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Joey Hess 2022-11-09 13:31:16 -04:00
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### Please describe the problem.
When exporting commits to S3 with versioning=yes and exporttree=yes, deleted annexed objects are marked as deleted but deleted git objects remain. This prevents a user from retrieving a consistent version of the exporttree commit without using git-annex.
### What steps will reproduce the problem?
* Create a repository and add annexed and git objects.
* Add S3 special remote with exporttree=yes and versioning=yes
* Export to the remote.
* Remove a git object and an annexed object.
* Export again and the annexed object will be removed while the git object remains.
Example repository and publicly readable remote having this issue here:
https://github.com/openneurodatasets/ds001705
Git files in the 1.0.0 tag are still present in the S3 1.0.1 export. sub-000101/ses-baseline/pet/sub-000101_ses-baseline_rec-MLEM_pet.json is an example file not present in 1.0.1 that is still present on S3.
### What version of git-annex are you using? On what operating system?
Debian bullseye
```
git-annex version: 10.20220927-ga92546587
build flags: Assistant Webapp Pairing Inotify DBus DesktopNotify TorrentParser MagicMime Benchmark Feeds Testsuite S3 WebDAV
dependency versions: aws-0.22 bloomfilter-2.0.1.0 cryptonite-0.26 DAV-1.3.4 feed-1.3.0.1 ghc-8.8.4 http-client-0.6.4.1 persistent-sqlite-2.10.6.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.1.0
key/value backends: SHA256E SHA256 SHA512E SHA512 SHA224E SHA224 SHA384E SHA384 SHA3_256E SHA3_256 SHA3_512E SHA3_512 SHA3_224E SHA3_224 SHA3_384E SHA3_384 SKEIN256E SKEIN256 SKEIN512E SKEIN512 BLAKE2B256E BLAKE2B256 BLAKE2B512E BLAKE2B512 BLAKE2B160E BLAKE2B160 BLAKE2B224E BLAKE2B224 BLAKE2B384E BLAKE2B384 BLAKE2BP512E BLAKE2BP512 BLAKE2S256E BLAKE2S256 BLAKE2S160E BLAKE2S160 BLAKE2S224E BLAKE2S224 BLAKE2SP256E BLAKE2SP256 BLAKE2SP224E BLAKE2SP224 SHA1E SHA1 MD5E MD5 WORM URL X*
remote types: git gcrypt p2p S3 bup directory rsync web bittorrent webdav adb tahoe glacier ddar git-lfs httpalso borg hook external
operating system: linux x86_64
supported repository versions: 8 9 10
upgrade supported from repository versions: 0 1 2 3 4 5 6 7 8 9 10
local repository version: 10
```
### Please provide any additional information below.
[[!format sh """
# git annex export 1.0.0 --to=s3-PUBLIC
export s3-PUBLIC .bidsignore
ok
export s3-PUBLIC .datalad/.gitattributes
ok
export s3-PUBLIC .datalad/config
ok
export s3-PUBLIC .gitattributes
ok
export s3-PUBLIC CHANGES
ok
export s3-PUBLIC README
ok
export s3-PUBLIC dataset_description.json
ok
export s3-PUBLIC sub-000101/ses-baseline/anat/sub-000101_ses-baseline_T1w.nii.gz
ok
export s3-PUBLIC sub-000101/ses-baseline/anat/sub-000101_ses-baseline_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/.bidsignore
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_K1.nii.gz
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_Vb.nii.gz
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_k2.nii.gz
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_k3.nii.gz
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_k4.nii.gz
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000101/ses-displaced/anat/sub-000101_ses-displaced_T1w.nii.gz
ok
export s3-PUBLIC sub-000101/ses-displaced/anat/sub-000101_ses-displaced_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000101/ses-displaced/pet/.bidsignore
ok
export s3-PUBLIC sub-000101/ses-displaced/pet/sub-000101_ses-displaced_k3.nii.gz
ok
export s3-PUBLIC sub-000101/ses-displaced/pet/sub-000101_ses-displaced_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000101/ses-displaced/pet/sub-000101_ses-displaced_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000102/ses-baseline/anat/sub-000102_ses-baseline_T1w.nii.gz
ok
export s3-PUBLIC sub-000102/ses-baseline/anat/sub-000102_ses-baseline_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/.bidsignore
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_K1.nii.gz
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_Vb.nii.gz
