Page contents:
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.
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If you are updating Spectre, we advise deleting the previous installation to ensure a clean update. |
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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.
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## Install (if not already installed)
if(!require('devtools')) {install.packages('devtools')} |
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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.
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## Install Spectre
library('devtools')
devtools::install_github("immunedynamics/spectre") |
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If you are updating Spectre (rather than installing for the first time), we recommend re-starting RStudio at this point. |
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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.
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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: |
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# 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
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✓ 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) |
Installation troubleshooting
Occasionally during installation, you may run into errors, such as the one below relating to 'flowCore'. Check out our installation troubleshooting page for help.
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Error in library("flowCore") : there is no package called ‘flowCore’
Error: unable to load R code in package ‘Spectre’
Execution halted |
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Check libraries (packages)
Once the packages have been installed, you can check the libraries (packages) by running the 'package.check()' function. If installation of any specific package was not successful, see our installation troubleshooting page for help.
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## Check if all required packages have been installed Spectre::package.check() |
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'All packages successfully installed' |
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'dplyr is required but not installed' |
Load libraries (packages)
You can then load the required packages using the 'package.load()' function.
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## Load all required packages Spectre::package.load() |
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Package installations can fail due to a number of reasons, including R version incompatibilities (for example, Spectre v0.1 will not work in R v3.3.0), or package incompatibilities. If you are having problems installing Spectre, please see our installation troubleshooting page or submit an issue on the Spectre Github repository. Alternatively, you can install Spectre using one of our self-contained docker images. |
