Skip to content

Commit

Permalink
Update mac documentation to include arm64 (#330)
Browse files Browse the repository at this point in the history
  • Loading branch information
@jwokaty
jwokaty authored Sep 27, 2023
1 parent 4bba266 commit d858ff4
Showing 1 changed file with 119 additions and 54 deletions.
173 changes: 119 additions & 54 deletions Doc/Prepare-macOS-Big-Sur-HOWTO.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,9 +9,11 @@ https://github.com/Bioconductor/bioconductor_salt.
- For how to uninstall Mac packages (`.pkg` files) using native `pkgutil`:
https://wincent.com/wiki/Uninstalling_packages_(.pkg_files)_on_Mac_OS_X
- Watch https://mac.r-project.org/ for changes in requirements. Binaries can be
found at https://mac.r-project.org/bin/.
found at https://mac.r-project.org/bin/. These binaries should be preferred
over others.
- As of April 2023, the minimum supported OS is MacOSX11.

- This document describes how to prepare both x86_64 and arm64 machines for
the BBS.


## 1. Initial setup (from the administrator account)
Expand Down Expand Up @@ -591,7 +593,13 @@ TESTING:
We need to make sure that, by default, the **reticulate** package will
use the system-wide Python interpreter that is in the `PATH`.
In `/etc/profile` add:
In the terminal, execute
which python3
This is the reticulate path that must be set in `/etc/profile`. For example, if
the output of `which python3` is `/usr/local/bin/python3` then in `/etc/profile`
add
export RETICULATE_PYTHON="/usr/local/bin/python3" # same as 'which python3'
Expand All @@ -609,7 +617,7 @@ TESTING: If R is already installed on the machine, start it, and do:
#### Install Python 3 modules needed by BBS
`BBS_UBUNTU_PATH` must be the path to `BBS/Ubuntu-files/20.04`.
`BBS_UBUNTU_PATH` must be the path to `BBS/Ubuntu-files/22.04`.
sudo -H pip3 install -r $BBS_UBUNTU_PATH/pip_bbs.txt
Expand All @@ -621,10 +629,13 @@ TESTING: If R is already installed on the machine, start it, and do:
sudo -H pip3 install -r $BBS_UBUNTU_PATH/pip_pkgs.txt
Optionally, install all of the above with
Optionally, install all of the above with
python3 -m pip install $(cat $BBS_UBUNTU_PATH/pip_*.txt | awk '/^[^#]/ {print $1}')
Note: it's ok if jupyter lab is not installed but everything else should be.
Tensorflow is currently not available for Mac OS arm64.
TESTING:
- `jupyter --version` should display something like this:
Expand All @@ -642,8 +653,6 @@ TESTING:
nbformat : 5.0.8
traitlets : 5.0.5
```
Note that it's ok if jupyter lab is not installed but everything else
should be.
- Start python3 and try to import the above modules. Quit.
Expand Down Expand Up @@ -687,6 +696,8 @@ to the `PATH` take effect. Then:
### 2.15 Install Pandoc
#### x86_64
Install Pandoc 2.7.3 instead of the latest Pandoc (2.9.2.1 as of April 2020).
The latter breaks `R CMD build` for 8 Bioconductor software packages
(**FELLA**, **flowPloidy**, **MACPET**, **profileScoreDist**, **projectR**,
Expand All @@ -696,12 +707,22 @@ The latter breaks `R CMD build` for 8 Bioconductor software packages
Download with:
cd ~/Downloads/
curl -LO https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-macOS.pkg
curl -LO https://github.com/jgm/pandoc/releases/download/2.7.3/pandoc-2.7.3-macOS.pkg > ~/Downloads/pandoc.pkg
#### arm64
Earlier releases are not available for arm64, so the latest version of pandoc
should be installed.
Download
curl -LO https://github.com/jgm/pandoc/releases/download/3.1.8/pandoc-3.1.8-arm64-macOS.pkg > ~/Downloads/pandoc.pkg
#### For all macs
Install with:
sudo installer -pkg pandoc-2.7.3-macOS.pkg -target /
sudo installer -pkg pandoc.pkg -target /
# Fix /usr/local/ permissions:
sudo chown -R biocbuild:admin /usr/local/*
Expand Down Expand Up @@ -853,9 +874,9 @@ the tarball (`.tar.gz` file) does NOT include Tcl/Tk (which is needed
by R base package **tcltk**) so make sure to grab the former.
