Created
April 22, 2020 03:13
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| $ java -jar ~/Desktop/bfg-1.13.0.jar --strip-blobs-bigger-than 600K . | |
| Using repo : /Users/lcollado/Dropbox/Code/spatialLIBD/./.git | |
| This repo has been processed by The BFG before! Will prune repo before proceeding - to avoid unnecessary cleaning work on unused objects... | |
| Completed prune of old objects - will now proceed with the main job! | |
| Scanning packfile for large blobs: 4459 | |
| Scanning packfile for large blobs completed in 133 ms. | |
| Found 33 blob ids for large blobs - biggest=1542678 smallest=660317 | |
| Total size (unpacked)=28483493 | |
| Found 125 objects to protect | |
| Found 5 commit-pointing refs : HEAD, refs/heads/master, refs/remotes/origin/gh-pages, ... | |
| Protected commits | |
| ----------------- | |
| These are your protected commits, and so their contents will NOT be altered: | |
| * commit f245d61a (protected by 'HEAD') - contains 2 dirty files : | |
| - man/figures/README-access_data-1.png (987.6 KB) | |
| - man/figures/paper_figure1.jpg (1.2 MB) | |
| WARNING: The dirty content above may be removed from other commits, but as | |
| the *protected* commits still use it, it will STILL exist in your repository. | |
| Details of protected dirty content have been recorded here : | |
| /Users/lcollado/Dropbox/Code/spatialLIBD/..bfg-report/2020-04-21/21-14-31/protected-dirt/ | |
| If you *really* want this content gone, make a manual commit that removes it, | |
| and then run the BFG on a fresh copy of your repo. | |
| Cleaning | |
| -------- | |
| Found 147 commits | |
| Cleaning commits: 100% (147/147) | |
| Cleaning commits completed in 2,067 ms. | |
| Updating 4 Refs | |
| --------------- | |
| Ref Before After | |
| -------------------------------------------------- | |
| refs/heads/master | f245d61a | c0493593 | |
| refs/remotes/origin/gh-pages | 22c0b18b | 95df6597 | |
| refs/remotes/origin/master | 504155ea | cb522dbd | |
| refs/tags/bioc_submission | df19c0d9 | 94810672 | |
| Updating references: 100% (4/4) | |
| ...Ref update completed in 29 ms. | |
| Commit Tree-Dirt History | |
| ------------------------ | |
| Earliest Latest | |
| | | | |
| .......................mmmmmmmmm...mmmmmmmmmmmmmmmmmmmmmmmmm | |
| D = dirty commits (file tree fixed) | |
| m = modified commits (commit message or parents changed) | |
| . = clean commits (no changes to file tree) | |
| Before After | |
| ------------------------------------------- | |
| First modified commit | 8bf29d77 | 1922efc8 | |
| Deleted files | |
| ------------- | |
| Filename Git id | |
| ----------------------------------------------------------------------- | |
| README-access_data-1.png | f04eedd4 (987.6 KB), 266da72e (988.1 KB) | |
| access_data-1.png | f9d35c4b (1001.7 KB), 266da72e (988.1 KB) | |
| geom_spatial-1.png | 07cde735 (962.8 KB), e6955fbe (1.5 MB) | |
| logo.ai | 3ac42c73 (870.9 KB) | |
| paper_figure1.jpg | c847a1e3 (1.2 MB) | |
| sce_image_clus-1.png | fd950f8d (1.4 MB), 5491266b (994.8 KB), ... | |
| sce_image_gene-1.png | 172664cb (785.9 KB), 03c173a8 (1.1 MB), ... | |
| sce_image_gene-2.png | 359f41d6 (1001.8 KB), 36188686 (1.0 MB), ... | |
| sig_genes_extract.html | 410a5f92 (1.4 MB), c551aa58 (1.4 MB), ... | |
| In total, 373 object ids were changed. Full details are logged here: | |
| /Users/lcollado/Dropbox/Code/spatialLIBD/..bfg-report/2020-04-21/21-14-31 | |
| BFG run is complete! When ready, run: git reflog expire --expire=now --all && git gc --prune=now --aggressive | |
| -- | |
| You can rewrite history in Git - don't let Trump do it for real! | |
| Trump's administration has lied consistently, to make people give up on ever | |
