diff --git a/LICENSE.html b/LICENSE.html index b5a47e0..8d2e0b9 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -52,7 +52,7 @@

GNU GENERAL PUBLIC LICENSE Version 2, June 1991

Copyright (C) 1989, 1991 Free Software Foundation, Inc., http://fsf.org/ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

-
                        Preamble
+
                        Preamble

The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software–to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation’s software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too.

When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things.

To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it.

@@ -61,47 +61,51 @@

Also, for each author’s protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors’ reputations.

Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone’s free use or not licensed at all.

The precise terms and conditions for copying, distribution and modification follow.

-
                GNU GENERAL PUBLIC LICENSE
+
                GNU GENERAL PUBLIC LICENSE

TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION

-
  1. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The “Program”, below, refers to any such program or work, and a “work based on the Program” means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term “modification”.) Each licensee is addressed as “you”.

Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does.

-
  1. You may copy and distribute verbatim copies of the Program’s source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.

You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.

-
  1. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
-stating that you changed the files and the date of any change.
-
-b) You must cause any work that you distribute or publish, that in
-whole or in part contains or is derived from the Program or any
-part thereof, to be licensed as a whole at no charge to all third
-parties under the terms of this License.
-
-c) If the modified program normally reads commands interactively
-when run, you must cause it, when started running for such
-interactive use in the most ordinary way, to print or display an
-announcement including an appropriate copyright notice and a
-notice that there is no warranty (or else, saying that you provide
-a warranty) and that users may redistribute the program under
-these conditions, and telling the user how to view a copy of this
-License.  (Exception: if the Program itself is interactive but
-does not normally print such an announcement, your work based on
-the Program is not required to print an announcement.)
+
  1. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The “Program”, below, refers to any such program or work, and a “work based on the Program” means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term “modification”.) Each licensee is addressed as “you”.
    2. +

Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does.

+
  1. You may copy and distribute verbatim copies of the Program’s source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program.
    2. +

You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee.

+
  1. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions:
    2. +
a) You must cause the modified files to carry prominent notices
+stating that you changed the files and the date of any change.
+
+b) You must cause any work that you distribute or publish, that in
+whole or in part contains or is derived from the Program or any
+part thereof, to be licensed as a whole at no charge to all third
+parties under the terms of this License.
+
+c) If the modified program normally reads commands interactively
+when run, you must cause it, when started running for such
+interactive use in the most ordinary way, to print or display an
+announcement including an appropriate copyright notice and a
+notice that there is no warranty (or else, saying that you provide
+a warranty) and that users may redistribute the program under
+these conditions, and telling the user how to view a copy of this
+License.  (Exception: if the Program itself is interactive but
+does not normally print such an announcement, your work based on
+the Program is not required to print an announcement.)

These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it.

Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program.

In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License.

-
  1. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable
-source code, which must be distributed under the terms of Sections
-1 and 2 above on a medium customarily used for software interchange; or,
-
-b) Accompany it with a written offer, valid for at least three
-years, to give any third party, for a charge no more than your
-cost of physically performing source distribution, a complete
-machine-readable copy of the corresponding source code, to be
-distributed under the terms of Sections 1 and 2 above on a medium
-customarily used for software interchange; or,
-
-c) Accompany it with the information you received as to the offer
-to distribute corresponding source code.  (This alternative is
-allowed only for noncommercial distribution and only if you
-received the program in object code or executable form with such
-an offer, in accord with Subsection b above.)
+
  1. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following:
    2. +
a) Accompany it with the complete corresponding machine-readable
+source code, which must be distributed under the terms of Sections
+1 and 2 above on a medium customarily used for software interchange; or,
+
+b) Accompany it with a written offer, valid for at least three
+years, to give any third party, for a charge no more than your
+cost of physically performing source distribution, a complete
+machine-readable copy of the corresponding source code, to be
+distributed under the terms of Sections 1 and 2 above on a medium
+customarily used for software interchange; or,
+
+c) Accompany it with the information you received as to the offer
+to distribute corresponding source code.  (This alternative is
+allowed only for noncommercial distribution and only if you
+received the program in object code or executable form with such
+an offer, in accord with Subsection b above.)

The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable.

