bootstrap goes into infinite loop of installing findutils and gnu-sed

[tobiiasl]

Summary: When I run bootstrap it complains that findutils is not installed with the right options: [ERR ] findutils is already installed with options '', [ERR ] but not the required '--with-default-names'. [ERR ] Consider uninstalling findutils with 'brew uninstall findutils' and rerun the bootstrap!

After uninstalling findutils and running bootstrap again: [ERR ] gnu-sed is already installed with options '', [ERR ] but not the required '--with-default-names'. [ERR ] Consider uninstalling gnu-sed with 'brew uninstall gnu-sed' and rerun the bootstrap!

After uninstalling gnu-sed and running bootstrap again I get the first error. And so it goes on.

Full log below:

`~/git/firecloud/support-firecloud/ci/darwin$ ./bootstrap Installing/Upgrading homebrew... ==> This script will install: /usr/local/bin/brew /usr/local/share/doc/homebrew /usr/local/share/man/man1/brew.1 /usr/local/share/zsh/site-functions/_brew /usr/local/etc/bash_completion.d/brew /usr/local/Homebrew

Press RETURN to continue or any other key to abort ==> /usr/bin/sudo /bin/mkdir -p /Library/Caches/Homebrew Password: ==> /usr/bin/sudo /bin/chmod g+rwx /Library/Caches/Homebrew ==> /usr/bin/sudo /usr/sbin/chown tobiaslindgren /Library/Caches/Homebrew ==> Downloading and installing Homebrew... remote: Counting objects: 97, done. remote: Compressing objects: 100% (40/40), done. remote: Total 97 (delta 73), reused 78 (delta 54), pack-reused 0 Unpacking objects: 100% (97/97), done. From https://github.com/Homebrew/brew 46821084..c8e81e86 master -> origin/master HEAD is now at c8e81e86 Merge pull request #4077 from reitermarkus/rubocop-cask Updated 2 taps (homebrew/core, caskroom/cask). ==> Cleaning up /Library/Caches/Homebrew... ==> Migrating /Library/Caches/Homebrew to /Users/tobiaslindgren/Library/Caches/Homebrew... ==> Deleting /Library/Caches/Homebrew... ==> New Formulae gitlab-gem mkl-dnn netdata patchelf phplint util-linux ==> Updated Formulae gnupg ✔ docker-compose libzip rancher-cli libgpg-error ✔ docker-compose-completion links recoverjpeg libtiff ✔ docker2aci lmod remctl sqlite ✔ dub log4cplus saltstack watch ✔ duti mapnik scm-manager abcmidi emscripten maxwell sdb abyss fibjs mediaconch sfk afsctool fig2dev metabase silk amqp-cpp firebase-cli mill singular annie fits mint skaffold apache-geode flow modd skafos apibuilder-cli fn monero softhsm arangodb fobis mutt sops armor freetds mypy sourcery artifactory frege nanopb-generator sox asio futhark ncmpcpp sparse aspectj gdcm nghttp2 spigot azure-cli gegl nginx sqldiff babeld ghostscript nomad sqlite-analyzer babl gist nss sqliteodbc bazel git-sizer nuget src bibtex2html git-town nvm subversion binaryen globus-toolkit ocrmypdf svgcleaner bit go-jira openimageio swift botan groonga openvdb teleport brotli grpc packmol terraform byteman heroku paket testssl chakra htmldoc pam_yubico timelimit chronograf htop percona-server-mongodb tmux cimg i2p perl@5.18 tup cliclick imlib2 php txr clojure influxdb php@5.6 vault composer jansson php@7.0 vim conan jenkins php@7.1 wildfly-as consul jenkins-lts phpunit wireguard-tools container-diff jhipster pick xonsh convox keychain pioneers xrootd coreos-ct knot pipenv xtensor cython kops poco yarn davmail kubernetes-cli pqiv yash dbhash launch proguard yaws di lcdf-typetools pstoedit yle-dl discount libhttpseverywhere py2cairo you-get dmd liblwgeom py3cairo youtube-dl dnscrypt-proxy libqalculate pycodestyle znapzend dnsdist librealsense qd docker libsoxr qscintilla2 docker-completion libspectre qtfaststart ==> Installation successful!