| being told the truth. Don't give up: https://www.theguardian.com/us-news/trump-administration | |
| -- | |
| $ git reflog expire --expire=now --all && git gc --prune=now --aggressive | |
| Enumerating objects: 1981, done. | |
| Counting objects: 100% (1981/1981), done. | |
| Delta compression using up to 4 threads | |
| Compressing objects: 100% (1859/1859), done. | |
| Writing objects: 100% (1981/1981), done. | |
| Total 1981 (delta 1352), reused 440 (delta 0), pack-reused 0 | |
| $ cd ~/Desktop/ | |
| $ git clone git@github.com:LieberInstitute/spatialLIBD.git | |
| Cloning into 'spatialLIBD'... | |
| remote: Enumerating objects: 954, done. | |
| remote: Counting objects: 100% (954/954), done. | |
| remote: Compressing objects: 100% (418/418), done. | |
| remote: Total 2171 (delta 635), reused 782 (delta 492), pack-reused 1217 | |
| Receiving objects: 100% (2171/2171), 36.23 MiB | 6.86 MiB/s, done. | |
| Resolving deltas: 100% (1377/1377), done. | |
| $ cd spatialLIBD/ | |
| 21:16 spatialLIBD $ du -sh . | |
| 46M . | |
| $ du -sh * | |
| 4.0K DESCRIPTION | |
| 4.0K NAMESPACE | |
| 4.0K NEWS.md | |
| 196K R | |
| 20K README.Rmd | |
| 24K README.md | |
| 4.0K _pkgdown.yml | |
| 4.0K app.R | |
| 4.0K codecov.yml | |
| 168K data | |
| 436K data-raw | |
| 136K dev | |
| 5.7M inst | |
| 2.3M man | |
| 236K pkgdown | |
| 8.0K tests | |
| 48K vignettes | |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| $ java -jar ~/Desktop/bfg-1.13.0.jar --strip-blobs-bigger-than 300K . | |
| Using repo : /Users/lcollado/Dropbox/Code/spatialLIBD/./.git | |
| This repo has been processed by The BFG before! Will prune repo before proceeding - to avoid unnecessary cleaning work on unused objects... | |
| Completed prune of old objects - will now proceed with the main job! | |
| Scanning packfile for large blobs: 3967 | |
| Scanning packfile for large blobs completed in 92 ms. | |
| Found 23 blob ids for large blobs - biggest=1270074 smallest=307427 | |
| Total size (unpacked)=11718638 | |
| Found 113 objects to protect | |
| Found 5 commit-pointing refs : HEAD, refs/heads/master, refs/remotes/origin/gh-pages, ... | |
| Protected commits | |
| ----------------- | |
| These are your protected commits, and so their contents will NOT be altered: | |
| * commit 94b172ae (protected by 'HEAD') - contains 3 dirty files : | |
| - data-raw/tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.csv (385.0 KB) | |
| - man/figures/README-access_data-1.png (987.6 KB) | |
| - man/figures/paper_figure1.jpg (1.2 MB) | |
| WARNING: The dirty content above may be removed from other commits, but as | |
| the *protected* commits still use it, it will STILL exist in your repository. | |
| Details of protected dirty content have been recorded here : | |
| /Users/lcollado/Dropbox/Code/spatialLIBD/..bfg-report/2020-04-21/21-22-03/protected-dirt/ | |
| If you *really* want this content gone, make a manual commit that removes it, | |
| and then run the BFG on a fresh copy of your repo. | |
| Cleaning | |
| -------- | |
| Found 148 commits | |
| Cleaning commits: 100% (148/148) | |
| Cleaning commits completed in 1,592 ms. | |
| Updating 4 Refs | |
| --------------- | |
| Ref Before After | |
| -------------------------------------------------- | |
| refs/heads/master | 94b172ae | 793d28c9 | |
| refs/remotes/origin/gh-pages | 95df6597 | fec455e7 | |
| refs/remotes/origin/master | c0493593 | 3a2de842 | |
| refs/tags/bioc_submission | 94810672 | 29bcc915 | |
| Updating references: 100% (4/4) | |
| ...Ref update completed in 64 ms. | |
| Commit Tree-Dirt History | |
| ------------------------ | |
| Earliest Latest | |
| | | | |
| .......DDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD | |
| D = dirty commits (file tree fixed) | |
| m = modified commits (commit message or parents changed) | |