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_k2.nii.gz
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_k3.nii.gz
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_k4.nii.gz
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000102/ses-displaced/anat/sub-000102_ses-displaced_T1w.nii.gz
ok
export s3-PUBLIC sub-000102/ses-displaced/anat/sub-000102_ses-displaced_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000102/ses-displaced/pet/.bidsignore
ok
export s3-PUBLIC sub-000102/ses-displaced/pet/sub-000102_ses-displaced_k3.nii.gz
ok
export s3-PUBLIC sub-000102/ses-displaced/pet/sub-000102_ses-displaced_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000102/ses-displaced/pet/sub-000102_ses-displaced_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000103/ses-baseline/anat/sub-000103_ses-baseline_T1w.nii.gz
ok
export s3-PUBLIC sub-000103/ses-baseline/anat/sub-000103_ses-baseline_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/.bidsignore
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_K1.nii.gz
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_Vb.nii.gz
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_k2.nii.gz
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_k3.nii.gz
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_k4.nii.gz
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000103/ses-displaced/anat/sub-000103_ses-displaced_T1w.nii.gz
ok
export s3-PUBLIC sub-000103/ses-displaced/anat/sub-000103_ses-displaced_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000103/ses-displaced/pet/.bidsignore
ok
export s3-PUBLIC sub-000103/ses-displaced/pet/sub-000103_ses-displaced_k3.nii.gz
ok
export s3-PUBLIC sub-000103/ses-displaced/pet/sub-000103_ses-displaced_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000103/ses-displaced/pet/sub-000103_ses-displaced_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000104/ses-baseline/anat/sub-000104_ses-baseline_T1w.nii.gz
ok
export s3-PUBLIC sub-000104/ses-baseline/anat/sub-000104_ses-baseline_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/.bidsignore
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_K1.nii.gz
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_Vb.nii.gz
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_k2.nii.gz
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_k3.nii.gz
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_k4.nii.gz
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000104/ses-displaced/anat/sub-000104_ses-displaced_T1w.nii.gz
ok
export s3-PUBLIC sub-000104/ses-displaced/anat/sub-000104_ses-displaced_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000104/ses-displaced/pet/.bidsignore
ok
export s3-PUBLIC sub-000104/ses-displaced/pet/sub-000104_ses-displaced_k3.nii.gz
ok
export s3-PUBLIC sub-000104/ses-displaced/pet/sub-000104_ses-displaced_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000104/ses-displaced/pet/sub-000104_ses-displaced_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000105/ses-baseline/anat/sub-000105_ses-baseline_T1w.nii.gz
ok
export s3-PUBLIC sub-000105/ses-baseline/anat/sub-000105_ses-baseline_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/.bidsignore
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_K1.nii.gz
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_Vb.nii.gz
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_k2.nii.gz
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_k3.nii.gz
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_k4.nii.gz
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_rec-MLEM_pet.nii.gz
ok
export s3-PUBLIC sub-000105/ses-displaced/anat/sub-000105_ses-displaced_T1w.nii.gz
ok
export s3-PUBLIC sub-000105/ses-displaced/anat/sub-000105_ses-displaced_label-displacementROI_dseg.nii.gz
ok
export s3-PUBLIC sub-000105/ses-displaced/pet/.bidsignore
ok
export s3-PUBLIC sub-000105/ses-displaced/pet/sub-000105_ses-displaced_k3.nii.gz
ok
export s3-PUBLIC sub-000105/ses-displaced/pet/sub-000105_ses-displaced_rec-MLEM_pet.json
ok
export s3-PUBLIC sub-000105/ses-displaced/pet/sub-000105_ses-displaced_rec-MLEM_pet.nii.gz
ok
(recording state in git...)