==> Homebrew has enabled anonymous aggregate user behaviour analytics. Read the analytics documentation (and how to opt-out) here: https://docs.brew.sh/Analytics.html

==> Next steps:

• Run brew help to get started
• Further documentation: https://docs.brew.sh Already up-to-date. libtiff (4.0.7, 4.0.7_2, 4.0.9, 4.0.9_2) < 4.0.9_3 awscli (1.11.26, 1.11.63, 1.14.60, 1.14.70) < 1.15.0 sqlite (3.15.2, 3.17.0, 3.23.0) < 3.23.1 libgpg-error (1.27) < 1.29 watch (3.3.12, 3.3.13) < 3.3.14 node (7.2.1, 7.7.3, 8.5.0, 9.2.1, 9.10.1) < 9.11.1 gnupg (2.2.3, 2.2.5) < 2.2.6 ==> Upgrading 7 outdated packages, with result: libtiff 4.0.9_2 -> 4.0.9_3, awscli 1.14.70 -> 1.15.0, sqlite 3.23.0 -> 3.23.1, libgpg-error 1.27 -> 1.29, watch 3.3.13 -> 3.3.14, node 9.10.1 -> 9.11.1, gnupg 2.2.5 -> 2.2.6 ==> Upgrading sqlite ==> Downloading https://homebrew.bintray.com/bottles/sqlite-3.23.1.high_sierra.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/0b/0b5f0e6d1096fbed10367e53c13c0e1300841f8f47739a0874abba8cc769a6d7?__gda__=ex ######################################################################## 100.0% ==> Pouring sqlite-3.23.1.high_sierra.bottle.tar.gz ==> Caveats This formula is keg-only, which means it was not symlinked into /usr/local, because macOS provides an older sqlite3.

If you need to have this software first in your PATH run: echo 'export PATH="/usr/local/opt/sqlite/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set: LDFLAGS: -L/usr/local/opt/sqlite/lib CPPFLAGS: -I/usr/local/opt/sqlite/include

==> Summary 🍺 /usr/local/Cellar/sqlite/3.23.1: 11 files, 3MB ==> Upgrading libtiff ==> Downloading https://homebrew.bintray.com/bottles/libtiff-4.0.9_3.high_sierra.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/23/2338c777aad152907291b35f40f2767771038a4812d2460e045b9ef4a7f3b565?__gda__=ex ######################################################################## 100.0% ==> Pouring libtiff-4.0.9_3.high_sierra.bottle.tar.gz 🍺 /usr/local/Cellar/libtiff/4.0.9_3: 246 files, 3.5MB ==> Upgrading awscli ==> Downloading https://homebrew.bintray.com/bottles/awscli-1.15.0.high_sierra.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/13/13ffeccef35d420fa9dd7b8cb34e9d86391ae2dda106f1eb8c5ee36a3cf105f5?__gda__=ex ######################################################################## 100.0% ==> Pouring awscli-1.15.0.high_sierra.bottle.tar.gz ==> Caveats The "examples" directory has been installed to: /usr/local/share/awscli/examples