| . = clean commits (no changes to file tree) | |
| Before After | |
| ------------------------------------------- | |
| First modified commit | 6750fc63 | 25e22590 | |
| Last dirty commit | c0493593 | 3a2de842 | |
| Deleted files | |
| ------------- | |
| Filename Git id | |
| ----------------------------------------------------------------------------------------------- | |
| README-access_data-1.png | f04eedd4 (987.6 KB) | |
| paper_figure1.jpg | c847a1e3 (1.2 MB) | |
| sce_image_clus-2.png | 5a0a2f55 (439.8 KB) | |
| sce_image_clus_no_spatial-1.png | 526fda11 (438.4 KB) | |
| sce_image_clus_p-1.png | 5a0a2f55 (439.8 KB) | |
| sce_image_gene-3.png | f676c919 (494.1 KB), 582494a6 (364.0 KB) | |
| sce_image_gene_p-1.png | 24221fb9 (391.3 KB) | |
| sce_image_grid-1.png | 9a35512c (300.2 KB), fe551f20 (360.5 KB) | |
| sce_image_grid_gene-1.png | 6d1cb9cb (399.5 KB) | |
| tissue_lowres_image.png | 4e3f6064 (453.7 KB), 57e78ddc (442.2 KB), ... | |
| tstats_Human_DLPFC_snRNAseq_Nguyen_topLayer.csv | 8bc27c0b (385.0 KB) | |
| In total, 423 object ids were changed. Full details are logged here: | |
| /Users/lcollado/Dropbox/Code/spatialLIBD/..bfg-report/2020-04-21/21-22-03 | |
| BFG run is complete! When ready, run: git reflog expire --expire=now --all && git gc --prune=now --aggressive | |
| -- | |
| You can rewrite history in Git - don't let Trump do it for real! | |
| Trump's administration has lied consistently, to make people give up on ever | |
| being told the truth. Don't give up: https://github.com/bkeepers/stop-trump | |
| -- | |
| $ | |
| $ git reflog expire --expire=now --all && git gc --prune=now --aggressive | |
| Enumerating objects: 1980, done. | |
| Counting objects: 100% (1980/1980), done. | |
| Delta compression using up to 4 threads | |
| Compressing objects: 100% (1839/1839), done. | |
| Writing objects: 100% (1980/1980), done. | |
| Total 1980 (delta 1354), reused 376 (delta 0), pack-reused 0 | |
| $ git status | |
| On branch master | |
| Your branch is ahead of 'origin/master' by 1 commit. | |
| (use "git push" to publish your local commits) | |
| Untracked files: | |
| (use "git add <file>..." to include in what will be committed) | |
| ..bfg-report/ | |
| inst/app/www/data/ | |
| nothing added to commit but untracked files present (use "git add" to track) | |
| $ git add inst/* | |
| $ git status | |
| On branch master | |
| Your branch is ahead of 'origin/master' by 1 commit. | |
| (use "git push" to publish your local commits) | |
| Changes to be committed: | |
| (use "git restore --staged <file>..." to unstage) | |
| new file: inst/app/www/data/151507/tissue_lowres_image.png | |
| new file: inst/app/www/data/151508/tissue_lowres_image.png | |
| new file: inst/app/www/data/151509/tissue_lowres_image.png | |
| new file: inst/app/www/data/151510/tissue_lowres_image.png | |
| new file: inst/app/www/data/151669/tissue_lowres_image.png | |
| new file: inst/app/www/data/151670/tissue_lowres_image.png | |
| new file: inst/app/www/data/151671/tissue_lowres_image.png | |
| new file: inst/app/www/data/151672/tissue_lowres_image.png | |
| new file: inst/app/www/data/151673/tissue_lowres_image.png | |
| new file: inst/app/www/data/151674/tissue_lowres_image.png | |
| new file: inst/app/www/data/151675/tissue_lowres_image.png | |
| new file: inst/app/www/data/151676/tissue_lowres_image.png | |
| Untracked files: | |
| (use "git add <file>..." to include in what will be committed) | |
| ..bfg-report/ | |
| 21:23 spatialLIBD $ git ci -am "Re-add the images after running bfg" | |
| [master 07663ae] Re-add the images after running bfg | |
| 12 files changed, 0 insertions(+), 0 deletions(-) | |
