Mojave upgrade issues

DELL P2715Q Issues

  • Firefox/Yahoo mail screen went largely white, had to refresh page.

  • Screen locked broken unreadable display, open close macbook to refresh screen.

Xcode CLI broken

$ git status
xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

$ xcode-select --install
xcode-select: note: install requested for command line developer tools

$ git status
On branch read-the-docs

Python3 upgraded

$ make html
/bin/sh: /usr/local/bin/sphinx-build: /usr/local/opt/python3/bin/python3.6: bad interpreter: No such file or directory
make: *** [html] Error 126
$ python3
Python 3.7.0 (default, Sep 18 2018, 18:47:08)
[Clang 10.0.0 (clang-1000.10.43.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

$ cat Pipfile
[[source]]
url = "https://pypi.python.org/simple"
verify_ssl = true
name = "pypi"

[packages]
sphinx = "*"
sphinx-rtd-theme = "*"

[dev-packages]

[requires]
python_version = "3.6"

Update Brew (just in case)

$ brew list
gdbm            openssl         pipenv          python          python3         readline        sqlite          xz

$ brew upgrade
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 2 taps (homebrew/core, homebrew/cask).
==> New Formulae
aravis       carla        diceware     hyperkit     llvm@6       nng          nwchem       oclgrind     picat        smimesign    vfuse
==> Updated Formulae
sqlite ✔                           fmsx                               kubernetes-service-catalog-client  pyinvoke
ace                                fn                                 kumo                               pyside
angular-cli                        folly                              kustomize                          qcachegrind
anjuta                             fonttools                          libcouchbase                       qd
annie                              fortio                             libdazzle                          qt
apache-flink                       fossil                             libetpan                           ranger
apr                                freetds                            libiscsi                           rebar3
arangodb                           freexl                             libphonenumber                     root
aria2                              frugal                             libsoup                            roswell
ark                                futhark                            libspectre                         rust
arp-scan                           fzy                                libuv                              rustup-init
arpack                             gdb                                libvirt                            sbt
aurora-cli                         geckodriver                        libwbxml                           selenium-server-standalone
avfs                               gedit                              links                              shellharden
avrdude                            ghostscript                        llvm                               simutrans
avro-c                             git                                logstash                           skaffold
awk                                git-archive-all                    luaradio                           skafos
aws-shell                          git-cola                           lxc                                sops
awscli                             git-credential-manager             lynis                              sourcery
azure-cli                          git-lfs                            lz4                                sphinx-doc
babel                              git-sizer                          mariadb@10.2                       spotbugs
bat                                gjs                                mbedtls                            sqldiff
bind                               glances                            mdds                               sqlite-analyzer
bitcoin                            glib                               megatools                          stellar-core
bitrise                            glm                                menhir                             stlink
brew-gem                           gloox                              metabase                           stunnel
brotli                             gocr                               mmark                              svgo
bullet                             gradle                             mongodb@3.6                        swift-protobuf
cabal-install                      grakn                              mosquitto                          syncthing
cargo-completion                   grpc                               mpd                                tcpflow
cash-cli                           grunt-completion                   nano                               telegraf
chakra                             gst-editing-services               neko                               terragrunt
chapel                             gst-libav                          nginx                              tgui
circleci                           gst-plugins-bad                    node                               tiger-vnc
clang-format                       gst-plugins-base                   ntopng                             tomcat
clojure                            gst-plugins-good                   opam                               tomcat@7
cmark-gfm                          gst-plugins-ugly                   opensc                             tomcat@8
cnats                              gst-python                         orc-tools                          ttyd
codequery                          gst-rtsp-server                    ortp                               twarc
coffeescript                       gst-validate                       packer                             uhd
compcert                           gstreamer                          paket                              unp64
conan                              gtk-mac-integration                pandoc                             urh
consul                             hapi-fhir-cli                      pandoc-citeproc                    v8
convox                             hcloud                             pandoc-crossref                    vagrant-completion
cpmtools                           helmfile                           parallel                           vala
crowdin                            help2man                           pdftoedn                           vegeta
crystal                            heroku                             pdftoipe                           vim
dbhash                             homebank                           pgbadger                           vips
dependency-check                   httpd                              pgrouting                          vnu
diff-pdf                           hugo                               php                                vorbis-tools
diffoscope                         hwloc                              php@5.6                            vte3
digdag                             ice                                php@7.0                            wdiff
docker-machine-nfs                 imagemagick                        php@7.1                            weaver
double-conversion                  imagemagick@6                      pmd                                webpack
dub                                immortal                           poppler                            wireguard-tools
duck                               influxdb                           postgis                            wtf
duplicity                          jenkins                            povray                             xcodegen
elasticsearch                      jenkins-lts                        pqiv                               xerces-c
elasticsearch@5.6                  jerasure                           pre-commit                         xonsh
erlang                             jfrog-cli-go                       prettier                           xtensor
erlang@19                          jhipster                           profanity                          yarn
erlang@20                          json-glib                          proj                               yelp-tools
eslint                             jump                               prometheus                         youtube-dl
faas-cli                           kerl                               protobuf-swift                     zpython
fabric                             kibana                             prototool                          zsh
file-roller                        kibana@5.6                         pulumi
flow                               krakend                            pygobject3
==> Deleted Formulae
submarine