If installing R release: download R from CRAN (e.g. from
https://cloud.r-project.org/bin/macosx/). Pick up the 1st file. Make sure to
pick the installer, not the source tarball, as the former contains Tcl/Tk
libraries that will install in `/usr/local`.
https://cloud.r-project.org/bin/macosx/). Make sure to pick the installer, not
the source tarball, as the former contains Tcl/Tk libraries that will install
in `/usr/local`.
#### Download and install
Expand All @@ -864,11 +885,11 @@ Remove the previous R installation:
cd /Library/Frameworks/
sudo rm -rf R.framework
Download and install with:
For example, if installing for x86_64 mac, download and install with:
cd ~/Downloads/
curl -O https://cran.r-project.org/bin/macosx/base/R-4.3.0.pkg
sudo installer -pkg R-4.3.0.pkg -target /
curl -O https://cloud.r-project.org/bin/macosx/big-sur-x86_64/base/R-4.3.1-x86_64.pkg
sudo installer -pkg R-4.3.1-x86_64.pkg -target /
Note that, unlike what we do on the Linux and Windows builders, this is a
*system-wide* installation of R i.e. it's in the `PATH` for all users on the
Expand Down Expand Up @@ -1160,14 +1181,14 @@ Everything in this section must be done **from the biocbuild account**.
### 4.1 Install Java
Go to https://jdk.java.net/ and follow the link to the latest JDK (JDK
14 as of April 1, 2020). Then download the tarball for macOS/x64 (e.g.
`openjdk-14.0.1_osx-x64_bin.tar.gz`) to `~/Downloads/`.
Go to https://jdk.java.net/ and follow the link to the latest JDK. Then
download the tarball for your specific mac (e.g. `openjdk-18.0.1.1_macos-x64_bin.tar.gz`
or `openjdk-18.0.1.1_macos-aarch64_bin.tar.gz`) to `~/Downloads/`.
Install with:
cd /usr/local/
sudo tar zxvf ~/Downloads/openjdk-14.0.1_osx-x64_bin.tar.gz
sudo tar zxvf ~/Downloads/openjdk-18.0.1.1_macos-x64_bin.tar.gz
# Fix /usr/local/ permissions:
sudo chown -R biocbuild:admin /usr/local/*
Expand All @@ -1176,24 +1197,24 @@ Install with:
Then:
cd /usr/local/bin/
ln -s ../jdk-14.0.1.jdk/Contents/Home/bin/java
ln -s ../jdk-14.0.1.jdk/Contents/Home/bin/javac
ln -s ../jdk-14.0.1.jdk/Contents/Home/bin/jar
ln -s ../jdk-18.0.1.1.jdk/Contents/Home/bin/java
ln -s ../jdk-18.0.1.1.jdk/Contents/Home/bin/javac
ln -s ../jdk-18.0.1.1.jdk/Contents/Home/bin/jar
In `/etc/profile` add the following line:
export JAVA_HOME=/usr/local/jdk-14.0.1.jdk/Contents/Home
export JAVA_HOME=/usr/local/jdk-18.0.1.1.jdk/Contents/Home
TESTING: Logout and login again so that the changes to `/etc/profile` take
effect. Then:
java --version
# openjdk 14.0.1 2020-04-14
# OpenJDK Runtime Environment (build 14.0.1+7)
# OpenJDK 64-Bit Server VM (build 14.0.1+7, mixed mode, sharing)
# openjdk 18.0.1.1 2022-04-22
# OpenJDK Runtime Environment (build 18.0.1.1+2-6)
# OpenJDK 64-Bit Server VM (build 18.0.1.1+2-6, mixed mode, sharing)
javac --version
# javac 14.0.1
# javac 18.0.1.1
Finally reconfigure R to use this new Java installation:
Expand All @@ -1206,7 +1227,7 @@ TESTING: Try to install the **rJava** package:
library(rJava)
.jinit()
.jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
# [1] "14.0.1+7"
# [1] "18.0.1.1+2-6"
### 4.2 Install NetCDF and HDF5 system library
Expand All @@ -1215,13 +1236,22 @@ NetCDF is needed only if CRAN package **ncdf4** needs to be installed from
source which is usually NOT the case (most of the time a Mac binary should
be available on CRAN).
