R News

You just committed a large file and can’t push to GitHub

by L. Collado-Torres · March 18, 2020

This article is originally published at https://lcolladotor.github.io/

Oh ohh! ???? What do you do now?

The data me and my colleagues work with is typically too big for our personal computers, so we use a high performance computing environment (cluster) and mostly interact with it through the command line terminal. As you might know, I’m a big fan of version control and I use git plus GitHub for sharing our code ¹. That’s why I’ve been advocating others to use it for a while and when they do, they run to me if they have some issues. A while back, my former student Amy Peterson wrote a blog post titled git to know git: an 8 minute introduction which is useful if you are getting started. Amy also links to the excellent Happy Git and GitHub for the useR book.

Recurrent problem: you just commited a large file and can’t push to GitHub

One situation that I’ve frequently helped others with is when they use git add * or git add . and version control every file in their project. They then do a commit such as git commit -m "added all files" and run git push to sync their files to GitHub. But oops, GitHub complains that you are trying to commit files larger than 50 Mb and even grinds to a halt if they are larger than 100 Mb. Which given that we work with large data, happens frequently (even a PDF file can be that big!).

Ok, so what can you do at this point? Remember, this is the scenario where you just made that commit. That is, it’s the last commit. At that point, it’s best to undo your last git commit which is well described in this website. However, when you undo a commit, you can either fully wipe out any changes (wipe them out fully from your disk, not only git’s version control!) or undo the version control step but also keep your files intact. The main solution then is to use:

git reset --soft HEAD~1

However, maybe you tried other commands and it’s a bit more complicated than that. Which is why I greatly advise that you create a local backup of your main_project directory before you dive into commands such as git reset, specially whenever you see the --hard option being suggested. That is, do something like this:

## Nagivate to the parent directory of your main_project
cd directory_containing_your_project

## Check the full size of your project directory
du -sh main_project

## Do you have enough disk space?
df -h .

## If you have enough disk space, then create a full backup
cp -r main_project main_project_backup/

Once you are able to roll back the offending commit, instead of running git add * or git add . and similar commands, repeat the following cycle:

Check which files are not being version controlled (untracked) with git status.
Check how big each of your untracked files is. You can do so with ls -lh and ls -lh some_pattern.
Add the files or file patterns you want to avoid version controlling (the large files) to your .gitignore file ².
Double check that your pattern worked by confirming that these files do not show up as untracked when you run git status.

Repeat this until the only remaining untracked files are those you actually want to version control and that are small enough ³.

And that’s it! Keep version controlling your code and reap the benefits later on when you need to.

via GIPHY

We all run into this situation at some point (or multiple times), so please keep using version control. The benefits will outweigh the negatives!

Use case story: the issue

Thanks to a colleague who gave me permission to share their use case, here we can dive down into a real life example. First, this was their description (edited for anonymity):

Ran these, as per GitHub’s instructions, and it went fine

git init
git add README.md
git commit -m "first commit"
git remote add origin [email protected]:LieberInstitute/some_repository.git
git push -u origin master

Even added a .gitignore with some instructions on what to ignore when committing

But it wasn’t enough and I hadn’t come to appreciate yet that there’s no need to commit .rda’s or other very large files, so my git push died.

Since these were already staged, I thought the next move was to make another commit with an edited .gitignore listing anything in my rdas/

Putting me two branches ahead of master (Leo: commits I think)

I got frustrated and thought then that ok, I want to go back two commits…

my Googling suggested me to go for git reset --hard HEAD~2…

That’s when I started panicking ????

My colleague started panicking at this point because they couldn’t see the files anymore. That is, running ls -lh rdas/ didn’t list the files they had worked on really hard to create over the past months. But at this point, these large files were under version control by git ⁴, just not available on GitHub due to the file size limitations.