==> Upgrading 6 outdated packages, with result:
pipenv 2018.5.18 -> 2018.7.1, gdbm 1.14.1_1 -> 1.18, python 3.6.5 -> 3.7.0, readline 7.0.3_1 -> 7.0.5, sqlite 3.24.0 -> 3.25.2, openssl 1.0.2o_1 -> 1.0.2p
==> Upgrading readline
==> Downloading https://homebrew.bintray.com/bottles/readline-7.0.5.mojave.bottle.tar.gz
==> Downloading from https://akamai.bintray.com/59/5976a79f0dbd5ccb2a261f692763319d612309caa2b8cf703f209270764c657c?__gda__=exp=1537980679~hm
######################################################################## 100.0%
==> Pouring readline-7.0.5.mojave.bottle.tar.gz
==> Caveats
readline is keg-only, which means it was not symlinked into /usr/local,
because macOS provides the BSD libedit library, which shadows libreadline.
In order to prevent conflicts when programs look for libreadline we are
defaulting this GNU Readline installation to keg-only.

For compilers to find readline you may need to set:
  export LDFLAGS="-L/usr/local/opt/readline/lib"
  export CPPFLAGS="-I/usr/local/opt/readline/include"

==> Summary
🍺  /usr/local/Cellar/readline/7.0.5: 46 files, 1.5MB
==> Upgrading sqlite
==> Downloading https://homebrew.bintray.com/bottles/sqlite-3.25.2.mojave.bottle.tar.gz
==> Downloading from https://akamai.bintray.com/59/59e23f50f8a87b151578dbd38334b49df6488ea835d3b99c0bcbe50726032b1f?__gda__=exp=1537980682~hm
######################################################################## 100.0%
==> Pouring sqlite-3.25.2.mojave.bottle.tar.gz
==> Caveats
Homebrew has detected an existing SQLite history file that was created
with the editline library. The current version of this formula is
built with Readline. To back up and convert your history file so that
it can be used with Readline, run:

  sed -i~ 's/\\040/ /g' ~/.sqlite_history

before using the `sqlite` command-line tool again. Otherwise, your
history will be lost.

sqlite is keg-only, which means it was not symlinked into /usr/local,
because macOS provides an older sqlite3.

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

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

==> Summary
🍺  /usr/local/Cellar/sqlite/3.25.2: 11 files, 3.7MB
==> Upgrading openssl
==> Downloading https://homebrew.bintray.com/bottles/openssl-1.0.2p.mojave.bottle.tar.gz
==> Downloading from https://akamai.bintray.com/ca/cabda4ca62a0b206366658e36ce7175e7da5f8ad24846843611ed19d7759404b?__gda__=exp=1537980685~hm
######################################################################## 100.0%
==> Pouring openssl-1.0.2p.mojave.bottle.tar.gz
==> Caveats
A CA file has been bootstrapped using certificates from the SystemRoots
keychain. To add additional certificates (e.g. the certificates added in
the System keychain), place .pem files in
  /usr/local/etc/openssl/certs

and run
  /usr/local/opt/openssl/bin/c_rehash

openssl is keg-only, which means it was not symlinked into /usr/local,
because Apple has deprecated use of OpenSSL in favor of its own TLS and crypto libraries.