Bash completion has been installed to: /usr/local/etc/bash_completion.d

zsh completions and functions have been installed to: /usr/local/share/zsh/site-functions ==> Summary 🍺 /usr/local/Cellar/awscli/1.15.0: 4,401 files, 40.3MB ==> Upgrading libgpg-error ==> Downloading https://homebrew.bintray.com/bottles/libgpg-error-1.29.high_sierra.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/75/759835f6fc52907db4219d3587ea91a85b87c002d5009de8eecf848016a80250?__gda__=ex ######################################################################## 100.0% ==> Pouring libgpg-error-1.29.high_sierra.bottle.tar.gz 🍺 /usr/local/Cellar/libgpg-error/1.29: 25 files, 805.6KB ==> Upgrading watch ==> Downloading https://homebrew.bintray.com/bottles/watch-3.3.14.high_sierra.bottle.tar.gz ######################################################################## 100.0% ==> Pouring watch-3.3.14.high_sierra.bottle.tar.gz 🍺 /usr/local/Cellar/watch/3.3.14: 9 files, 80KB ==> Upgrading node ==> Downloading https://homebrew.bintray.com/bottles/node-9.11.1.high_sierra.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/a4/a4c2d90a60930aa6e2cff330a81d8cec3636cdd9fc002ce79da30540499052d2?__gda__=ex ######################################################################## 100.0% ==> Pouring node-9.11.1.high_sierra.bottle.tar.gz ==> Caveats Bash completion has been installed to: /usr/local/etc/bash_completion.d ==> Summary 🍺 /usr/local/Cellar/node/9.11.1: 5,125 files, 49.7MB ==> Upgrading gnupg ==> Downloading https://homebrew.bintray.com/bottles/gnupg-2.2.6.high_sierra.bottle.tar.gz ==> Downloading from https://akamai.bintray.com/38/38302b573c7a247dec8aae9645c2164071b911ad572521d0bc16df1dad1843ec?__gda__=ex ######################################################################## 100.0% ==> Pouring gnupg-2.2.6.high_sierra.bottle.tar.gz Error: The brew link step did not complete successfully The formula built, but is not symlinked into /usr/local Could not symlink bin/gpg Target /usr/local/bin/gpg already exists. You may want to remove it: rm '/usr/local/bin/gpg'

To force the link and overwrite all conflicting files: brew link --overwrite gnupg

To list all files that would be deleted: brew link --overwrite --dry-run gnupg

Possible conflicting files are: /usr/local/bin/gpg -> /usr/local/MacGPG2/bin/gpg2 ==> Caveats Once you run this version of gpg you may find it difficult to return to using a prior 1.4.x or 2.0.x. Most notably the prior versions will not automatically know about new secret keys created or imported by this version. We recommend creating a backup of your ~/.gnupg prior to first use.

For full details on each change and how it could impact you please see https://www.gnupg.org/faq/whats-new-in-2.1.html ==> Summary 🍺 /usr/local/Cellar/gnupg/2.2.6: 133 files, 10.4MB Installing/Upgrading git... [DO ] Installing basic/GNU packages... ==> Downloading https://homebrew.bintray.com/bottles/diffutils-3.6.high_sierra.b ==> Downloading from https://akamai.bintray.com/fd/fd411d030058f27f1ce31cdb5d8a4 ######################################################################## 100.0% ==> Pouring diffutils-3.6.high_sierra.bottle.tar.gz 🍺 /usr/local/Cellar/diffutils/3.6: 17 files, 671.6KB Traceback (most recent call last): File "", line 1, in IndexError: list index out of range [ERR ] findutils is already installed with options '', [ERR ] but not the required '--with-default-names'. [ERR ] Consider uninstalling findutils with 'brew uninstall findutils' and rerun the bootstrap! ~/git/firecloud/support-firecloud/ci/darwin$ brew uninstall findutils Uninstalling /usr/local/Cellar/findutils/4.6.0... (33 files, 1.6MB) ~/git/firecloud/support-firecloud/ci/darwin$ ./bootstrap Installing/Upgrading homebrew... ==> This script will install: /usr/local/bin/brew /usr/local/share/doc/homebrew /usr/local/share/man/man1/brew.1 /usr/local/share/zsh/site-functions/_brew /usr/local/etc/bash_completion.d/brew /usr/local/Homebrew

Press RETURN to continue or any other key to abort ==> /usr/bin/sudo /bin/mkdir -p /Library/Caches/Homebrew Password: ==> /usr/bin/sudo /bin/chmod g+rwx /Library/Caches/Homebrew ==> /usr/bin/sudo /usr/sbin/chown tobiaslindgren /Library/Caches/Homebrew ==> Downloading and installing Homebrew... HEAD is now at c8e81e86 Merge pull request #4077 from reitermarkus/rubocop-cask Updated 1 tap (homebrew/core). ==> Cleaning up /Library/Caches/Homebrew... ==> Migrating /Library/Caches/Homebrew to /Users/tobiaslindgren/Library/Caches/Homebrew... ==> Deleting /Library/Caches/Homebrew... ==> Updated Formulae file-formula libmagic ==> Installation successful!

