Update Sys Deps (#127)

* Fix link

* Fixes typo Fix #109

* Update what to expect

* strengthen wording for basilisk requirement instead of reticulate as requested
by Vince

* Update System Dependency section with @vjctin suggested text

Author: lshep

description-file.Rmd

@@ -157,7 +157,8 @@ If the installation process is non-trivial, a top-level [`INSTALL` file](#sysdep
 be included to document the process. If a user facing [`README`](#readme) is included it
 is also recommended to document the process there; do not try to install a
 dependency for a user anywhere in the package (i.e. readme, r code, man pages,
-vignette). You may show instructions only in unevaluated sections.
+vignette). You may show instructions only in unevaluated sections. See also
+[Additional files and dependencies](#rcode-sysdep)
 
 ## `biocViews` {#description-biocviews}
 

install-file.Rmd

@@ -3,8 +3,11 @@
 An INSTALL file does not have to be included with the package. An INSTALL file
 is utilized for specifying external system requirements needed. It should be
 used in combination with the `SystemRequirements` field of the [Description
-file](#description-sysdep). This file should contain installation instructions
-for the required system dependency.
+file](#description-sysdep). This file should provide instructions for installing
+the external software on the 3 major OS that we support: Linux, Windows, and
+Mac. This will not only help your users get the external software on their
+machines, but it will also help us install it on the build machines if it's not
+already there.
 
 Specifying this requirement does not guarantee that _Bioconductor_ will agree to
 install the external system requirement. It is encouraged to discuss any

r-code.Rmd

@@ -206,20 +206,32 @@ helper functions.
 
 #### Additional files and dependencies {#rcode-sysdep}
 
-Do NOT install anything on a users system.
-
-System dependencies, applications, and additionally needed packages should be
-assumed already present on the user's system.
-
-If necessary, package maintainers should provide instructions for download and
-setup, but should not execute those instructions on behalf of a
-user. Complicated or additional system dependency instructions could be part of
-the [README file](#readme) and/or [INSTALL file](#sysdep). All package
-dependencies must actively be on CRAN or [_Bioconductor_][].  
+Do NOT install anything on a users system! System dependencies, applications,
+and additionally needed packages should be assumed already present on the user's
+system.
+
+Direct calls to external commands via
+system() or system2() are not ideal so should only be used when there is no
+other alternative. For example, if a CRAN or Bioconductor package already
+provides the functionality that you are after, you should use that instead.
+
+Now if your package **absolutely** must rely on external software then you
+need to make sure that those requirements are listed in
+the SystemRequirements field of the DESCRIPTION file of the package. These
+requirements should be "reasonable" requirements, that is, trusted software
+only, open source, and relatively easy to install.
+
+Additionally we ask that the package contains an [INSTALL file](#sysdep) (in the
+top-level folder) that provides instructions for installing the external
+software on the 3 major OS that we support: Linux, Windows, and Mac. This
+will not only help your users get the external software on their machines,
+but it will also help us install it on the build machines if it's not
+already there.
 
 All system and package dependencies should be the latest publically available
-version.
-
+version. All package dependencies must actively be on CRAN or
+Bioconductor. Bioconductor will not recognize Remotes in Description and will
+not install a lower version of a package or dependency.  
 
 ####  Namespaces {#rcode-namespaces}