So then my panic Googling took me to https://stackoverflow.com/questions/5788037/recover-from-git-reset-hard

where I thought ok I just can run git reset HEAD@{2} , which was

7cb9bac HEAD@{0}: reset: moving to HEAD@{2}
1e8499d HEAD@{1}: reset: moving to HEAD~2
f03b884 HEAD@{2}: commit: Committing EVERYTHING
7cb9bac HEAD@{3}: commit: Commiting EVERYTHING          <- this one
1e8499d HEAD@{4}: commit (initial): first commit

And there it looked like not everything was quite lost, as I could see

$ git status
# On branch master
# Your branch is ahead of 'origin/master' by 1 commit.
#   (use "git push" to publish your local commits)
#
# Changes not staged for commit:
#   (use "git add/rm <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#   deleted:    .RData
#   deleted:    .gitignore
#   deleted:    *.R ## Lots of files with this pattern
#   deleted:    *.sh ## same story about the file pattern
#   deleted:    pdfs/*.pdf
#   deleted:    rdas/*.rda
#   deleted:    tables/*.csv
#
# Untracked files:
#   (use "git add <file>..." to include in what will be committed)
#
#   logs/
#   pdfs/*other*.pdf
#   rdas/*other*.rda
#   *other*.R
no changes added to commit (use "git add" and/or "git commit -a")

So now my colleague realizes that somehow git is version controlling the files, but the deleted label is still VERY scary!!

And then I thought ok I just need to re-stage those deleted files…

So I ran git add -A , but now I see

$ 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 reset HEAD <file>..." to unstage)
#
#   deleted:    .RData
#   deleted:    .gitignore
#   deleted:    *.R ## Lots of files with this pattern
#   deleted:    *.sh ## same story about the file pattern
#   deleted:    pdfs/*.pdf
#   deleted:    rdas/*.rda
#   deleted:    tables/*.csv
#   new file:   logs/*.Rout
#   new file:   logs/*.sh.*
#   new file:   pdfs/*other*.pdf
#   new file:   rdas/*other*.rda
#   new file:   *other*.R
#   renamed:    pdfs/*something*.pdf -> pdfs/*something_else*.pdf
#   renamed:    rdas/*something*.rda -> rdas/*something_else*.rda

and clearly I don’t know what I’m doing so I stopped

And thanked the lord you were online. ????????

I promise I did some reviewing of resources and testing with local and JHPCE test dirs before

My colleague then pointed me to the directory with the files and we fixed their files.

Use case story: the solution

Like I mentioned earlier, the first thing to do in cases like this is to create a backup.

## Check how big it is
du -sh project_FINAL

## Create a backup
cp -r project_FINAL project_leo_backup/

## To wipe out the original copy
## proceed with EXTREME caution!
# rm -fr project_FINAL

## Then restore everything from your backup copy
cp -r project_leo_backup project_FINAL/

I actually messed up at one point and had to rely on this backup!! So, like I said,

Please backup everything before you start using git reset and similar commands!

Next, to undo all the git rm (deleting a file), I undid the git add -A step using a combination of git reset and git checkout (to restore files).

# https://stackoverflow.com/a/2125713/9374370
$ git reset HEAD
$ git checkout .

## check things
$ git status
On branch master
Your branch is ahead of 'origin/master' by 1 commit.
  (use "git push" to publish your local commits)
nothing to commit, working tree clean
$ git log
commit 7cb9bac5378500b35a0c22480a5961248ecf67ea (HEAD -> master)
Author: xx <[email protected]>
Date:   Tue Mar 17 19:27:31 2020 -0400
    Commiting EVERYTHING
commit 1e8499d7d41cab6c12ea23ccdb2da8120b00a7f7 (origin/master)
Author: XX <[email protected]>
Date:   Tue Mar 17 19:04:03 2020 -0400
    first commit

$ ls -lh rdas
total 6.2G
## I see tons of stuff (many of which I'm now the "owner" of)

I then finally used git reset --soft to undo the last commit.

# https://www.git-tower.com/learn/git/faq/undo-last-commit
git reset --soft HEAD~1 ## note that I'm not using --hard

## Everything is back to before that big commit
$ git log
commit 1e8499d7d41cab6c12ea23ccdb2da8120b00a7f7 (HEAD -> master, origin/master)
Author: XX <[email protected]>
Date:   Tue Mar 17 19:04:03 2020 -0400
    first commit

## and the files are there =)
$ ls -lh rdas
total 6.2G
-rwxrwx--- 1 lcollado lieber_jaffe 690M Mar 18 00:22 *.rda ## exmaple file

Now that the directory and files have been restored to before all files were committed, we can proceed to ignore large files. For example, we can ignore the rdas/ directory that has many large files that we don’t want to version control ⁵.