==> Homebrew has enabled anonymous aggregate user behaviour analytics. Read the analytics documentation (and how to opt-out) here: https://docs.brew.sh/Analytics.html

==> Next steps:

• Run brew help to get started
• Further documentation: https://docs.brew.sh Already up-to-date. Installing/Upgrading git... [DO ] Installing basic/GNU packages... ==> Downloading https://ftp.gnu.org/gnu/findutils/findutils-4.6.0.tar.gz ######################################################################## 100.0% ==> ./configure --prefix=/usr/local/Cellar/findutils/4.6.0 --localstatedir=/usr/ ==> make install 🍺 /usr/local/Cellar/findutils/4.6.0: 25 files, 1.6MB, built in 3 minutes 24 seconds Traceback (most recent call last): File "", line 1, in IndexError: list index out of range [ERR ] gnu-sed is already installed with options '', [ERR ] but not the required '--with-default-names'. [ERR ] Consider uninstalling gnu-sed with 'brew uninstall gnu-sed' and rerun the bootstrap! ~/git/firecloud/support-firecloud/ci/darwin$ brew uninstall gnu-sed Uninstalling /usr/local/Cellar/gnu-sed/4.5... (12 files, 529KB) gnu-sed 4.2.2, 4.4 2 are still installed. Remove all versions with brew uninstall --force gnu-sed. ~/git/firecloud/support-firecloud/ci/darwin$ ./bootstrap Installing/Upgrading homebrew... ==> This script will install: /usr/local/bin/brew /usr/local/share/doc/homebrew /usr/local/share/man/man1/brew.1 /usr/local/share/zsh/site-functions/_brew /usr/local/etc/bash_completion.d/brew /usr/local/Homebrew

Press RETURN to continue or any other key to abort ==> /usr/bin/sudo /bin/mkdir -p /Library/Caches/Homebrew Password: ==> /usr/bin/sudo /bin/chmod g+rwx /Library/Caches/Homebrew ==> /usr/bin/sudo /usr/sbin/chown tobiaslindgren /Library/Caches/Homebrew ==> Downloading and installing Homebrew... HEAD is now at c8e81e86 Merge pull request #4077 from reitermarkus/rubocop-cask Updated 1 tap (homebrew/core). ==> Cleaning up /Library/Caches/Homebrew... ==> Migrating /Library/Caches/Homebrew to /Users/tobiaslindgren/Library/Caches/Homebrew... ==> Deleting /Library/Caches/Homebrew... ==> Updated Formulae cockatrice dnscrypt-proxy folly hugo vala convox embulk gollum tippecanoe ==> Installation successful!

==> Homebrew has enabled anonymous aggregate user behaviour analytics. Read the analytics documentation (and how to opt-out) here: https://docs.brew.sh/Analytics.html

==> Next steps:

• Run brew help to get started
• Further documentation: https://docs.brew.sh Already up-to-date. gnu-sed (4.2.2, 4.4) < 4.5 ==> Upgrading 1 outdated package, with result: gnu-sed 4.5 ==> Upgrading gnu-sed ==> Downloading https://homebrew.bintray.com/bottles/gnu-sed-4.5.high_sierra.bottle.tar.gz Already downloaded: /Users/tobiaslindgren/Library/Caches/Homebrew/gnu-sed-4.5.high_sierra.bottle.tar.gz ==> Pouring gnu-sed-4.5.high_sierra.bottle.tar.gz ==> Caveats The command has been installed with the prefix "g". If you do not want the prefix, install using the "with-default-names" option.

