From 1d7696655496f4fd0d24f9642dd930eefa06b001 Mon Sep 17 00:00:00 2001 From: hong-revo Date: Wed, 20 Sep 2017 23:50:25 +1000 Subject: [PATCH 1/3] start fixing vignettes --- .gitattributes | 63 +++++++++++++++++++++++++++++++++++++ .gitignore | 8 +++++ vignettes/10Deploy.Rmd | 16 +++++----- vignettes/11Extend.Rmd | 4 +++ vignettes/20Multi.Rmd | 4 +-- vignettes/30Compute.Rmd | 4 +-- vignettes/40Cost.Rmd | 4 +-- vignettes/60Kmeans.Rmd | 4 +-- vignettes/70Hotspot.Rmd | 4 +-- vignettes/80ModelSelect.Rmd | 4 +-- 10 files changed, 95 insertions(+), 20 deletions(-) create mode 100644 .gitattributes diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..1ff0c42 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,63 @@ +############################################################################### +# Set default behavior to automatically normalize line endings. +############################################################################### +* text=auto + +############################################################################### +# Set default behavior for command prompt diff. +# +# This is need for earlier builds of msysgit that does not have it on by +# default for csharp files. +# Note: This is only used by command line +############################################################################### +#*.cs diff=csharp + +############################################################################### +# Set the merge driver for project and solution files +# +# Merging from the command prompt will add diff markers to the files if there +# are conflicts (Merging from VS is not affected by the settings below, in VS +# the diff markers are never inserted). Diff markers may cause the following +# file extensions to fail to load in VS. An alternative would be to treat +# these files as binary and thus will always conflict and require user +# intervention with every merge. To do so, just uncomment the entries below +############################################################################### +#*.sln merge=binary +#*.csproj merge=binary +#*.vbproj merge=binary +#*.vcxproj merge=binary +#*.vcproj merge=binary +#*.dbproj merge=binary +#*.fsproj merge=binary +#*.lsproj merge=binary +#*.wixproj merge=binary +#*.modelproj merge=binary +#*.sqlproj merge=binary +#*.wwaproj merge=binary + +############################################################################### +# behavior for image files +# +# image files are treated as binary by default. +############################################################################### +#*.jpg binary +#*.png binary +#*.gif binary + +############################################################################### +# diff behavior for common document formats +# +# Convert binary document formats to text before diffing them. This feature +# is only available from the command line. Turn it on by uncommenting the +# entries below. +############################################################################### +#*.doc diff=astextplain +#*.DOC diff=astextplain +#*.docx diff=astextplain +#*.DOCX diff=astextplain +#*.dot diff=astextplain +#*.DOT diff=astextplain +#*.pdf diff=astextplain +#*.PDF diff=astextplain +#*.rtf diff=astextplain +#*.RTF diff=astextplain diff --git a/.gitignore b/.gitignore index a1e2348..c3b74da 100644 --- a/.gitignore +++ b/.gitignore @@ -27,3 +27,11 @@ inst/doc .Rproj.user *_credentials.R *~ + + +# VS files +.vs +*.tss +*.suo +*.sln +*.rxproj diff --git a/vignettes/10Deploy.Rmd b/vignettes/10Deploy.Rmd index 565e8cf..44babe1 100644 --- a/vignettes/10Deploy.Rmd +++ b/vignettes/10Deploy.Rmd @@ -1,6 +1,6 @@ --- -title = "Using Azure Data Science Virtual Machine: Deployment of a single DSVM" -author = "Graham Williams and Le Zhang" +title: "Using Azure Data Science Virtual Machine: Deployment of a single DSVM" +author: "Graham Williams and Le Zhang" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} @@ -68,7 +68,7 @@ account creation on a Windows DSVM. We can simply source the credentials file in R. -```{r setup} +```{r, setup} # Load the required subscription resources: TID, CID, and KEY. # Also includes the ssh PUBKEY for the user. @@ -143,7 +143,7 @@ HOST cat("\n") ``` -```{r connect} +```{r, connect} # Connect to the Azure subscription and use this as the context for # our activities. @@ -165,7 +165,7 @@ cat("Resource group", RG, "at", LOC, Create the resource group within which all resources we create will be grouped. -```{r create resource group} +```{r, create resource group} # Create a new resource group into which we create the VMs and related # resources. Resource group name is RG. Note that to create a new # resource group one needs to add access control of Active Directory @@ -219,7 +219,7 @@ formals(deployDSVM)$os The following code deploys a Linux DSVM which will take a