{"action":"created","issue":{"url":"https://api.github.com/repos/sylabs/singularity/issues/1899","repository_url":"https://api.github.com/repos/sylabs/singularity","labels_url":"https://api.github.com/repos/sylabs/singularity/issues/1899/labels{/name}","comments_url":"https://api.github.com/repos/sylabs/singularity/issues/1899/comments","events_url":"https://api.github.com/repos/sylabs/singularity/issues/1899/events","html_url":"https://github.com/sylabs/singularity/issues/1899","id":355242524,"node_id":"MDU6SXNzdWUzNTUyNDI1MjQ=","number":1899,"title":"Whiteout Marker Error","user":{"login":"aureliooo","id":40893404,"node_id":"MDQ6VXNlcjQwODkzNDA0","avatar_url":"https://avatars0.githubusercontent.com/u/40893404?v=4","gravatar_id":"","url":"https://api.github.com/users/aureliooo","html_url":"https://github.com/aureliooo","followers_url":"https://api.github.com/users/aureliooo/followers","following_url":"https://api.github.com/users/aureliooo/following{/other_user}","gists_url":"https://api.github.com/users/aureliooo/gists{/gist_id}","starred_url":"https://api.github.com/users/aureliooo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aureliooo/subscriptions","organizations_url":"https://api.github.com/users/aureliooo/orgs","repos_url":"https://api.github.com/users/aureliooo/repos","events_url":"https://api.github.com/users/aureliooo/events{/privacy}","received_events_url":"https://api.github.com/users/aureliooo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-08-29T16:37:11Z","updated_at":"2018-10-03T08:07:58Z","closed_at":null,"author_association":"NONE","body":"## Version of Singularity:\r\n\r\nSingularity 2.5.2\r\n\r\n### Expected behavior\r\n\r\nBuild a Singularity Image using --sandbox\r\n\r\n### Actual behavior\r\n\r\nWARNING: Warning reading tar header: Ignoring malformed pax extended attribute\r\nSingularity: docker-extract (U=0,P=58)> Warning reading tar header: Ignoring malformed pax extended attribute\r\n\r\nWARNING: Warning reading tar header: Ignoring malformed pax extended attribute\r\nExploding layer: sha256:6f01ad3510b4aabf658455837f53c3bd0f735349ae1e178bc51226639e317fa1.tar.gz\r\nExploding layer: sha256:a3bffaefcb2e89763e9d4c213a6ebe17da731b4d0263cff91cc78887042ea357.tar.gz\r\nExploding layer: sha256:4f299991da429308446f1430ce9af52c30117ceadd18c7406449ce9c0f6c653e.tar.gz\r\nExploding layer: sha256:b879d6190031218c185fd5aa00dab3b6e91966cb3caf6e755390aac5ee24060e.tar.gz\r\nExploding layer: sha256:689624b1325509f81b91919cb6d9b9199efed74f8f326c7ae580dae0c5a46cd6.tar.gz\r\nExploding layer: sha256:f6ae1e0236383b8575de2ae0af2000441fb88eeb1697062a25ba7b08a57c03ff.tar.gz\r\nExploding layer: sha256:94280402e42b298865e4ba41f7e097f0a9123a89b09914413edff6effeeae55d.tar.gz\r\nSingularity: docker-extract (U=0,P=72)> Failed removing file: /pipeline/usr/local/miniconda/pkgs/cache\r\n\r\nWARNING: Failed removing file: /pipeline/usr/local/miniconda/pkgs/cache\r\nSingularity: docker-extract (U=0,P=72)> Error applying whiteout marker from docker layer.\r\n\r\nERROR  : Error applying whiteout marker from docker layer.\r\nSingularity: docker-extract (U=0,P=72)> Retval = 255\r\n\r\nABORT  : Retval = 255\r\n\r\n### Steps to reproduce behavior\r\n\r\nsingularity build --sandbox pipeline docker://mindandbrain/pipeline\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/sylabs/singularity/issues/comments/426548018","html_url":"https://github.com/sylabs/singularity/issues/1899#issuecomment-426548018","issue_url":"https://api.github.com/repos/sylabs/singularity/issues/1899","id":426548018,"node_id":"MDEyOklzc3VlQ29tbWVudDQyNjU0ODAxOA==","user":{"login":"sinonkt","id":13428859,"node_id":"MDQ6VXNlcjEzNDI4ODU5","avatar_url":"https://avatars2.githubusercontent.com/u/13428859?v=4","gravatar_id":"","url":"https://api.github.com/users/sinonkt","html_url":"https://github.com/sinonkt","followers_url":"https://api.github.com/users/sinonkt/followers","following_url":"https://api.github.com/users/sinonkt/following{/other_user}","gists_url":"https://api.github.com/users/sinonkt/gists{/gist_id}","starred_url":"https://api.github.com/users/sinonkt/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sinonkt/subscriptions","organizations_url":"https://api.github.com/users/sinonkt/orgs","repos_url":"https://api.github.com/users/sinonkt/repos","events_url":"https://api.github.com/users/sinonkt/events{/privacy}","received_events_url":"https://api.github.com/users/sinonkt/received_events","type":"User","site_admin":false},"created_at":"2018-10-03T08:07:58Z","updated_at":"2018-10-03T08:07:58Z","author_association":"NONE","body":"Hi, I