If you need to use these commands with their normal names, you can add a "gnubin" directory to your PATH from your bashrc like: PATH="/usr/local/opt/gnu-sed/libexec/gnubin:$PATH"

Additionally, you can access their man pages with normal names if you add the "gnuman" directory to your MANPATH from your bashrc as well: MANPATH="/usr/local/opt/gnu-sed/libexec/gnuman:$MANPATH" ==> Summary 🍺 /usr/local/Cellar/gnu-sed/4.5: 12 files, 529KB Installing/Upgrading git... [DO ] Installing basic/GNU packages... Traceback (most recent call last): File "", line 1, in IndexError: list index out of range [ERR ] findutils is already installed with options '', [ERR ] but not the required '--with-default-names'. [ERR ] Consider uninstalling findutils with 'brew uninstall findutils' and rerun the bootstrap! ~/git/firecloud/support-firecloud/ci/darwin$ brew uninstall findutils Uninstalling /usr/local/Cellar/findutils/4.6.0... (25 files, 1.6MB) ~/git/firecloud/support-firecloud/ci/darwin$ ./bootstrap Installing/Upgrading homebrew... ==> This script will install: /usr/local/bin/brew /usr/local/share/doc/homebrew /usr/local/share/man/man1/brew.1 /usr/local/share/zsh/site-functions/_brew /usr/local/etc/bash_completion.d/brew /usr/local/Homebrew

Press RETURN to continue or any other key to abort ==> /usr/bin/sudo /bin/mkdir -p /Library/Caches/Homebrew Password: ==> /usr/bin/sudo /bin/chmod g+rwx /Library/Caches/Homebrew ==> /usr/bin/sudo /usr/sbin/chown tobiaslindgren /Library/Caches/Homebrew ==> Downloading and installing Homebrew... HEAD is now at c8e81e86 Merge pull request #4077 from reitermarkus/rubocop-cask ==> Cleaning up /Library/Caches/Homebrew... ==> Migrating /Library/Caches/Homebrew to /Users/tobiaslindgren/Library/Caches/Homebrew... ==> Deleting /Library/Caches/Homebrew... Already up-to-date. ==> Installation successful!

==> Homebrew has enabled anonymous aggregate user behaviour analytics. Read the analytics documentation (and how to opt-out) here: https://docs.brew.sh/Analytics.html

==> Next steps:

• Run brew help to get started
• Further documentation: https://docs.brew.sh Already up-to-date. Installing/Upgrading git... [DO ] Installing basic/GNU packages... ==> Downloading https://ftp.gnu.org/gnu/findutils/findutils-4.6.0.tar.gz Already downloaded: /Users/tobiaslindgren/Library/Caches/Homebrew/findutils-4.6.0.tar.gz ==> ./configure --prefix=/usr/local/Cellar/findutils/4.6.0 --localstatedir=/usr/ ==> make install 🍺 /usr/local/Cellar/findutils/4.6.0: 25 files, 1.6MB, built in 3 minutes 15 seconds Traceback (most recent call last): File "", line 1, in IndexError: list index out of range [ERR ] gnu-sed is already installed with options '', [ERR ] but not the required '--with-default-names'. [ERR ] Consider uninstalling gnu-sed with 'brew uninstall gnu-sed' and rerun the bootstrap! ~/git/firecloud/support-firecloud/ci/darwin$`

[tobiiasl]

Even after I manually install findutils with the right flags I get an error: brew uninstall findutils brew install findutils --with-default-names

Still gives the error: [ERR ] findutils is already installed with options '', [ERR ] but not the required '--with-default-names'. [ERR ] Consider uninstalling findutils with 'brew uninstall findutils' and rerun the bootstrap!

[tobiiasl]

Running brew info manually gives nothing: ~/git/firecloud/support-firecloud/ci/darwin$ brew info --json=v1 []