# git annex export 1.0.1 --to=s3-PUBLIC
unexport s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_K1.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_k2.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_k3.nii.gz ok
unexport s3-PUBLIC .bidsignore ok
unexport s3-PUBLIC sub-000101/ses-baseline/anat/sub-000101_ses-baseline_T1w.nii.gz ok
rename s3-PUBLIC sub-000101/ses-baseline/anat/sub-000101_ses-baseline_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9793--13db6c96808070211b8987c327240ff8.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_Vb.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_K1.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_Vb.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-baseline/anat/sub-000104_ses-baseline_T1w.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-displaced/pet/sub-000104_ses-displaced_rec-MLEM_pet.nii.gz ok
unexport s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_k4.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_k3.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-displaced/anat/sub-000103_ses-displaced_T1w.nii.gz ok
unexport s3-PUBLIC sub-000105/ses-displaced/pet/sub-000105_ses-displaced_k3.nii.gz ok
rename s3-PUBLIC sub-000102/ses-displaced/anat/sub-000102_ses-displaced_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9794--419a63ecba6de7235554c1f5a7fbc7d8.nii.gz ok
rename s3-PUBLIC sub-000102/ses-baseline/anat/sub-000102_ses-baseline_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9793--45358ccfe2d8a7455c3202691ee632eb.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_rec-MLEM_pet.nii.gz ok
rename s3-PUBLIC sub-000105/ses-baseline/anat/sub-000105_ses-baseline_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9793--508a92de80b90e3030d2e46bb920f051.nii.gz ok
rename s3-PUBLIC sub-000101/ses-displaced/anat/sub-000101_ses-displaced_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9794--512f12576f0f99de20f12aa715000251.nii.gz ok
unexport s3-PUBLIC dataset_description.json ok
unexport s3-PUBLIC sub-000105/ses-displaced/pet/sub-000105_ses-displaced_rec-MLEM_pet.nii.gz ok
unexport s3-PUBLIC CHANGES ok
unexport s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_Vb.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-displaced/anat/sub-000101_ses-displaced_T1w.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_K1.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_K1.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_rec-MLEM_pet.nii.gz ok
rename s3-PUBLIC sub-000105/ses-displaced/anat/sub-000105_ses-displaced_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9794--726e1c95511fb7b8bc94f275e9d6e9e7.nii.gz ok
unexport s3-PUBLIC sub-000105/ses-baseline/anat/sub-000105_ses-baseline_T1w.nii.gz ok
unexport s3-PUBLIC sub-000105/ses-displaced/pet/.bidsignore ok
unexport s3-PUBLIC sub-000105/ses-displaced/anat/sub-000105_ses-displaced_T1w.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_Vb.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-displaced/pet/sub-000103_ses-displaced_rec-MLEM_pet.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_rec-MLEM_pet.nii.gz ok
rename s3-PUBLIC sub-000103/ses-displaced/anat/sub-000103_ses-displaced_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9794--887598ee2277aeebae901fd7d97a7f4c.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_k4.nii.gz ok
unexport s3-PUBLIC sub-000105/ses-displaced/pet/sub-000105_ses-displaced_rec-MLEM_pet.json ok
unexport s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_Vb.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_k3.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-displaced/pet/sub-000103_ses-displaced_k3.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_k4.nii.gz ok
unexport s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_k3.nii.gz ok
unexport s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_rec-MLEM_pet.nii.gz ok
unexport s3-PUBLIC sub-000103/ses-baseline/anat/sub-000103_ses-baseline_T1w.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-displaced/anat/sub-000102_ses-displaced_T1w.nii.gz ok
unexport s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_k2.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-displaced/pet/sub-000101_ses-displaced_k3.nii.gz ok
unexport s3-PUBLIC README ok
