tagged as jump3:base sha256:2eaa0ec96fec9015eca1fa4543180086674bc2c17672f3c80e73f165435d86e4 Docker container for LEAP is built and tagged as leap:base sha256:da240e4e3563e3d39043caeef35c8eff9f87b8b472441bf6a387ff9e7238bb5f Docker container for PIDC is built and tagged as pidc:base sha256:11237a3eea66916c814cb63de5403040e1ee4f591f2e8fe2e342dd7b1612a81d Docker container for PNI is built and tagged as pni:base sha256:95eb7ae68608a327e9935e3abf6ade7305c7abcce48b495a7135804d611fcbbd Docker container for PPCOR is built and tagged as ppcor:base sha256:d7f50b91e5db5a33e2237f852431be184440b390639f75ade3a36a6f804cbacc Docker container for SINGE is built and tagged as singe:base sha256:11f8db0dbea60ed5eeb663634df37544acc35ebfb2297a8d072ff2252da778a3 Docker container for SCNS is built and tagged as scns:base Sending build context to Docker daemon 2.048kB Step 1/11 : FROM r-base:3.5.3 ---> 62c848eeb175 Step 2/11 : LABEL maintainer = "Aditya Pratapa adyprat@vt.edu" ---> Using cache ---> 237e322b4cab Step 3/11 : USER root ---> Using cache ---> 7f1a56b2d021 Step 4/11 : WORKDIR / ---> Using cache ---> 4d18d0b99acc Step 5/11 : RUN apt-get update && apt-get install -y git ---> Running in 31d7696d4254 Get:1 http://deb.debian.org/debian testing InRelease [116 kB] Get:3 http://deb.debian.org/debian testing/main amd64 Packages [7,676 kB] Get:2 http://cdn-fastly.deb.debian.org/debian sid InRelease [146 kB] Get:4 http://cdn-fastly.deb.debian.org/debian sid/main amd64 Packages [8,388 kB] Fetched 16.3 MB in 3s (4,902 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: libc6-dev : Breaks: libgcc-8-dev (< 8.4.0-2~) but 8.3.0-3 is to be installed E: Error, pkgProblemResolver::Resolve generated breaks, this may be caused by held packages. The command '/bin/sh -c apt-get update && apt-get install -y git' returned a non-zero code: 100 Docker container for SCODE is built and tagged as scode:base sha256:3d796d4a560d420dfb9a87007bef6a2dc45a684cf671310b734fac96238bdf9e Docker container for SCRIBE is built and tagged as sincerities:base sha256:aa23db1a591b082f38694babbd4883aed5cb47b1b355a32a88f35cead33e07ee Docker container for SINCERITIES is built and tagged as sincerities:base

Hsu-Che-Wei commented 3 years ago

![Uploading Screenshot 2020-09-22 at 01.02.06.png…]()

adyprat commented 3 years ago

Hi @Hsu-Che-Wei, Looks like your error is not with SCNS, but rather with SCODE docker. I fixed this in 2a5a095 Let me know if this is still an issue.