Install Spectre from Github
Check Spectre version
To see if you have Spectre installed, you can open RStudio and look under the 'packages' tab. The version will be listed in the right hand column. Hit the 
button to refresh the package list if you need. If you have the latest version installed, R won't install it again. If you have an older version, the R will install the latest version. If you wish, you can check the Spectre Home Page for the latest version.
Tip
If you are updating Spectre, we advise deleting the previous installation to ensure a clean update.
remove.packages('Spectre')
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Install Devtools
In R, install and load the 'devtools' package. The devtools package has a number of dependencies (packages that it needs to use) that it will automatically install when you install 'devtools' – this might take some time.
## Install (if not already installed)
if(!require('devtools')) {install.packages('devtools')}
Tip
After installing devtools, we recommend restarting RStudio.
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Install Spectre
Subsequently, use the 'install_github' function to install and load the Spectre package. By default this will load the 'master' branch, which is the same as the latest stable release version (listed at https://immunedynamics.github.io/spectre). To install a specific release version, see https://cran.r-project.org/web/packages/githubinstall/vignettes/githubinstall.html.
## Install Spectre
library('devtools')
devtools::install_github("immunedynamics/spectre")
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Confirm or decline updates
During installation, you may see a message like the following. You can update all the packages if you wish, but if you are unsure, or using multiple packages in other contexts, it might be wise to wait until you have time to update everything and test your scripts afterwards.
These packages have more recent versions available. Which would you like to update? 1: All 2: CRAN packages only 3: None 4: rlang (0.4.1 -> 0.4.2 ) [CRAN] 5: digest (0.6.22 -> 0.6.23) [CRAN] 6: roxygen2 (7.0.0 -> 7.0.1 ) [CRAN] Enter one or more numbers, or an empty line to skip updates:
# Type '1' and press enter to update all packages, or '3' and press enter for no updates 3
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Possible queries during installation
R will inform you of which additional package are being installed.
As each dependency (package) is being installed, you will see updates.
If you see the following prompt, click 'Install'.
You may be asked for permission to compile the code for certain pages, type 'Yes' and run the code.
Yes
Successful installation
If the installation was successful,
✓ checking for file ‘/private/var/folders/zf/7wygqzns5vx7ycttdgcc4byc0000gp/T/RtmpDchxP7/remotes9a66a1a4064/ImmuneDynamics-Spectre-c1401e6/DESCRIPTION’ ... ─ preparing ‘Spectre’: (879ms) ✓ checking DESCRIPTION meta-information ... ─ checking for LF line-endings in source and make files and shell scripts ─ checking for empty or unneeded directories ─ building ‘Spectre_0.5.4.tar.gz’ * installing *source* package ‘Spectre’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help Warning: /private/var/folders/zf/7wygqzns5vx7ycttdgcc4byc0000gp/T/RtmpQekn8e/R.INSTALL231e7ae0ba82/Spectre/man/demo.exp.Rd: docType ‘demo.exp’ is unrecognized *** installing help indices ** building package indices ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (Spectre)
You can check on the status of Spectre and the other package dependencies by running 'package.check()'.
## Check if all required packages have been installed Spectre::package.check()
You should see the following returned.
Package: Spectre
-- Version (on disk): 0.5.3
-- Version (loaded): 0.5.3
-- Install date: 2021-06-19
-- Install source: Github (immunedynamics/spectre@c1401e6)
-- Install path: /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Spectre
-- R version: R version 4.1.0 (2021-05-18)
-- OS: macOS Catalina 10.15.7
Please note, your 'on disk' version of Spectre is different to the 'loaded' version (i.e. you appear to have had the Spectre library loaded and active while installing a new version. To address this, either:
a) run 'detach('package:Spectre', unload = TRUE)' followed by 'library('Spectre'), or
b) re-start RStudio
Checking dependency packages...
-- All packages successfully installed.
Check out 'https://immunedynamics.github.io/spectre/' for protocols
Load libraries (packages)
You can then load the required packages using the 'package.load()' function.
## Load all required packages Spectre::package.load()
Unsuccessful installation
If Spectre or any of the dependencies was not installed successfully, you may see some error messages like the following.
Alternatively, if Spectre was successfully installed, but when running 'package.check()' some of the dependencies were not been installed correctly, you will see something like the following:
Checking dependency packages...
-- Biobase is required but not installed. Please install from BioConductor.
Check out 'https://immunedynamics.github.io/spectre/getting-started/' for help with installation
Installation troubleshooting
If you run into problems during installation, check out our installation troubleshooting page. Alternatively, you can report an issue on Github, ask for help on our discussion board, or email us.