If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code.

  1. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance.

    2. @@ -116,39 +120,39 @@

Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and “any later version”, you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation.

  1. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally.

    -
                      NO WARRANTY
    +
                      NO WARRANTY

  2. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM “AS IS” WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION.

  3. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

    -
               END OF TERMS AND CONDITIONS
-
-  How to Apply These Terms to Your New Programs
    +
               END OF TERMS AND CONDITIONS
+
+  How to Apply These Terms to Your New Programs

If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms.

To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the “copyright” line and a pointer to where the full notice is found.

-
{description}
-Copyright (C) {year}  {fullname}
-
-This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or
-(at your option) any later version.
-
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along
-with this program; if not, write to the Free Software Foundation, Inc.,
-51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
{description}
+Copyright (C) {year}  {fullname}
+
+This program is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+You should have received a copy of the GNU General Public License along
+with this program; if not, write to the Free Software Foundation, Inc.,
+51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

Also add information on how to contact you by electronic and paper mail.

If the program is interactive, make it output a short notice like this when it starts in an interactive mode:

-
Gnomovision version 69, Copyright (C) year name of author
-Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-This is free software, and you are welcome to redistribute it
-under certain conditions; type `show c' for details.
+
Gnomovision version 69, Copyright (C) year name of author
+Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+This is free software, and you are welcome to redistribute it
+under certain conditions; type `show c' for details.

The hypothetical commands show w' andshow c’ should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than show w' andshow c’; they could even be mouse-clicks or menu items–whatever suits your program.

You should also get your employer (if you work as a programmer) or your school, if any, to sign a “copyright disclaimer” for the program, if necessary. Here is a sample; alter the names:

Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision’ (which makes passes at compilers) written by James Hacker.

diff --git a/articles/miniCRAN-dependency-graph.html b/articles/miniCRAN-dependency-graph.html index 1a14bb9..e16dfff 100644 --- a/articles/miniCRAN-dependency-graph.html +++ b/articles/miniCRAN-dependency-graph.html @@ -74,12 +74,14 @@ -
+ +

Using miniCRAN to identify package dependencies

-

Andrie de Vries

+

Andrie de +Vries

-

March 20, 2024

+

March 23, 2024

Source: vignettes/miniCRAN-dependency-graph.rmd
miniCRAN-dependency-graph.rmd
@@ -87,28 +89,50 @@

March 20, 2024

-

The miniCRAN package exposes two functions that provide information about dependencies:

+

The miniCRAN package exposes two functions that provide +information about dependencies:

    -

  • The function pkgDep() returns a character vector with the names of dependencies. Internally, pkgDep() is a wrapper around tools::package_dependencies(), a base R function that, well, tells you about package dependencies. My pkgDep() function is in one way a convenience, but more importantly it sets different defaults (more about this later).

    • -

  • The function makeDepGraph() creates a graph representation of the dependencies.

    • +

  • The function pkgDep() returns a character vector +with the names of dependencies. Internally, pkgDep() is a +wrapper around tools::package_dependencies(), a base R +function that, well, tells you about package dependencies. My +pkgDep() function is in one way a convenience, but more +importantly it sets different defaults (more about this later).

    • +

  • The function makeDepGraph() creates a graph +representation of the dependencies.

-

The package chron neatly illustrates the different roles of Imports, Suggests and Enhances:

+

The package chron neatly illustrates the different roles +of Imports, Suggests and Enhances:

    -

  • chron Imports the base packages graphics and stats. This means that chron internally makes use of graphics and stats and will always load these packages.

    • -

  • chron Suggests the packages scales and ggplot2. This means that chron uses some functions from these packages in examples or in its vignettes. However, these functions are not necessary to use chron

    • -

  • chron Enhances the package zoo, meaning that it adds something to zoo packages. These enhancements are made available to you if you have zoo installed.

    • +

  • chron Imports the base packages +graphics and stats. This means that chron internally makes +use of graphics and stats and will always load these packages.

    • +

  • chron Suggests the packages scales +and ggplot2. This means that chron uses some functions from +these packages in examples or in its vignettes. However, these functions +are not necessary to use chron

    • +

  • chron Enhances the package +zoo, meaning that it adds something to zoo +packages. These enhancements are made available to you if you have +zoo installed.