$ git status
On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
    modified:   README.md

Untracked files:
  (use "git add <file>..." to include in what will be committed)
    .RData
    .gitignore
    *.R ## Lots of files with this pattern
    *.sh ## Lots of files with this pattern
    pdfs/
    rdas/
    tables/

$ echo "rdas" >> .gitignore

## Notice that rdas is not there anymore ^^
$ git status
On branch master
Your branch is up to date with 'origin/master'.

Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git restore <file>..." to discard changes in working directory)
    modified:   README.md

Untracked files:
  (use "git add <file>..." to include in what will be committed)
    .RData
    .gitignore
    *.R ## Lots of files with this pattern
    *.sh ## Lots of files with this pattern
    pdfs/
    tables/

And now we can update our .gitignore and push this small change (ignoring the rdas/ directory) to GitHub.

$ git add .gitignore

$ git commit -m "Ignore rdas"
[master 52f1850] Ignore rdas
 1 file changed, 14 insertions(+)
 create mode 100755 .gitignore

$ git push
X11 forwarding request failed on channel 0
Enumerating objects: 4, done.
Counting objects: 100% (4/4), done.
Delta compression using up to 20 threads
Compressing objects: 100% (3/3), done.
Writing objects: 100% (3/3), 420 bytes | 210.00 KiB/s, done.
Total 3 (delta 0), reused 0 (delta 0)
To github.com:LieberInstitute/some_repository.git
   1e8499d..52f1850  master -> master

And we are done!

via GIPHY

And I’ll get some free beers hehe ????????

Omg you’re amazing beautiful lord n savior jesus christ

Your next 10 beers are on me.

plus 2 for the promotion ????????????????????

To which I replied

hehe, I’ve simply only have had more practice at this than you (fixing xx’s repos mostly hehe)

but yeah, backing up is the best thing you can do

that actually saved me from my one git reset --hard HEAD~1 command that should have been git reset --soft HEAD~1

Misc notes

Note that you might also want to use git status-size in some situations.

## From https://github.com/jtloong/git-status-size
$ git status-size

Finally, if you are a JHPCE user, I recommend including these lines in your ~/.bashrc file.

## Load the git module by default when qrsh/qsub
## thanks to Jiong Yang
if [[ $HOSTNAME == compute-* ]]; then
    echo "Adding LIBD modules"
    module use /jhpce/shared/jhpce/modulefiles/libd
    echo "Loading git"
    module load git
    module load git-status-size/github
    module load git-lfs/2.8.0
    module load rmate/1.5.9 ## macOS users
    module load conda_R/3.6.x ## default R version
fi

Acknowledgments

I greatly appreciate the anonymous user who reached out to me about this issue and had an excellent history of commands which allowed me to figure out a possible solution and then write this blog post (with their permission). We both hope that this information will be useful to ourselves and others in the future.

This blog post was made possible thanks to:

References

[1] C. Boettiger. knitcitations: Citations for ‘Knitr’ Markdown Files. R package version 1.0.10. 2019. URL: https://CRAN.R-project.org/package=knitcitations.

[2] G. Csárdi, R. core, H. Wickham, W. Chang, et al. sessioninfo: R Session Information. R package version 1.1.1. 2018. URL: https://CRAN.R-project.org/package=sessioninfo.

[3] A. Oleś, M. Morgan, and W. Huber. BiocStyle: Standard styles for vignettes and other Bioconductor documents. R package version 2.14.4. 2020. URL: https://github.com/Bioconductor/BiocStyle.

[4] Y. Xie, A. P. Hill, and A. Thomas. blogdown: Creating Websites with R Markdown. ISBN 978-0815363729. Boca Raton, Florida: Chapman and Hall/CRC, 2017. URL: https://github.com/rstudio/blogdown.