rename s3-PUBLIC sub-000104/ses-displaced/anat/sub-000104_ses-displaced_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9794--bd645a943d74dda136f4e0c421d49c85.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-displaced/pet/sub-000104_ses-displaced_k3.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_K1.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-displaced/pet/sub-000101_ses-displaced_rec-MLEM_pet.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-displaced/pet/sub-000102_ses-displaced_k3.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-baseline/anat/sub-000102_ses-baseline_T1w.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_k2.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_k4.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_k2.nii.gz ok
rename s3-PUBLIC sub-000104/ses-baseline/anat/sub-000104_ses-baseline_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9793--de819fa10f3f6253e4eeec3b77158726.nii.gz ok
unexport s3-PUBLIC sub-000102/ses-displaced/pet/sub-000102_ses-displaced_rec-MLEM_pet.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_k3.nii.gz ok
rename s3-PUBLIC sub-000103/ses-baseline/anat/sub-000103_ses-baseline_label-displacementROI_dseg.nii.gz -> .git-annex-tmp-content-MD5E-s9793--e6f2a37df1a0a47325fc9cb065117e0d.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_k2.nii.gz ok
unexport s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_rec-MLEM_pet.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_k4.nii.gz ok
unexport s3-PUBLIC sub-000104/ses-displaced/anat/sub-000104_ses-displaced_T1w.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9793--13db6c96808070211b8987c327240ff8.nii.gz -> derivatives/masks/sub-000101/ses-baseline/sub-000101_ses-baseline_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9794--419a63ecba6de7235554c1f5a7fbc7d8.nii.gz -> derivatives/masks/sub-000102/ses-displaced/sub-000102_ses-displaced_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9793--45358ccfe2d8a7455c3202691ee632eb.nii.gz -> derivatives/masks/sub-000102/ses-baseline/sub-000102_ses-baseline_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9793--508a92de80b90e3030d2e46bb920f051.nii.gz -> derivatives/masks/sub-000105/ses-baseline/sub-000105_ses-baseline_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9794--512f12576f0f99de20f12aa715000251.nii.gz -> derivatives/masks/sub-000101/ses-displaced/sub-000101_ses-displaced_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9794--726e1c95511fb7b8bc94f275e9d6e9e7.nii.gz -> derivatives/masks/sub-000105/ses-displaced/sub-000105_ses-displaced_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9794--887598ee2277aeebae901fd7d97a7f4c.nii.gz -> derivatives/masks/sub-000103/ses-displaced/sub-000103_ses-displaced_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9794--bd645a943d74dda136f4e0c421d49c85.nii.gz -> derivatives/masks/sub-000104/ses-displaced/sub-000104_ses-displaced_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9793--de819fa10f3f6253e4eeec3b77158726.nii.gz -> derivatives/masks/sub-000104/ses-baseline/sub-000104_ses-baseline_label-displacementROI_dseg.nii.gz ok
rename s3-PUBLIC .git-annex-tmp-content-MD5E-s9793--e6f2a37df1a0a47325fc9cb065117e0d.nii.gz -> derivatives/masks/sub-000103/ses-baseline/sub-000103_ses-baseline_label-displacementROI_dseg.nii.gz ok
export s3-PUBLIC .bidsignore
ok
export s3-PUBLIC CHANGES
ok
export s3-PUBLIC LICENSE
ok
export s3-PUBLIC README
ok
export s3-PUBLIC dataset_description.json
ok
export s3-PUBLIC derivatives/masks/dseg.tsv
ok
export s3-PUBLIC participants.json
ok
export s3-PUBLIC participants.tsv
ok
export s3-PUBLIC sub-000101/ses-baseline/anat/sub-000101_ses-baseline_T1w.json
ok
export s3-PUBLIC sub-000101/ses-baseline/anat/sub-000101_ses-baseline_T1w.nii
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_pet.json
ok
export s3-PUBLIC sub-000101/ses-baseline/pet/sub-000101_ses-baseline_pet.nii
ok
export s3-PUBLIC sub-000101/ses-displaced/anat/sub-000101_ses-displaced_T1w.json
ok
export s3-PUBLIC sub-000101/ses-displaced/anat/sub-000101_ses-displaced_T1w.nii
ok
export s3-PUBLIC sub-000101/ses-displaced/pet/sub-000101_ses-displaced_pet.json
ok
export s3-PUBLIC sub-000101/ses-displaced/pet/sub-000101_ses-displaced_pet.nii
ok
export s3-PUBLIC sub-000102/ses-baseline/anat/sub-000102_ses-baseline_T1w.json
ok
export s3-PUBLIC sub-000102/ses-baseline/anat/sub-000102_ses-baseline_T1w.nii
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_pet.json
ok
export s3-PUBLIC sub-000102/ses-baseline/pet/sub-000102_ses-baseline_pet.nii
ok
