rm from image don't work

[sbvitok]

Describe the bug
RUN rm -vf /etc/yum.repos.d/* do not delete files

To Reproduce

viktor@viktor:~/skopeo$ cat Dockerfile
FROM centos:7
RUN rm -vf /etc/yum.repos.d/*
RUN ls -la /etc/yum.repos.d/
viktor@viktor:~/skopeo$ 

function makisu_build() {
    makisu_version=${MAKISU_VERSION:-latest}
    cd ${@: -1}
    docker run -i --rm --net host \
        -v /var/run/docker.sock:/docker.sock \
        -e DOCKER_HOST=unix:///docker.sock \
        -v $(pwd):/makisu-context \
        -v /tmp/makisu-storage:/makisu-storage \
        gcr.io/uber-container-tools/makisu:$makisu_version build \
            --commit=explicit \
            --modifyfs=true \
            --load \
            ${@:1:${#@}-1} /makisu-context
    cd -
}

makisu_build -t myimage .

Log:

Unable to find image 'gcr.io/uber-container-tools/makisu:latest' locally
latest: Pulling from uber-container-tools/makisu
b3399c6d8f6e: Pull complete 
b917792f5627: Pull complete 
Digest: sha256:4cf8eed574a4721e05d2d183d269233ad609048f36555880f8414a5952ac4a1e
Status: Downloaded newer image for gcr.io/uber-container-tools/makisu:latest
{"level":"info","ts":1584001610.9922383,"msg":"Starting Makisu build (version=v0.1.14)"}
{"level":"info","ts":1584001610.992901,"msg":"Using build context: /makisu-context"}
{"level":"info","ts":1584001610.9929953,"msg":"Using local file at /makisu-storage/cache_key_value.json for cacheID storage"}
{"level":"info","ts":1584001610.993019,"msg":"No registry information provided, using cached layers"}
{"level":"info","ts":1584001610.9931283,"msg":"* Stage 1/1 : (alias=0,latestfetched=-1)"}
{"level":"info","ts":1584001610.993147,"msg":"* Step 1/3 (commit,modifyfs) : FROM centos:7  (793cfec8)"}
{"level":"info","ts":1584001610.9931998,"msg":"* Started pulling image index.docker.io/library/centos:7"}
{"level":"info","ts":1584001612.9689603,"msg":"* Started pulling layer index.docker.io/library/centos:sha256:ab5ef0e5819490abe86106fd9f4381123e37a03e80e650be39f7938d30ecb530"}
{"level":"info","ts":1584001613.372902,"msg":"* Started pulling layer index.docker.io/library/centos:sha256:5e35e350aded98340bc8fcb0ba392d809c807bc3eb5c618d4a0674d98d88bccd"}
{"level":"info","ts":1584001614.0140715,"msg":"* Finished pulling layer library/centos:5e35e350aded98340bc8fcb0ba392d809c807bc3eb5c618d4a0674d98d88bccd"}
{"level":"info","ts":1584001618.0624764,"msg":"* Finished pulling layer library/centos:ab5ef0e5819490abe86106fd9f4381123e37a03e80e650be39f7938d30ecb530"}
{"level":"info","ts":1584001618.062845,"msg":"* Pulled image index.docker.io/library/centos:7","duration":7.069613329}
{"level":"info","ts":1584001618.065863,"msg":"* Processing FROM layer ab5ef0e5819490abe86106fd9f4381123e37a03e80e650be39f7938d30ecb530"}
{"level":"info","ts":1584001620.9950323,"msg":"* Untarred 10735 files to /","duration":2.929}
{"level":"info","ts":1584001621.3382373,"msg":"* Merged 10735 headers from tar to memfs"}
{"level":"info","ts":1584001621.3382676,"msg":"* Executed FROM centos:7  (793cfec8)","duration":10.345111911}
{"level":"info","ts":1584001621.3385255,"msg":"* Committed gzipped layer sha256:ab5ef0e5819490abe86106fd9f4381123e37a03e80e650be39f7938d30ecb530 (75780712 bytes)"}