few minutes. -```{r deploy} +```{r, deploy} # Create the required Linux DSVM - generally 4 minutes. ldsvm <- deployDSVM(context, @@ -238,7 +238,7 @@ azureListVM(context, RG) Prove that the deployed DSVM exists. -```{r prove exists} +```{r, prove exists} # Send a simple system() command across to the new server to test its # existence. Expect a single line with an indication of how long the @@ -273,7 +273,7 @@ server through the secure shell and manually run that command. We then reboot the server so that, for example, kernel updates, take effect. -```{r useful tools} +```{r, useful tools} system(paste(ssh, "sudo locale-gen 'en_AU.UTF-8'")) system(paste(ssh, "sudo apt-get -y install wajig")) system(paste(ssh, "wajig install -y lsb htop")) diff --git a/vignettes/11Extend.Rmd b/vignettes/11Extend.Rmd index 6caf0bd..b72710f 100644 --- a/vignettes/11Extend.Rmd +++ b/vignettes/11Extend.Rmd @@ -3,6 +3,10 @@ title: "Using Azure Data Science Virtual Machine: Extension of DSVM" author: "Graham Williams and Le Zhang" date: "July 10, 2017" output: html_document +vignette: > + %\VignetteIndexEntry{Vignette Title} + %\VignetteEngine{knitr::rmarkdown} + \usepackage[utf8]{inputenc} --- # Use case diff --git a/vignettes/20Multi.Rmd b/vignettes/20Multi.Rmd index 6cecfa0..e59ec5d 100644 --- a/vignettes/20Multi.Rmd +++ b/vignettes/20Multi.Rmd @@ -1,6 +1,6 @@ --- -title = "Using Azure Data Science Virtual Machine: Multi-deployment of DSVMs Quick Start" -author= "Graham Williams" +title: "Using Azure Data Science Virtual Machine: Multi-deployment of DSVMs Quick Start" +author: "Graham Williams" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} diff --git a/vignettes/30Compute.Rmd b/vignettes/30Compute.Rmd index 4f22eaa..23277b8 100644 --- a/vignettes/30Compute.Rmd +++ b/vignettes/30Compute.Rmd @@ -1,6 +1,6 @@ --- -title = "Using Azure Data Science Virtual Machine: Compute on Linux DSVM Quick Start" -author= "Graham Williams" +title: "Using Azure Data Science Virtual Machine: Compute on Linux DSVM Quick Start" +author: "Graham Williams" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} diff --git a/vignettes/40Cost.Rmd b/vignettes/40Cost.Rmd index e3ccba4..f9c3872 100644 --- a/vignettes/40Cost.Rmd +++ b/vignettes/40Cost.Rmd @@ -1,6 +1,6 @@ --- -title = "Using Azure Data Science Virtual Machine: Data consumption and cost calculation" -author= "Graham Williams" +title: "Using Azure Data Science Virtual Machine: Data consumption and cost calculation" +author: "Graham Williams" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} diff --git a/vignettes/60Kmeans.Rmd b/vignettes/60Kmeans.Rmd index ea4ba5d..702dae1 100644 --- a/vignettes/60Kmeans.Rmd +++ b/vignettes/60Kmeans.Rmd @@ -1,6 +1,6 @@ --- -title = "Using Azure Data Science Virtual Machine: a use case - kmeans clustering" -author= "Le Zhang and Graham Williams" +title: "Using Azure Data Science Virtual Machine: a use case - kmeans clustering" +author: "Le Zhang and Graham Williams" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} diff --git a/vignettes/70Hotspot.Rmd b/vignettes/70Hotspot.Rmd index 837a404..232137d 100644 --- a/vignettes/70Hotspot.Rmd +++ b/vignettes/70Hotspot.Rmd @@ -1,6 +1,6 @@ --- -title = "Using Azure Data Science Virtual Machine: a use case - hotspot" -author= "Le Zhang and Graham Williams" +title: "Using Azure Data Science Virtual Machine: a use case - hotspot" +author: "Le Zhang and Graham Williams" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} diff --git a/vignettes/80ModelSelect.Rmd b/vignettes/80ModelSelect.Rmd index 94fe7c9..067c210 100644 --- a/vignettes/80ModelSelect.Rmd +++ b/vignettes/80ModelSelect.Rmd @@ -1,6 +1,6 @@ --- -title = "Using Azure Data Science Virtual Machine: a use case - binary classification" -author= "Graham Williams" +title: "Using Azure Data Science Virtual Machine: a use case - binary classification" +author: "Graham Williams" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Vignette Title} From 7e0f05380a51ef029397d127ba719302b02a954c Mon Sep 17 00:00:00 2001 From: hong-revo Date: Thu, 21 Sep 2017 00:05:58 +1000 Subject: [PATCH 2/3] add remotes: line so install will actually work --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index 8b13fcc..f6a420c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -35,3 +35,4 @@ Suggests: testthat VignetteBuilder: knitr RoxygenNote: 5.0.1 +Remotes: Microsoft/AzureSMR From a20cef10117c090c3291916763997be9d2e7c418 Mon Sep 17 00:00:00 2001 From: hong-revo Date: Thu, 21 Sep 2017 01:05:30 +1000 Subject: [PATCH 3/3] update .Rbuildignore --- .Rbuildignore | 1 + 1 file changed, 1 insertion(+) diff --git a/.Rbuildignore b/.Rbuildignore index 77fbde6..978011a 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -1,5 +1,6 @@ \.git \.gitignore +\.gitattributes Makefile ^.*\.Rproj$ ^\.Rproj\.user$