| create mode 100755 inst/app/www/data/151507/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151508/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151509/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151510/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151669/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151670/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151671/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151672/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151673/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151674/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151675/tissue_lowres_image.png | |
| create mode 100755 inst/app/www/data/151676/tissue_lowres_image.png | |
| $ git push --force | |
| Enumerating objects: 1294, done. | |
| Counting objects: 100% (1294/1294), done. | |
| Delta compression using up to 4 threads | |
| Compressing objects: 100% (375/375), done. | |
| Writing objects: 100% (1294/1294), 8.59 MiB | 1.07 MiB/s, done. | |
| Total 1294 (delta 839), reused 1262 (delta 837), pack-reused 0 | |
| remote: Resolving deltas: 100% (839/839), done. | |
| To github.com:LieberInstitute/spatialLIBD.git | |
| + c049359...07663ae master -> master (forced update) | |
| $ ~/Desktop | |
| $ git clone git@github.com:LieberInstitute/spatialLIBD.git | |
| Cloning into 'spatialLIBD'... | |
| remote: Enumerating objects: 989, done. | |
| remote: Counting objects: 100% (989/989), done. | |
| remote: Compressing objects: 100% (431/431), done. | |
| remote: Total 2206 (delta 645), reused 818 (delta 502), pack-reused 1217 | |
| Receiving objects: 100% (2206/2206), 36.23 MiB | 6.84 MiB/s, done. | |
| Resolving deltas: 100% (1387/1387), done. | |
| 21:25 Desktop $ | |
| 21:25 Desktop $ | |
| 21:25 Desktop $ cd spatialLIBD/ | |
| 21:25 spatialLIBD $ du -sh . | |
| 46M . | |
| 21:25 spatialLIBD $ du -sh * | |
| 4.0K DESCRIPTION | |
| 4.0K NAMESPACE | |
| 4.0K NEWS.md | |
| 196K R | |
| 20K README.Rmd | |
| 24K README.md | |
| 4.0K _pkgdown.yml | |
| 4.0K app.R | |
| 4.0K codecov.yml | |
| 168K data | |
| 436K data-raw | |
| 136K dev | |
| 5.7M inst | |
| 2.3M man | |
| 236K pkgdown | |
| 8.0K tests | |
| 48K vignettes | |
| 21:27 spatialLIBD $ du -sh .git | |
| 37M .git |
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| $ git clone git@github.com:LieberInstitute/spatialLIBD.git | |
| Cloning into 'spatialLIBD'... | |
| remote: Enumerating objects: 621, done. | |
| remote: Counting objects: 100% (621/621), done. | |
| remote: Compressing objects: 100% (290/290), done. | |
| remote: Total 1490 (delta 323), reused 555 (delta 284), pack-reused 869 | |
| Receiving objects: 100% (1490/1490), 11.47 MiB | 5.77 MiB/s, done. | |
| Resolving deltas: 100% (866/866), done. | |
| $ cd spatialLIBD/ | |
| $ du -sh .git | |
| 12M .git | |
| 21:28 spatialLIBD $ du -sh * | |
| 4.0K DESCRIPTION | |
| 4.0K NAMESPACE | |
| 4.0K NEWS.md | |
| 196K R | |
| 20K README.Rmd | |
| 24K README.md | |
| 4.0K _pkgdown.yml | |
| 4.0K app.R | |
| 4.0K codecov.yml | |
| 168K data | |
| 436K data-raw | |
| 136K dev | |
| 5.7M inst | |
| 2.3M man | |
| 236K pkgdown | |
| 8.0K tests | |
| 48K vignettes | |
| $ du -sh . | |
| 22M . |
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| $ git clone -b master --single-branch git@github.com:LieberInstitute/spatialLIBD.git | |
| Cloning into 'spatialLIBD'... | |
| remote: Enumerating objects: 75, done. | |
| remote: Counting objects: 100% (75/75), done. | |
| remote: Compressing objects: 100% (5/5), done. | |
| remote: Total 1294 (delta 71), reused 70 (delta 70), pack-reused 1219 | |
| Receiving objects: 100% (1294/1294), 8.59 MiB | 5.96 MiB/s, done. | |
| Resolving deltas: 100% (840/840), done. | |
| $ cd spatialLIBD/ | |
| $ du -sh . | |
| 18M . |
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