also faced quite similar issue. @dctrud and try what you suggest but my docker Storage Driver already be `overlay2`. my other docker-based image was succesfully pull by singularity-2.6 except this one.\r\n## Version of Singularity:\r\n\r\nSingularity=2.6.0-HEAD.579c415\r\nDockerForMacVersion=2.0.0.0-beta1-mac75 (27117)\r\nDockerEngine=18.09.0-ce-beta1\r\n\r\n### Expected behavior\r\n\r\nCan run my custom centos/systemd derived image `sinonkt/docker-slurm-simulator` normally like when run on docker.\r\n*** plain centos/sysmted:latest can run fine on singularity. but don't know why my variant go wrongs.\r\n\r\n### Actual behavior\r\n\r\n```\r\nWARNING: pull for Docker Hub is not guaranteed to produce the\r\nWARNING: same image on repeated pull. Use Singularity Registry\r\nWARNING: (shub://) to pull exactly equivalent images.\r\nDocker image path: index.docker.io/sinonkt/docker-slurm-simulator:latest\r\nCache folder set to /root/.singularity/docker\r\n[17/17] |===================================| 100.0%\r\nImporting: base Singularity environment\r\nSingularity: docker-extract (U=0,P=50)> Provide a single docker tar file to extract\r\nSingularity: docker-extract (U=0,P=50)> Retval = 255\r\nExploding layer: sha256:7dc0dca2b1516961d6b3200564049db0a6e0410b370bb2189e2efae0d368616f.tar.gz\r\nSingularity: docker-extract (U=0,P=53)> Warning reading tar header: Ignoring malformed pax extended attribute\r\nWARNING: Warning reading tar header: Ignoring malformed pax extended attribute\r\nSingularity: docker-extract (U=0,P=53)> Warning reading tar header: Ignoring malformed pax extended attribute\r\nWARNING: Warning reading tar header: Ignoring malformed pax extended attribute\r\nSingularity: docker-extract (U=0,P=53)> Warning reading tar header: Ignoring malformed pax extended attribute\r\nWARNING: Warning reading tar header: Ignoring malformed pax extended attribute\r\nExploding layer: sha256:1eb7c4a06796bfe72361978971297c959e102630ff43fc016495e1da7fec4236.tar.gz\r\nExploding layer: sha256:ce36c489b0dda0f85eae0b5acbebe2f387911485192de2033565065dc5e56c61.tar.gz\r\nExploding layer: sha256:911e73949586049765f24eceef0fefa423147d8822c10d26052178ddb7b48a4f.tar.gz\r\nExploding layer: sha256:1e3d0657a09e69261566b90c8444984707b2d3359e69d7aec1d82a5b0397f341.tar.gz\r\nSingularity: docker-extract (U=0,P=61)> Failed removing file: /tmp/.singularity-build.FWD4uX/var/lib/yum/yumdb/a/26cb720a7995364140e82e072b2171e73d64759c-audit-libs-2.8.1-3.el7-x86_64\r\nWARNING: Failed removing file: /tmp/.singularity-build.FWD4uX/var/lib/yum/yumdb/a/26cb720a7995364140e82e072b2171e73d64759c-audit-libs-2.8.1-3.el7-x86_64\r\nSingularity: docker-extract (U=0,P=61)> Error applying whiteout marker from docker layer.\r\nERROR  : Error applying whiteout marker from docker layer.\r\nSingularity: docker-extract (U=0,P=61)> Retval = 255\r\nABORT  : Retval = 255\r\nCleaning up...\r\nERROR: pulling container failed!\r\n```\r\n\r\n### Steps to reproduce behavior\r\nI run singularity inside my docker-singularity-image also propagate host /sys/fs/cgroup for downstream image to use\r\n```\r\ndocker run -it --cap-add=SYS_ADMIN \\\r\n  -v /sys/fs/cgroup:/sys/fs/cgroup:ro \\\r\n  -v $(pwd):/home/dev/Code \\\r\n  sinonkt/docker-centos7-singularity-nextflow \\\r\n  /bin/bash \\\r\n```\r\n```\r\nsingularity pull --name sinonkt-docker-slurm-simulator-latest.img docker://sinonkt/docker-slurm-simulator:latest\r\n```\r\n\r\n"}}
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