{"level":"info","ts":1584001621.3385367,"msg":"* Pushing with cache ID 793cfec8"}
{"level":"info","ts":1584001621.338705,"msg":"* Step 2/3 (modifyfs) : RUN rm -vf /etc/yum.repos.d/*  (a4de2c2e)"}
{"level":"info","ts":1584001621.3407612,"msg":"removed '/etc/yum.repos.d/CentOS-Base.repo'\nremoved '/etc/yum.repos.d/CentOS-CR.repo'\nremoved '/etc/yum.repos.d/CentOS-Debuginfo.repo'\nremoved '/etc/yum.repos.d/CentOS-Media.repo'\nremoved '/etc/yum.repos.d/CentOS-Sources.repo'\nremoved '/etc/yum.repos.d/CentOS-Vault.repo'\nremoved '/etc/yum.repos.d/CentOS-fasttrack.repo'\n"}
{"level":"info","ts":1584001621.3409705,"msg":"* Executed RUN rm -vf /etc/yum.repos.d/*  (a4de2c2e)","duration":0.002247052}
{"level":"info","ts":1584001621.3410249,"msg":"* Not committing step RUN rm -vf /etc/yum.repos.d/*  (a4de2c2e)"}
{"level":"info","ts":1584001621.3413975,"msg":"* Step 3/3 (commit,modifyfs) : RUN ls -la /etc/yum.repos.d/  (a8d9861b)"}
{"level":"info","ts":1584001621.3441672,"msg":"total 8\ndrwxr-xr-x 2 root root 4096 Mar 12 08:27 .\ndrwxr-xr-x 1 root root 4096 Oct  1 01:16 ..\n"}
{"level":"info","ts":1584001621.3444872,"msg":"* Executed RUN ls -la /etc/yum.repos.d/  (a8d9861b)","duration":0.003066722}
{"level":"info","ts":1584001622.472696,"msg":"* Collecting filesystem diff"}
{"level":"info","ts":1584001622.9690194,"msg":"* Collected diff: 2639 files found","duration":0.496}
{"level":"info","ts":1584001623.1695855,"msg":"* Created layer by scanning filesystem; 2639 files found"}
{"level":"info","ts":1584001623.1705265,"msg":"* Committed gzipped layer sha256:4113c0e748f1d67bcb1863cabcd607b09a58030fe90957997248533595da4f8f (2564597 bytes)"}
{"level":"info","ts":1584001623.17054,"msg":"* Pushing with cache ID a8d9861b"}
{"level":"error","ts":1584001623.513886,"msg":"Failed to push cache: registry client not configured to push cache; registry client not configured to push cache"}
{"level":"info","ts":1584001623.5143762,"msg":"Computed total image size 78345309","total_image_size":78345309}
{"level":"info","ts":1584001623.51439,"msg":"Successfully built image myimage:latest"}
{"level":"info","ts":1584001623.5143943,"msg":"Loading image myimage:latest"}
{"level":"info","ts":1584001623.5145717,"msg":"Image tarrer dir: /makisu-storage/sandbox/sandbox243799103/myimage/latest"}
{"level":"info","ts":1584001625.1112688,"msg":"Successfully loaded image myimage:latest"}
{"level":"info","ts":1584001625.111357,"msg":"Finished building myimage:latest"}
/home/viktor/skopeo

$ docker run --rm myimage:latest ls -la /etc/yum.repos.d/
drwxr-xr-x 1 root root 4096 Mar 12 08:27 .
drwxr-xr-x 1 root root 4096 Mar 12 08:28 ..
-rw-r--r-- 1 root root 1664 Sep  5  2019 CentOS-Base.repo
-rw-r--r-- 1 root root 1309 Sep  5  2019 CentOS-CR.repo
-rw-r--r-- 1 root root  649 Sep  5  2019 CentOS-Debuginfo.repo
-rw-r--r-- 1 root root  630 Sep  5  2019 CentOS-Media.repo
-rw-r--r-- 1 root root 1331 Sep  5  2019 CentOS-Sources.repo
-rw-r--r-- 1 root root 6639 Sep  5  2019 CentOS-Vault.repo
-rw-r--r-- 1 root root  314 Sep  5  2019 CentOS-fasttrack.repo

Expected behavior
docker run --rm myimage:latest ls -la /etc/yum.repos.d/
must display 0 files

[sbvitok]

any news?

[yiranwang52]

we are seeing this issue in our production environment too; working on fix.