Reproducibility

## ─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
##  setting  value                       
##  version  R version 3.6.3 (2020-02-29)
##  os       macOS Catalina 10.15.3      
##  system   x86_64, darwin15.6.0        
##  ui       X11                         
##  language (EN)                        
##  collate  en_US.UTF-8                 
##  ctype    en_US.UTF-8                 
##  tz       America/New_York            
##  date     2020-03-18                  
## 
## ─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
##  package       * version date       lib source                            
##  assertthat      0.2.1   2019-03-21 [1] CRAN (R 3.6.0)                    
##  bibtex          0.4.2.2 2020-01-02 [1] CRAN (R 3.6.0)                    
##  BiocManager     1.30.10 2019-11-16 [1] CRAN (R 3.6.1)                    
##  BiocStyle     * 2.14.4  2020-01-09 [1] Bioconductor                      
##  blogdown        0.18    2020-03-04 [1] CRAN (R 3.6.0)                    
##  bookdown        0.18    2020-03-05 [1] CRAN (R 3.6.0)                    
##  cli             2.0.2   2020-02-28 [1] CRAN (R 3.6.0)                    
##  colorout      * 1.2-1   2019-05-07 [1] Github (jalvesaq/colorout@7ea9440)
##  crayon          1.3.4   2017-09-16 [1] CRAN (R 3.6.0)                    
##  digest          0.6.25  2020-02-23 [1] CRAN (R 3.6.0)                    
##  evaluate        0.14    2019-05-28 [1] CRAN (R 3.6.0)                    
##  fansi           0.4.1   2020-01-08 [1] CRAN (R 3.6.0)                    
##  glue            1.3.2   2020-03-12 [1] CRAN (R 3.6.0)                    
##  htmltools       0.4.0   2019-10-04 [1] CRAN (R 3.6.0)                    
##  httr            1.4.1   2019-08-05 [1] CRAN (R 3.6.0)                    
##  jsonlite        1.6.1   2020-02-02 [1] CRAN (R 3.6.0)                    
##  knitcitations * 1.0.10  2019-09-15 [1] CRAN (R 3.6.0)                    
##  knitr           1.28    2020-02-06 [1] CRAN (R 3.6.0)                    
##  lubridate       1.7.4   2018-04-11 [1] CRAN (R 3.6.0)                    
##  magrittr        1.5     2014-11-22 [1] CRAN (R 3.6.0)                    
##  plyr            1.8.6   2020-03-03 [1] CRAN (R 3.6.2)                    
##  R6              2.4.1   2019-11-12 [1] CRAN (R 3.6.1)                    
##  Rcpp            1.0.3   2019-11-08 [1] CRAN (R 3.6.0)                    
##  RefManageR      1.2.12  2019-04-03 [1] CRAN (R 3.6.0)                    
##  rlang           0.4.5   2020-03-01 [1] CRAN (R 3.6.0)                    
##  rmarkdown       2.1     2020-01-20 [1] CRAN (R 3.6.0)                    
##  sessioninfo   * 1.1.1   2018-11-05 [1] CRAN (R 3.6.0)                    
##  stringi         1.4.6   2020-02-17 [1] CRAN (R 3.6.0)                    
##  stringr         1.4.0   2019-02-10 [1] CRAN (R 3.6.0)                    
##  withr           2.1.2   2018-03-15 [1] CRAN (R 3.6.0)                    
##  xfun            0.12    2020-01-13 [1] CRAN (R 3.6.0)                    
##  xml2            1.2.5   2020-03-11 [1] CRAN (R 3.6.0)                    
##  yaml            2.2.1   2020-02-01 [1] CRAN (R 3.6.0)                    
## 
## [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library

Between our personal computers and the JHPCE cluster, but also with collaborators and the community at large.↩︎
Note that you can also create .gitignore files inside each directory if you want to have tighter control. You could also ignore a full directory and the use git add -f to forcibly version control files, for example, echo "my_subdir" >> .gitignore plus git add -f my_subdir/*.R to forcibly version control the R script files inside my_subdir but ignore everything else.↩︎
If you really want to version control large files, look into git lfs.↩︎
Stored and hidden in some way inside the .git directory.↩︎
Maybe later we’ll version control a few of them using git add -f rdas/some_file.rda but it’ll be a targeted version control command.↩︎

Thanks for visiting r-craft.org
This article is originally published at https://lcolladotor.github.io/
Please visit source website for post related comments.

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You just committed a large file and can’t push to GitHub

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You just committed a large file and can’t push to GitHub

Recurrent problem: you just commited a large file and can’t push to GitHub

Use case story: the issue

Use case story: the solution

Misc notes

Acknowledgments

References

Reproducibility

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