A worked example using the package chron

-

The function pkgDep() exposes not only these dependencies, but also all recursive dependencies. In other words, it answers the question which packages need to be installed to satisfy all dependencies of dependencies.

+

The function pkgDep() exposes not only these +dependencies, but also all recursive dependencies. In other words, it +answers the question which packages need to be installed to satisfy all +dependencies of dependencies.

This means that the algorithm is as follows:

    -
  • First retrieve a list of Suggests and Enhances, using a non-recursive dependency search
    • -
  • Next, perform a recursive search for all Imports, Depends and LinkingTo +
  • First retrieve a list of Suggests and +Enhances, using a non-recursive dependency search
    • +
  • Next, perform a recursive search for all Imports, +Depends and LinkingTo
-

The resulting list of packages should then contain the complete list necessary to satisfy all dependencies. In code:

+

The resulting list of packages should then contain the complete list +necessary to satisfy all dependencies. In code:

@@ -118,18 +142,23 @@ 
A worked example using the pac
 ##  [6] "labeling"     "colorspace"   "Rcpp"         "digest"       "gtable"      
 ## [11] "reshape2"     "scales"       "proto"        "MASS"         "stringr"     
 ## [16] "ggplot2"
-

To create an igraph plot of the dependencies, use the function makeDepGraph() and plot the results:

+

To create an igraph plot of the dependencies, use the function +makeDepGraph() and plot the results:

 dg <- makeDepGraph(tags, enhances = TRUE, availPkgs = cranJuly2014)
 set.seed(1)
 plot(dg, legendPosition = c(-1, 1), vertex.size = 20)

-

Note how the dependencies expand to zoo (enhanced), scales and ggplot (suggested) and then recursively from there to get all the Imports and LinkingTo dependencies.

+

Note how the dependencies expand to zoo (enhanced), +scales and ggplot (suggested) and then +recursively from there to get all the Imports and +LinkingTo dependencies.

An example with multiple input packages

-

As a final example, create a dependency graph of seven very popular R packages:

+

As a final example, create a dependency graph of seven very popular R +packages:

 tags <- c("ggplot2", "data.table", "plyr", "knitr", "shiny", "xts", "lattice")
 pkgDep(tags, suggests = TRUE, enhances = FALSE, availPkgs = cranJuly2014)
diff --git a/articles/miniCRAN-introduction.html b/articles/miniCRAN-introduction.html index 65d5a8b..881ec57 100644 --- a/articles/miniCRAN-introduction.html +++ b/articles/miniCRAN-introduction.html @@ -74,12 +74,14 @@ -
+ +

Using miniCRAN to create and maintain a local CRAN repository

-

Andrie de Vries and Alex Chubaty

+

Andrie de Vries +and Alex Chubaty

-

March 20, 2024

+

March 23, 2024

Source: vignettes/miniCRAN-introduction.rmd
miniCRAN-introduction.rmd
@@ -87,8 +89,11 @@

March 20, 2024

-

Start by creating the recursive dependency tree for your target packages.

-

For example, imagine a scenario where you want to create a repository that consists of the package foreach and its dependencies.

+

Start by creating the recursive dependency tree for your target +packages.

+

For example, imagine a scenario where you want to create a repository +that consists of the package foreach and its +dependencies.

Start by creating the dependency list:

 library("miniCRAN")
@@ -102,7 +107,9 @@ 
March 20, 2024

                   availPkgs = cranJuly2014)
 pkgList
## [1] "foreach"   "codetools" "iterators"
-

Next, create a repository with the function makeRepo(). In this example, get the required files for source packages as well as windows binaries:

+

Next, create a repository with the function makeRepo(). +In this example, get the required files for source packages +as well as windows binaries:

 # Create temporary folder for miniCRAN
 dir.create(pth <- file.path(tempdir(), "miniCRAN"))
@@ -113,14 +120,17 @@ 
March 20, 2024

 
 # List all files in miniCRAN
 list.files(pth, recursive = TRUE, full.names = FALSE)

-
Use pkgAvail to list available packages in your repository:

+
Use pkgAvail to list available packages in your
+repository:

 
 # Check for available packages
 pkgAvail(repos = pth, type = "win.binary")[, c(1:3, 5)]

 

 
Install packages from your local repository
 

-
To install packages from a local repository, you need to use the Uniform Resource Identifier (URI) convention file:/// to point to your file location.