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

For compilers to find openssl you may need to set:
  export LDFLAGS="-L/usr/local/opt/openssl/lib"
  export CPPFLAGS="-I/usr/local/opt/openssl/include"

==> Summary
🍺  /usr/local/Cellar/openssl/1.0.2p: 1,793 files, 12MB
==> Upgrading pipenv
==> Installing dependencies for pipenv: gdbm, python
==> Installing pipenv dependency: gdbm
==> Downloading https://homebrew.bintray.com/bottles/gdbm-1.18.mojave.bottle.tar.gz
######################################################################## 100.0%
==> Pouring gdbm-1.18.mojave.bottle.tar.gz
🍺  /usr/local/Cellar/gdbm/1.18: 20 files, 588.7KB
==> Installing pipenv dependency: python
==> Downloading https://homebrew.bintray.com/bottles/python-3.7.0.mojave.bottle.5.tar.gz
==> Downloading from https://akamai.bintray.com/60/600501d78904da7b5cbbf0d6e42d0028be2a9f85bdeb3b97724982c6453705ab?__gda__=exp=1537980698~hm
######################################################################## 100.0%
==> Pouring python-3.7.0.mojave.bottle.5.tar.gz
==> /usr/local/Cellar/python/3.7.0/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python
==> /usr/local/Cellar/python/3.7.0/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python
==> /usr/local/Cellar/python/3.7.0/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scripts=/usr/local/Cellar/python
==> Caveats
Python has been installed as
  /usr/local/bin/python3

Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
`python3`, `python3-config`, `pip3` etc., respectively, have been installed into
  /usr/local/opt/python/libexec/bin

If you need Homebrew's Python 2.7 run
  brew install python@2

Pip, setuptools, and wheel have been installed. To update them run
  pip3 install --upgrade pip setuptools wheel

You can install Python packages with
  pip3 install <package>
They will install into the site-package directory
  /usr/local/lib/python3.7/site-packages

See: https://docs.brew.sh/Homebrew-and-Python
==> Summary
🍺  /usr/local/Cellar/python/3.7.0: 4,790 files, 102.2MB
==> Installing pipenv
==> Downloading https://homebrew.bintray.com/bottles/pipenv-2018.7.1.mojave.bottle.tar.gz
==> Downloading from https://akamai.bintray.com/dc/dc136680cf0685e3ffc773a5863dc9d9b164959340732df500f3bfb3c15d14d4?__gda__=exp=1537980724~hm
######################################################################## 100.0%
==> Pouring pipenv-2018.7.1.mojave.bottle.tar.gz
==> Caveats
Bash completion has been installed to:
  /usr/local/etc/bash_completion.d
==> Summary
🍺  /usr/local/Cellar/pipenv/2018.7.1: 1,359 files, 18.7MB
==> Caveats
==> readline
readline is keg-only, which means it was not symlinked into /usr/local,
because macOS provides the BSD libedit library, which shadows libreadline.
In order to prevent conflicts when programs look for libreadline we are
defaulting this GNU Readline installation to keg-only.

For compilers to find readline you may need to set:
  export LDFLAGS="-L/usr/local/opt/readline/lib"
  export CPPFLAGS="-I/usr/local/opt/readline/include"

==> sqlite
Homebrew has detected an existing SQLite history file that was created
with the editline library. The current version of this formula is
built with Readline. To back up and convert your history file so that
it can be used with Readline, run:

  sed -i~ 's/\\040/ /g' ~/.sqlite_history

before using the `sqlite` command-line tool again. Otherwise, your
history will be lost.

sqlite is keg-only, which means it was not symlinked into /usr/local,
because macOS provides an older sqlite3.

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

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

==> openssl
A CA file has been bootstrapped using certificates from the SystemRoots
keychain. To add additional certificates (e.g. the certificates added in
the System keychain), place .pem files in
  /usr/local/etc/openssl/certs

and run
  /usr/local/opt/openssl/bin/c_rehash

openssl is keg-only, which means it was not symlinked into /usr/local,
because Apple has deprecated use of OpenSSL in favor of its own TLS and crypto libraries.