Download and extract Simon's binaries with:
Download and extract Simon's binaries:
cd ~/Downloads/
curl -O https://mac.r-project.org/bin/darwin17/x86_64/netcdf-4.8.1-darwin.17-x86_64.tar.xz
curl -O https://mac.r-project.org/bin/darwin17/x86_64/hdf5-1.12.1-darwin.17-x86_64.tar.xz
sudo tar fvxJ netcdf-4.8.1-darwin.17-x86_64.tar.xz -C /
sudo tar fvxJ hdf5-1.12.1-darwin.17-x86_64.tar.xz -C /
#### x86_64
curl -O https://mac.r-project.org/bin/darwin17/x86_64/netcdf-4.8.1-darwin.17-x86_64.tar.xz > ~/Downloads/netcdf.tar.xz
curl -O https://mac.r-project.org/bin/darwin17/x86_64/hdf5-1.12.1-darwin.17-x86_64.tar.xz > ~/Downloads/hdf5.tar.xz
#### arm64
curl -O https://mac.r-project.org/bin/darwin20/arm64/netcdf-4.8.1-darwin.20-arm64.tar.xz > ~/Downloads/netcdf.tar.xz
curl -O https://mac.r-project.org/bin/darwin20/arm64/hdf5-1.12.2-darwin.20-arm64.tar.xz > ~/Downloads/hdf5.tar.xz
#### All macs
sudo tar fvxJ netcdf.tar.xz -C /
sudo tar fvxJ hdf5.tar.xz -C /
# Fix /usr/local/ permissions:
sudo chown -R biocbuild:admin /usr/local/*
Expand All @@ -1240,11 +1270,19 @@ that this takes much longer:
### 4.3 Install GSL system library
Download and extract Simon's binary with:
Download and extract Simon's binary
cd ~/Downloads/
curl -O https://mac.r-project.org/bin/darwin17/x86_64/gsl-2.7-darwin.17-x86_64.tar.xz
sudo tar fvxJ gsl-2.7-darwin.17-x86_64.tar.xz -C /
#### x86_64
curl -O https://mac.r-project.org/bin/darwin17/x86_64/gsl-2.7-darwin.17-x86_64.tar.xz > ~/Downloads/gsl.tar.xz
#### arm64
curl -O https://mac.r-project.org/bin/darwin20/arm64/gsl-2.7.1-darwin.20-arm64.tar.xz > ~/Downloads/gsl.tar.xz
#### All macs
sudo tar fvxJ gsl.tar.xz -C /
# Fix /usr/local/ permissions:
sudo chown -R biocbuild:admin /usr/local/*
Expand Down Expand Up @@ -1280,7 +1318,7 @@ TESTING: Try to install the **rjags** package *from source*:
### 4.5 Install CMake
Needed for CRAN package **nlopter**, which is used by a few Bioconductor
Needed for CRAN package **nloptr**, which is used by a few Bioconductor
packages.
Home page: https://cmake.org/
Expand All @@ -1300,10 +1338,10 @@ you already have a brewed CMake on the machine, make sure to remove it:
Then:
cd ~/Downloads/
curl -LO https://github.com/Kitware/CMake/releases/download/v3.16.5/cmake-3.16.5-Darwin-x86_64.dmg
sudo hdiutil attach cmake-3.16.5-Darwin-x86_64.dmg
cp -ri /Volumes/cmake-3.16.5-Darwin-x86_64/CMake.app /Applications/
sudo hdiutil detach /Volumes/cmake-3.16.5-Darwin-x86_64
curl -LO https://github.com/Kitware/CMake/releases/download/v3.23.0/cmake-3.23.0-macos-universal.dmg
sudo hdiutil attach cmake-3.23.0-macos-universal.dmg
cp -ri /Volumes/cmake-3.23.0-macos-universal/CMake.app /Applications/
sudo hdiutil detach /Volumes/cmake-3.23.0-macos-universal
Then in `/etc/profile` *prepend* `/Applications/CMake.app/Contents/bin`
to `PATH`, or, if the file as not line setting `PATH` already, add the
Expand All @@ -1320,6 +1358,8 @@ effect. Then:
### 4.6 Install Open Babel
TODO: Modify instructions for arm64
The **ChemmineOB** package requires Open Babel 3. Note that the Open Babel
website seems very outdated:
Expand Down Expand Up @@ -1534,6 +1574,8 @@ Then try to install the **RMySQL** package *from source*:
### 4.9 Install Ensembl VEP script
TODO: Modify instructions for arm64
Required by Bioconductor packages **ensemblVEP** and **MMAPPR2**.