+
To install packages from a local repository, you need to use the Uniform
+Resource Identifier (URI) convention file:/// to point
+to your file location.

 
 install.packages(pkgs, 
                  repos = paste0("file:///", pth),
@@ -132,18 +142,28 @@ 
Adding packages to a
 

 
Adding new packages from CRAN
 

-
After creating a local miniCRAN repository, additional packages and their dependencies can easily be added. This mechanism can also be used to re-add an existing package to the miniCRAN repo.

+
After creating a local miniCRAN repository, additional packages and
+their dependencies can easily be added. This mechanism can also be used
+to re-add an existing package to the miniCRAN repo.

 
 # Add new packages (from CRAN) to the miniCRAN repo
 addPackage("Matrix", path = pth, repos = revolution, type = c("source", "win.binary"))
 pkgAvail(repos = pth, type = "win.binary")[, c(1:3, 5)]

-
The value that is returned (invisibly) via addPackage is the number of packages written to the index file, i.e., the total number of packages in the repo of that type.

+
The value that is returned (invisibly) via addPackage is
+the number of packages written to the index file, i.e., the
+total number of packages in the repo of that type.

 

 

 
Adding an older version of a package from CRAN
 

-
To add a specific version of a package from CRAN (or another CRAN-like repository), we can easily download the source packages from the CRAN archives. Dependencies for old package versions cannot be determined automatically and must be specified by the user.

-
Note: in order to to add binaries of older packages, you will need to download the source and build the binaries on the intended platform yourself. You will need the appropriate R development tools installed in order to build package binaries from source.

+
To add a specific version of a package from CRAN (or another
+CRAN-like repository), we can easily download the source packages from
+the CRAN archives. Dependencies for old package versions cannot be
+determined automatically and must be specified by the user.

+
Note: in order to to add binaries of older packages, you
+will need to download the source and build the binaries on the intended
+platform yourself. You will need the appropriate R development tools
+installed in order to build package binaries from source.

 
 # create a data frame with the package and version info
 oldVers <- data.frame(
@@ -154,8 +174,11 @@ 
Adding an older version
 
 # download old source package version and create repo index
 addOldPackage(pkgList, path = pth, vers = oldVers$version, repos = revolution, type = "source")

-
You will get a warning whenever there are multiple versions of a package saved in the repository. Currently, you need to manually remove duplicate versions before rebuilding the repository’s package index.

-
Note: This last step is important, otherwise you may end up with a repo in an inconsistent state.

+
You will get a warning whenever there are multiple versions of a
+package saved in the repository. Currently, you need to manually remove
+duplicate versions before rebuilding the repository’s package index.

+
Note: This last step is important, otherwise you may end up with a
+repo in an inconsistent state.

 
 # List package versions in the miniCRAN repo (produces warning about duplicates)
 pkgVersionsSrc <- checkVersions(pkgList, path = pth, type = "source")
@@ -169,7 +192,8 @@ 
Adding an older version
 
 # rebuild the package index after removing duplicate package versions
 updateRepoIndex(pth, type = c("source", "win.binary"))

-
To see the updated list of packages available in the miniCRAN repo:

+
To see the updated list of packages available in the miniCRAN
+repo:

 
 pkgAvail(pth, type = "source")[, c(1:3, 5)] # contains the old versions
 pkgAvail(pth, type = "win.binary")[, c(1:3, 5)] # contains the current versions

@@ -183,12 +207,17 @@ 
Adding packages from other sources
 
Updating the packages in a miniCRAN repository
 

-
Checking for updated versions of the packages currently stored in the miniCRAN repository:

+
Checking for updated versions of the packages currently stored in the
+miniCRAN repository:

 
 # Check if updated packages are available
 oldPackages(path = pth, repos = revolution, type = "source")[, 1:3] # should need update
 oldPackages(path = pth, repos = revolution, type = "win.binary")[, 1:3] # should be current

-
Update the versions of the packages currently stored in the miniCRAN repository. By default, a prompt is given to confirm the update for each package. This prompt can be suppressed using ask = FALSE, which will update all packages. Be careful using this option if you want to keep certain packages at an older version.