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

For compilers to find openssl you may need to set:
  export LDFLAGS="-L/usr/local/opt/openssl/lib"
  export CPPFLAGS="-I/usr/local/opt/openssl/include"

==> python
Python has been installed as
  /usr/local/bin/python3

Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to
`python3`, `python3-config`, `pip3` etc., respectively, have been installed into
  /usr/local/opt/python/libexec/bin

If you need Homebrew's Python 2.7 run
  brew install python@2

Pip, setuptools, and wheel have been installed. To update them run
  pip3 install --upgrade pip setuptools wheel

You can install Python packages with
  pip3 install <package>
They will install into the site-package directory
  /usr/local/lib/python3.7/site-packages

See: https://docs.brew.sh/Homebrew-and-Python
==> pipenv
Bash completion has been installed to:
  /usr/local/etc/bash_completion.d

Check brew

$ brew config
HOMEBREW_VERSION: 1.7.6
ORIGIN: https://github.com/Homebrew/brew
HEAD: f239b7a62790cfb4f33bda9aab7597d43f1b1e3b
Last commit: 13 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 6b72baa7d65ae0a742e8903f8d9afcdb26f55615
Core tap last commit: 16 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_GIT: git
HOMEBREW_MACOS_VERSION_NUMERIC: 101400
CPU: octa-core 64-bit haswell
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.17.1 => /Library/Developer/CommandLineTools/usr/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 10.0.1, 9.0.1
macOS: 10.14-x86_64
CLT: 10.0.0.0.1.1535735448
CLT headers: N/A
Xcode: N/A
XQuartz: N/A

$ brew doctor
Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: The following directories do not exist:
/usr/local/sbin

You should create these directories and change their ownership to your account.
  sudo mkdir -p /usr/local/sbin
  sudo chown -R $(whoami) /usr/local/sbin
$ sudo mkdir -p /usr/local/sbin
$ sudo chown -R $(whoami) /usr/local/sbin
$ brew doctor
Your system is ready to brew.
$ brew update
Already up-to-date.

Upgrade brew cask

$ brew cask upgrade
==> Casks with `auto_updates` or `version :latest` will not be upgraded
==> Upgrading 1 outdated package, with result:
eclipse-ptp 4.7.2,oxygen:2 -> 4.7.3a,oxygen:3a
==> Satisfying dependencies
==> Downloading https://www.eclipse.org/downloads/download.php?file=/technology/epp/downloads/release/oxygen/3a/ecl
==> Downloading from http://download.eclipse.org/technology/epp/downloads/release/oxygen/3a/eclipse-parallel-oxygen
######################################################################## 100.0%
==> Verifying SHA-256 checksum for Cask 'eclipse-ptp'.
==> Starting upgrade for Cask eclipse-ptp
==> Backing App 'Eclipse PTP.app' up to '/usr/local/Caskroom/eclipse-ptp/4.7.2,oxygen:2/Eclipse.app'.
==> Removing App '/Applications/Eclipse PTP.app'.
hdiutil attach -plist -nobrowse -readonly -noidme -mountrandom /var/folders/06/6q5dfrq12qvcbkyd62kd65l00000gn/T/d20181005-19955-168p4tu /Users/gcollis/Library/Caches/Homebrew/downloads/7e067b39049e2c1e5f3bc862e840c0c1898eee11a8857da6e0c2d4e6d6ee76c1--eclipse-parallel-oxygen-3a-macosx-cocoa-x86_64.dmg
mkbom -s -i /var/folders/06/6q5dfrq12qvcbkyd62kd65l00000gn/T/20181005-19955-pzvf6t.list -- /var/folders/06/6q5dfrq12qvcbkyd62kd65l00000gn/T/20181005-19955-v0unqc.bom
ditto --bom /var/folders/06/6q5dfrq12qvcbkyd62kd65l00000gn/T/20181005-19955-v0unqc.bom -- /private/var/folders/06/6q5dfrq12qvcbkyd62kd65l00000gn/T/d20181005-19955-168p4tu/dmg.qV8IAl /var/folders/06/6q5dfrq12qvcbkyd62kd65l00000gn/T/d20181005-19955-nlqu5o
diskutil eject /private/var/folders/06/6q5dfrq12qvcbkyd62kd65l00000gn/T/d20181005-19955-168p4tu/dmg.qV8IAl
cp -pR /var/folders/06/6q5dfrq12qvcbkyd62kd65l00000gn/T/d20181005-19955-nlqu5o/Eclipse.app/. /usr/local/Caskroom/eclipse-ptp/4.7.3a,oxygen:3a/Eclipse.app
==> Moving App 'Eclipse.app' to '/Applications/Eclipse PTP.app'.
==> Purging files for version 4.7.2,oxygen:2 of Cask eclipse-ptp
🍺  eclipse-ptp was successfully upgraded!