Doxygen bottle is corrupted on Catalina

[fxcoudert]

• are reporting a bug others will be able to reproduce and not asking a question. If you're not sure or want to ask a question do so on our Discourse: https://discourse.brew.sh
• ran a brew command and reproduced the problem with multiple formulae? If it's a problem with a single, official formula (not cask) please file this issue at Homebrew/homebrew-core: https://github.com/Homebrew/homebrew-core/issues/new/choose. If it's a brew cask problem please file this issue at https://github.com/Homebrew/homebrew-cask/issues/new/choose. If it's a tap (e.g. Homebrew/homebrew-php) problem please file this issue at the tap.
• ran brew update and can still reproduce the problem?
• ran brew doctor, fixed all issues and can still reproduce the problem?
• ran brew config and brew doctor and included their output with your issue?

Bug description

On Catalina CI nodes:

• brew install --verbose --build-bottle doxygen (succeeds)
• brew test --verbose doxygen (works)
• brew bottle --verbose --json doxygen --keep-old

The bottle file produced contains an invalid doxygen binary, with many NUL bytes:

brew@Catalina ~ % tar xf doxygen--1.8.16.catalina.bottle.tar.gz doxygen/1.8.16/bin/doxygen
brew@Catalina ~ % xxd /usr/local/Cellar/doxygen/1.8.16/bin/doxygen | head -n 5           
00000000: cffa edfe 0700 0001 0300 0080 0200 0000  ................
00000010: 1300 0000 0808 0000 8580 2100 0000 0000  ..........!.....
00000020: 1900 0000 4800 0000 5f5f 5041 4745 5a45  ....H...__PAGEZE
00000030: 524f 0000 0000 0000 0000 0000 0000 0000  RO..............
00000040: 0000 0000 0100 0000 0000 0000 0000 0000  ................
brew@Catalina ~ % xxd ./doxygen/1.8.16/bin/doxygen | head -n 5
00000000: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000010: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000020: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000030: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000040: 0000 0000 0000 0000 0000 0000 0000 0000  ................

If I then reinstall from the bottle, brew test will fail as it cannot execute that binary. Note that brew test passes after the initial install (not installed from the bottle).

[fxcoudert]

This appears to be a system tar bug:

brew@Catalina ~ % cd /usr/local/Cellar 
brew@Catalina Cellar % file doxygen/1.8.16/bin/doxygen
doxygen/1.8.16/bin/doxygen: Mach-O 64-bit executable x86_64
brew@Catalina Cellar % xxd doxygen/1.8.16/bin/doxygen | head -n 5
00000000: cffa edfe 0700 0001 0300 0080 0200 0000  ................
00000010: 1300 0000 0808 0000 8580 2100 0000 0000  ..........!.....
00000020: 1900 0000 4800 0000 5f5f 5041 4745 5a45  ....H...__PAGEZE
00000030: 524f 0000 0000 0000 0000 0000 0000 0000  RO..............
00000040: 0000 0000 0100 0000 0000 0000 0000 0000  ................
brew@Catalina Cellar % tar cf ~/toto.tar doxygen/1.8.16 
brew@Catalina Cellar % cd
brew@Catalina ~ % tar xf toto.tar doxygen/1.8.16/bin/doxygen
brew@Catalina ~ % file doxygen/1.8.16/bin/doxygen           
doxygen/1.8.16/bin/doxygen: data
brew@Catalina ~ % xxd doxygen/1.8.16/bin/doxygen | head -n 5
00000000: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000010: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000020: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000030: 0000 0000 0000 0000 0000 0000 0000 0000  ................
00000040: 0000 0000 0000 0000 0000 0000 0000 0000  ................

[MikeMcQuaid]

@fxcoudert Has noted this does not seem to happen on the Catalina GM.

[MikeMcQuaid]

This still seems to be happening on the public release/Xcode 11.1.

[gvarisco]

I've also reported it to Apple via their Feedback Assistant, case ID: FB7378125

[fxcoudert]

• This still happens on Catalina CI nodes (VMs) after the Supplemental Update
• This does not happen with Catalina on my own hardware

[NoLooseEnds]

Happens on my Macbook Pro 2018, with latest update.

(tested with Syncthing, but same issue)

[bunjiboys]

The issue also occurs with the kustomize formula, and I noticed a difference in the tar archives. It seems the catalina archive, at least for kustomize, was created with the --sparse option.

If I open the archive using mc on the mojave bottle it looks normal, but when I open the catalina archive, browsing to the bin folder, instead of seeing the contents of the folder, I see an extra directory level called GNUSparseFile.0 and then inside there is the kustomize binary. Similarly to the original issue the file has a lot of NUL bytes at the beginning of the file

[Bo98]

For what it's worth, this also happens with brew libarchive as far as I can see.

[chenrui333]

git-lfs 2.9.2 #45467 has tar issue.

[MikeMcQuaid]

Closing this as there's no activity and we have an acceptable workaround for now.