+
Update the versions of the packages currently stored in the miniCRAN
+repository. By default, a prompt is given to confirm the update for each
+package. This prompt can be suppressed using ask = FALSE,
+which will update all packages. Be careful using this option if you want
+to keep certain packages at an older version.

 
 # Update available packages
 updatePackages(path = pth, repos = revolution, type = "source", ask = FALSE) # should need update
diff --git a/articles/miniCRAN-non-CRAN-repos.html b/articles/miniCRAN-non-CRAN-repos.html
index d16442e..5ec00d0 100644
--- a/articles/miniCRAN-non-CRAN-repos.html
+++ b/articles/miniCRAN-non-CRAN-repos.html
@@ -74,12 +74,14 @@
 
 
 
-

+
+

   

       
Using repositories other than CRAN with miniCRAN

-                        
Andrie de Vries

+                        
Andrie de
+Vries

             
-            
March 20, 2024

+            
March 23, 2024

       
       Source: vignettes/miniCRAN-non-CRAN-repos.rmd
       
miniCRAN-non-CRAN-repos.rmd

@@ -87,9 +89,15 @@ 
March 20, 2024

 
     
     
-
Although the package name miniCRAN seems to indicate you can only use CRAN as a repository, you can in fact use any CRAN-like repository.

-
This vignette contains some examples of how to refer to different package repositories, including CRAN, alternative mirrors of CRAN, R-Forge as well as BioConductor.

-
To simplify the code to show the salient features, we use a little helper function, index() that is a simple wrapper around available.packages():

+
Although the package name miniCRAN seems to indicate you
+can only use CRAN as a repository, you can in fact use any CRAN-like
+repository.

+
This vignette contains some examples of how to refer to different
+package repositories, including CRAN, alternative mirrors of CRAN,
+R-Forge as well as BioConductor.

+
To simplify the code to show the salient features, we use a little
+helper function, index() that is a simple wrapper around
+available.packages():

 
 # Wrapper around available.packages ---------------------------------------
  
@@ -109,7 +117,8 @@ 
Using CRAN
 
Using a different mirror
 

-
You can also point to any other mirror, for example the stable version hosted by Revolution Analytics:

+
You can also point to any other mirror, for example the stable
+version hosted by Revolution Analytics:

 
 revoStable <- "http://packages.revolutionanalytics.com/cran/3.1/stable"
 index(revoStable)
@@ -128,7 +137,8 @@ 
Using R-forge
 
Using BioConductor
 

-
Although BioConductor has a different preferred install mechanism, the underlying repository structure is also CRAN-like:

+
Although BioConductor has a different preferred install mechanism,
+the underlying repository structure is also CRAN-like:

 
 bioc <- local({
   env <- new.env()
diff --git a/index.html b/index.html
index 621292b..0982bc5 100644
--- a/index.html
+++ b/index.html
@@ -90,6 +90,7 @@
 

 

 
+
 
Create a mini version of CRAN containing only selected packages

 

 
Introduction
diff --git a/pkgdown.yml b/pkgdown.yml
index f2914c1..06802f4 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -1,11 +1,11 @@
-pandoc: 2.9.2.1
+pandoc: 3.1.11
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   miniCRAN-dependency-graph: miniCRAN-dependency-graph.html
   miniCRAN-introduction: miniCRAN-introduction.html
   miniCRAN-non-CRAN-repos: miniCRAN-non-CRAN-repos.html
-last_built: 2024-03-20T17:58Z
+last_built: 2024-03-23T14:22Z
 urls:
   reference: http://andrie.github.io/miniCRAN/reference
   article: http://andrie.github.io/miniCRAN/articles
diff --git a/reference/index.html b/reference/index.html
index cf3c39b..ad32f21 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -213,7 +213,7 @@ 
Other
List pre-built packages in a directory based on file extension
       

           
-          miniCRAN-package _PACKAGE miniCRAN minicran 
+          miniCRAN-package miniCRAN minicran 
         

         
description