Complete installation instructions are at
Expand Down Expand Up @@ -1629,10 +1671,13 @@ Then try to build the **GeneGA** package:
### 4.11 Set up ImmuneSpaceR package for connecting to ImmuneSpace
Required by Bioconductor package **ImmuneSpaceR**. Get credentials from
Bitwarden.
In `/etc/profile` add:
export ISR_login=[email protected]
export ISR_pwd=1notCRAN
export ISR_login=*****
export ISR_pwd=*****
TESTING: Logout and login again so that the changes to `/etc/profile` take
effect. Then try to build the **ImmuneSpaceR** package:
Expand Down Expand Up @@ -1667,14 +1712,17 @@ Required by Bioconductor package **Travel**.
Download latest stable release from https://osxfuse.github.io/ e.g.:
cd ~/Downloads/
curl -LO https://github.com/osxfuse/osxfuse/releases/download/macfuse-4.0.5/macfuse-4.0.5.dmg
curl -LO https://github.com/osxfuse/osxfuse/releases/download/macfuse-4.5.0/macfuse-4.5.0.dmg
Install with:
sudo hdiutil attach macfuse-4.0.5.dmg
sudo hdiutil attach macfuse-4.5.0.dmg
sudo installer -pkg "/Volumes/macFUSE/Install macFUSE.pkg" -target /
sudo hdiutil detach /Volumes/macFUSE
You may need to enable support for third party kernel extensions if installing
macFUSE for the first time. See https://github.com/macfuse/macfuse/wiki/Getting-Started.
TESTING: Try to install the **Travel** package *from source*:
library(BiocManager)
Expand All @@ -1690,9 +1738,18 @@ Required by Bioconductor package **rmspc**.
Visit https://docs.microsoft.com/en-us/dotnet/core/install/macos. Download and
install the 6.0 .NET runtime corresponding to the build system's macOS.
curl -O https://download.visualstudio.microsoft.com/download/pr/2ef12357-499b-4a5b-a488-da45a5f310e6/fbe35c354bfb50934a976fc91c6d8d81/dotnet-runtime-6.0.13-osx-x64.pkg
shasum -a 512 dotnet-runtime-6.0.13-osx-x64.pkg
sudo installer -pkg dotnet-runtime-6.0.13-osx-x64.pkg -target /
##### x86_64
curl -O https://download.visualstudio.microsoft.com/download/pr/2ef12357-499b-4a5b-a488-da45a5f310e6/fbe35c354bfb50934a976fc91c6d8d81/dotnet-runtime-6.0.13-osx-x64.pkg > ~/Downloads/dotnet.pkg
##### arm64
curl -O https://download.visualstudio.microsoft.com/download/pr/aa3b3150-80cb-4d30-87f8-dc36fa1dcf26/8ec9ff6836828175f1a6a60aefd4e63b/dotnet-runtime-6.0.13-osx-arm64.pkg > ~/Downloads/dotnet.pkg
##### For all macs
shasum -a 512 dotnet.pkg
sudo installer -pkg dotnet.pkg -target /
#### Testing
Expand All @@ -1709,9 +1766,17 @@ Required by Bioconductor package **MMUPHin**.
Download and extract Simon's binary with:
cd ~/Downloads/
curl -O https://mac.r-project.org/bin/darwin20/x86_64/glpk-5.0-darwin.20-x86_64.tar.xz
sudo tar fvxJ glpk-5.0-darwin.20-x86_64.tar.xz -C /
#### x86_64
curl -O https://mac.r-project.org/bin/darwin20/x86_64/glpk-5.0-darwin.20-x86_64.tar.xz > ~/Download/glpk.tar.xz
#### arm64
curl -O https://mac.r-project.org/bin/darwin20/arm64/glpk-5.0-darwin.20-arm64.tar.xz > ~/Download/glpk.tar.xz
#### For all macs
sudo tar fvxJ glpk.tar.xz -C /
# Fix /usr/local/ permissions:
sudo chown -R biocbuild:admin /usr/local/*
Expand Down

0 comments on commit d858ff4

Please sign in to comment.