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Upgrades #47

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merged 2 commits into from
Jan 8, 2025
Merged

Upgrades #47

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7097afd
Remove environment variables for TRE CA Certificate
AaronJackson Dec 11, 2024
4b3900c
Bump libreoffice, rstudio, vscode
AaronJackson Dec 11, 2024
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16 changes: 0 additions & 16 deletions modules/hic-tre-cert.ps1
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Original file line number Diff line number Diff line change
Expand Up @@ -58,19 +58,3 @@ New-Item -Path "C:\Program Files\Mozilla Firefox\" -Name distribution -ItemType
}
}
"@ | Out-File -Encoding ASCII -FilePath "C:\Program Files\Mozilla Firefox\distribution\policies.json"

# This covers both conda and CRAN, but it also overrides their own
# provided CA chain files. That's probably ok given we don't allow
# access to the internet.
[Environment]::SetEnvironmentVariable(
"SSL_CERT_FILE",
"C:\Tools\hic-tre.dundee.ac.uk.crt",
[System.EnvironmentVariableTarget]::User)
[Environment]::SetEnvironmentVariable(
"REQUESTS_CA_BUNDLE",
"C:\Tools\hic-tre.dundee.ac.uk.crt",
[System.EnvironmentVariableTarget]::User)
[Environment]::SetEnvironmentVariable(
"CURL_CA_BUNDLE",
"C:\Tools\hic-tre.dundee.ac.uk.crt",
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Ah, I remember encountering the S3 issue during a build now 🤣

[System.EnvironmentVariableTarget]::User)
4 changes: 2 additions & 2 deletions modules/libreoffice.ps1
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Expand Up @@ -3,8 +3,8 @@ $ProgressPreference = 'SilentlyContinue' # Disable (slow) progress bar

Set-Location C:\Tools

$LIBRE_VERSION = "24.2.5"
$LIBRE_HASH = "cad625d119db4720df5270fa2d860e0ed56d6e374b878e19a3cab4af68f1f54f"
$LIBRE_VERSION = "24.8.3"
$LIBRE_HASH = "b1808dbe14b22bb358a09f0edf83ab591e9d43b37dcd9dd35ff3880b85f1ad90"

$LIBRE_URL = "https://mirrors.ukfast.co.uk/sites/documentfoundation.org/tdf/libreoffice/stable/${LIBRE_VERSION}/win/x86_64/LibreOffice_${LIBRE_VERSION}_Win_x86-64.msi"

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10 changes: 5 additions & 5 deletions modules/rstudio.ps1
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Expand Up @@ -4,20 +4,20 @@ $ProgressPreference = "SilentlyContinue" # PS progress bar is slow
$ErrorActionPreference = "Stop"

# R environment
Invoke-WebRequest -Uri "https://cloud.r-project.org/bin/windows/base/R-4.4.1-win.exe" -OutFile C:\Tools\R-installer.exe
Invoke-WebRequest -Uri "https://cloud.r-project.org/bin/windows/base/R-4.4.2-win.exe" -OutFile C:\Tools\R-installer.exe
Start-Process C:\Tools\R-installer.exe -ArgumentList "/VERYSILENT","/NORESTART" -NoNewWindow -Wait -PassThru

Invoke-WebRequest -Uri "https://download1.rstudio.org/electron/windows/RStudio-2024.04.2-764.exe" -OutFile C:\Tools\RStudio-installer.exe
Invoke-WebRequest -Uri "https://s3.amazonaws.com/rstudio-ide-build/electron/windows/RStudio-2024.09.1-394.exe" -OutFile C:\Tools\RStudio-installer.exe
Start-Process C:\Tools\RStudio-installer.exe -ArgumentList "/S" -NoNewWindow -Wait -PassThru

Invoke-WebRequest -Uri "https://cran.r-project.org/bin/windows/Rtools/rtools44/files/rtools44-6104-6039.exe" -OutFile C:\Tools\RTools.exe
Invoke-WebRequest -Uri "https://cran.r-project.org/bin/windows/Rtools/rtools44/files/rtools44-6335-6327.exe" -OutFile C:\Tools\RTools.exe
Start-Process C:\Tools\RTools.exe -ArgumentList "/VERYSILENT" -NoNewWindow -Wait -PassThru

# Install some default packages
$pkgs = "tidyverse","odbc","dbi","qqman","metafor","tidyr","ggplot2",`
"hmisc","data.table","dplyr","lubridate","survival","survminer"
foreach ($pkg in $pkgs) {
& "C:\Program Files\R\R-4.4.1\bin\Rscript.exe" `
& "C:\Program Files\R\R-4.4.2\bin\Rscript.exe" `
-e "install.packages('$pkg', repos='http://cran.uk.r-project.org')"
}

Expand All @@ -34,5 +34,5 @@ local({r <- getOption("repos")
# Set timezone
Sys.setenv(TZ='Europe/London')
"@
Set-Content "C:\Program Files\R\R-4.4.1\etc\Rprofile.site" $RConfig
Set-Content "C:\Program Files\R\R-4.4.2\etc\Rprofile.site" $RConfig
Set-Content "C:\Users\Administrator\Documents\.Renviron" "RSTUDIO_DISABLE_SECURE_DOWNLOAD_WARNING=1"
4 changes: 2 additions & 2 deletions modules/vscode.ps1
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Expand Up @@ -2,8 +2,8 @@
Set-Location C:\Tools
$ProgressPreference = "SilentlyContinue" # PS progress bar is slow

$VSCODE_SHA256 = "f4cd3b2d845bd2a61152707c2b8626c10e8e9bcd1a8163944c34635172f6cdd9"
$VSCODE_URL = "https://az764295.vo.msecnd.net/stable/74b1f979648cc44d385a2286793c226e611f59e7/VSCodeUserSetup-x64-1.71.2.exe"
$VSCODE_SHA256 = "7ce997d7a80ff838c2b7312be6e26917a8b66a67c633ee0b3317b1ae70010077"
$VSCODE_URL = "https://vscode.download.prss.microsoft.com/dbazure/download/stable/f1a4fb101478ce6ec82fe9627c43efbf9e98c813/VSCodeUserSetup-x64-1.95.3.exe"

Invoke-WebRequest -Uri ${VSCODE_URL} -OutFile C:\Tools\vscode.exe

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