Hello, pore-c has a series of dependencies that are of interest for Debian as a whole and still missing
python3-pyarrow python3-streamz, python3-pyranges, python3-pairtools, python3-ncls, python3-intake The package builds but does not run without these. In an attempt to push what I have, I ran into remote: GitLab: LFS objects are missing. Ensure LFS is properly set up or try a manual "git lfs push --all". To salsa.debian.org:med-team/pore-c.git ! [remote rejected]master -> master (pre-receive hook declined) ! [remote rejected]pristine-tar -> pristine-tar (pre-receive hook declined) ! [remote rejected]upstream -> upstream (pre-receive hook declined) error: failed to push some refs to 'salsa.debian.org:med-team/pore-c.git' $ git lfs push --all Specify a remote and a remote branch name (`git lfs push origin master`) $ git lfs push origin master Locking support detected on remote "origin". Consider enabling it with: $ git config lfs.https://salsa.debian.org/med-team/pore-c.git/info/lfs.locksverify true LFS upload failed:cts: 0% (0/23), 0 B | 0 B/s (missing) tests/data/NlaIII_run01_GRCh38.haplotagged.bam (1214675dd07b5a072ecbe9bf22ae7513c6f2c6b1435a86c0b8b93e6e85da6293) (missing) tests/data/NlaIII_GRCh38.contacts.parquet/part.0.parquet (94b3ebd6d94f10a2de3093d46473a51c003cd41713c9b3712d56ab30b676e193) (missing) tests/data/NlaIII_GRCh38.concatemers.parquet/_metadata (91d16d1ec1483db8b8080179ba9b485dce5bb625110768c23c348df6bef19e60) (missing) tests/data/GM12878_NlaIII_reads.tsv (7ce4529be82183332f9f3e37fa85f19a0a2aa5afa887f742145016bb2edcca53) (missing) tests/data/GRCh38.chromsizes (50e35247e1305e2a0a1fd1b7c07ff3576cec9389382d611c19eb0055633fc82b) (missing) tests/data/GM12878.phased.conf.vcf.gz (a7efa2fe2641ac2c76c0596ad628f90d9a8531856115f8b840379e95ee0709c8) (missing) tests/data/GM12878_NlaIII_reads.fq.gz (9d722847361b9c2d037d50d7e9cd126c958f5a0f689694fe5dfef37ae3ac1c4a) (missing) tests/data/GRCh38.fasta.gz.gzi (be5698ffc76f644f9483d04b3d58c8c2c7f0ba6a1fd37e78ac5eb99f5901e4f3) (missing) tests/data/NlaIII_GRCh38.contacts.parquet/_common_metadata (950401c687f40c995d415799583fa38ed1e063ceddd500d77c182388dda35d00) (missing) tests/data/NlaIII_run01_GRCh38.align_table.parquet/_common_metadata (82b94a7abce2fe49c8321de6ce5cb127c832e6de3dd74aa1c0e756098ab26e86) (missing) tests/data/NlaIII_GRCh38.vd.fragments.parquet/_metadata (b97516f9b93688053d27efe7f604fde9573e63444354e42d31507922df8ca3b1) (missing) tests/data/GRCh38.fasta.gz.fai (cbd68404c124a5e3ee4e4335bf907cbd0db00b1a077d695042495260716dfd9b) (missing) tests/data/GRCh38.fasta.gz (79582e1bbeec718000027048849a6413ee576f17c1d9aa877211db1f8d6a7b1b) (missing) tests/data/NlaIII_run01_GRCh38.read_sort.bam (b451a851e775d7c364eb844feafa1a0054939be6035b0e6cfb808d2e13db2f82) (missing) tests/data/test_ns.sam (d9a0a31551e5cec6444e9fbfb6b87f0b644ef5a4ab9bad09329a856eb39160de) (missing) tests/data/GM12878.phased.conf.vcf.gz.tbi (0db1dcb337cfe2d23dd6d2369b49ec1414961ee2305e635ca6af7289aacf16ab) (missing) tests/data/NlaIII_GRCh38.contacts.parquet/_metadata (83aaf5e4f09b9cafa30446bd3f8016164c450d23ba840cbd62bcef55049e3356) Uploading LFS objects: 0% (0/23), 0 B | 0 B/s, done. (missing) tests/data/NlaIII_GRCh38.concatemers.parquet/part.0.parquet (24ce696c45a21106d36ca97278f49ac707c1d77b97f86c77408ae0ee42c9905f) (missing) tests/data/NlaIII_run01_GRCh38.align_table.parquet/_metadata (42660830367bfa83ef9b4a5a501bdf0e19fd6c3a826210e8098e297443aad04e) (missing) tests/data/NlaIII_GRCh38.vd.fragments.parquet/part.0.parquet (6684beefe4fa555e3ef5ba2dca13769cda043424c08ac8f2b647471d7b587c80) (missing) tests/data/NlaIII_run01_GRCh38.align_table.parquet/part.0.parquet (8fecdb8434662f0c0892dcdd103078ff2c48c96f40cc3546a9e76638b9c42740) (missing) tests/data/NlaIII_GRCh38.concatemers.parquet/_common_metadata (ec1a8f121551b7d0bccc8f2eb4097742029b30068313dc15a932b701e4d91b0c) (missing) tests/data/NlaIII_GRCh38.vd.fragments.parquet/_common_metadata (2902630654ed49ea1ea6648dc21bba0c20b499fa6182a6b2ec6b531b7564cb6e) hint: Your push was rejected due to missing or corrupt local objects. hint: You can disable this check with: 'git config lfs.allowincompletepush true' Well, kind of curious I did enable it, but could not push --all. After also pushing upstream, I went for pristine-tar without lsf $ git push --set-upstream origin pristine-tar Enumerating objects: 4, done. Counting objects: 100% (4/4), done. Delta compression using up to 2 threads Compressing objects: 100% (3/3), done. Writing objects: 100% (4/4), 3.11 KiB | 3.11 MiB/s, done. Total 4 (delta 0), reused 0 (delta 0), pack-reused 0 To salsa.debian.org:med-team/pore-c.git * [new branch] pristine-tar -> pristine-tar Branch 'pristine-tar' set up to track remote branch 'pristine-tar' from 'origin'. moeller@steffen-laptop-debian:~/git/med-team/pore-c/pore-c$ git checkout master Downloading tests/data/GM12878.phased.conf.vcf.gz (516 KB) Error downloading object: tests/data/GM12878.phased.conf.vcf.gz (a7efa2f): Smudge error: Error downloading tests/data/GM12878.phased.conf.vcf.gz (a7efa2fe2641ac2c76c0596ad628f90d9a853 1856115f8b840379e95ee0709c8): [a7efa2fe2641ac2c76c0596ad628f90d9a8531856115f8b840379e95ee0709c8] Object does not exist on the server or you don't have permissions to access it: [404] Object does not exist on the server or you don't have permissions to access it Errors logged to /home/moeller/git/med-team/pore-c/pore-c/.git/lfs/logs/20200608T030628.335563029.log Use `git lfs logs last` to view the log. error: external filter 'git-lfs filter-process' failed fatal: tests/data/GM12878.phased.conf.vcf.gz: smudge filter lfs failed moeller@steffen-laptop-debian:~/git/med-team/pore-c/pore-c$ git branch master * pristine-tar upstream Hm. Ok. This is all new to me. I know about the large file support, but why is this enforced on me when working with a regular tarball that is not even big (most likely because of those special files pointing to external data). My immediate response would be to remove the test data and find other ways to perform the testing. Steffen