export s3-PUBLIC sub-000102/ses-displaced/anat/sub-000102_ses-displaced_T1w.json
ok
export s3-PUBLIC sub-000102/ses-displaced/anat/sub-000102_ses-displaced_T1w.nii
ok
export s3-PUBLIC sub-000102/ses-displaced/pet/sub-000102_ses-displaced_pet.json
ok
export s3-PUBLIC sub-000102/ses-displaced/pet/sub-000102_ses-displaced_pet.nii
ok
export s3-PUBLIC sub-000103/ses-baseline/anat/sub-000103_ses-baseline_T1w.json
ok
export s3-PUBLIC sub-000103/ses-baseline/anat/sub-000103_ses-baseline_T1w.nii
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_pet.json
ok
export s3-PUBLIC sub-000103/ses-baseline/pet/sub-000103_ses-baseline_pet.nii
ok
export s3-PUBLIC sub-000103/ses-displaced/anat/sub-000103_ses-displaced_T1w.json
ok
export s3-PUBLIC sub-000103/ses-displaced/anat/sub-000103_ses-displaced_T1w.nii
ok
export s3-PUBLIC sub-000103/ses-displaced/pet/sub-000103_ses-displaced_pet.json
ok
export s3-PUBLIC sub-000103/ses-displaced/pet/sub-000103_ses-displaced_pet.nii
ok
export s3-PUBLIC sub-000104/ses-baseline/anat/sub-000104_ses-baseline_T1w.json
ok
export s3-PUBLIC sub-000104/ses-baseline/anat/sub-000104_ses-baseline_T1w.nii
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_pet.json
ok
export s3-PUBLIC sub-000104/ses-baseline/pet/sub-000104_ses-baseline_pet.nii
ok
export s3-PUBLIC sub-000104/ses-displaced/anat/sub-000104_ses-displaced_T1w.json
ok
export s3-PUBLIC sub-000104/ses-displaced/anat/sub-000104_ses-displaced_T1w.nii
ok
export s3-PUBLIC sub-000104/ses-displaced/pet/sub-000104_ses-displaced_pet.json
ok
export s3-PUBLIC sub-000104/ses-displaced/pet/sub-000104_ses-displaced_pet.nii
ok
export s3-PUBLIC sub-000105/ses-baseline/anat/sub-000105_ses-baseline_T1w.json
ok
export s3-PUBLIC sub-000105/ses-baseline/anat/sub-000105_ses-baseline_T1w.nii
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_pet.json
ok
export s3-PUBLIC sub-000105/ses-baseline/pet/sub-000105_ses-baseline_pet.nii
ok
export s3-PUBLIC sub-000105/ses-displaced/anat/sub-000105_ses-displaced_T1w.json
ok
export s3-PUBLIC sub-000105/ses-displaced/anat/sub-000105_ses-displaced_T1w.nii
ok
export s3-PUBLIC sub-000105/ses-displaced/pet/sub-000105_ses-displaced_pet.json
ok
export s3-PUBLIC sub-000105/ses-displaced/pet/sub-000105_ses-displaced_pet.nii
ok
(recording state in git...)
# End of transcript or log.
"""]]
### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
Thank you for all your work making this wonderful tool!

51
doc/bugs/introduction_of_aws-0.23_causes_stack_bld_to_fail.mdwn Normal file
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@ -0,0 +1,51 @@
### Please describe the problem.
After aws-0.23 was introduced into extra-deps of `stack.yaml`, a stack build fails
in the dependency resolution phase (a plan construction problem). Adding `aeson-2.1.1.0`
into extra-deps as advised leads to a dependency hell with conflicting versions of
attoparsec being required amongst other troubles.
### What steps will reproduce the problem?
`stack setup && stack build`. Observe the following output:
[[!format sh """
Error: While constructing the build plan, the following exceptions were encountered:
In the dependencies for aws-0.23:
aeson-1.5.6.0 from stack configuration does not match >=2.0.0.0 (latest matching version
is 2.1.1.0)
needed due to git-annex-10.20221103 -> aws-0.23
Some different approaches to resolving this:
* Set 'allow-newer: true'
in C:\hs-stack\config.yaml to ignore all version constraints and build anyway.
* Recommended action: try adding the following to your extra-deps
in C:\Projektit\git-annex.branchable.com\git-annex--BUILD-221108-4f6c6114f\stack.yaml:
- aeson-2.1.1.0@sha256:103ceb1421cd0ffa810bfb1acb1261d60addbde1a041fb5cce0056ff7d7dcdc2,5980
Plan construction failed.
# End of transcript or log.
"""]]
### What version of git-annex are you using? On what operating system?
I was trying to build master or [[!commit 4f6c6114fb487b5f84aa7e6922786b0e19806525]], but alas no luck.
Windows 10 version 22H2 (build 19045.2130), 64 bit.
Stack version 2.9.1, Git revision 409d56031b4240221d656db09b2ba476fe6bb5b1 x86_64 hpack-0.35.0 .
### Please provide any additional information below.
.
### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
Sure, I use it several times a week with my multigigabyte backups, where it gives structure to my image-based backup routines, so you could say I'm a believer. :)
[[!meta author=jkniiv]]
[[!meta title="introduction of aws-0.23 causes stack build to fail"]]