diff --git a/inst/doc/miniCRAN-dependency-graph.html b/inst/doc/miniCRAN-dependency-graph.html index e453bba..a2ed658 100644 --- a/inst/doc/miniCRAN-dependency-graph.html +++ b/inst/doc/miniCRAN-dependency-graph.html @@ -254,7 +254,7 @@

A worked example using the package chron

plot(dg, legendPosition = c(-1, 1), vertex.size=20) -

plot of chunk makeDepGraph

+

plot of chunk makeDepGraph

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.

@@ -294,7 +294,7 @@

An example with multiple input packages

plot(dg, legendPosition = c(-1, -1), vertex.size=10, cex=0.7) -

plot of chunk so-tags

+

plot of chunk so-tags

diff --git a/inst/doc/miniCRAN-introduction.html b/inst/doc/miniCRAN-introduction.html index 97932e7..3bf2be4 100644 --- a/inst/doc/miniCRAN-introduction.html +++ b/inst/doc/miniCRAN-introduction.html @@ -227,12 +227,21 @@

Creating a miniCRAN repository

# Create temporary folder for miniCRAN
 dir.create(pth <- file.path(tempdir(), "miniCRAN"))
+
+ +
## Warning in dir.create(pth <- file.path(tempdir(), "miniCRAN")):
+## 'C:\Users\ANDRIE~1\AppData\Local\Temp\Rtmpm2fNyk\miniCRAN' already exists
+
-# Make repo for source and win.binary +
# Make repo for source and win.binary
 makeRepo(pkgList, path=pth, repos=revolution, type="source")
-
## Created new folder: C:/Users/ANDRIE~1/AppData/Local/Temp/RtmpcRONMK/miniCRAN/src/contrib
+
## Created new folder: C:/Users/ANDRIE~1/AppData/Local/Temp/Rtmpm2fNyk/miniCRAN/src/contrib
+

+
+
## Warning in download.file(url, destfile, method, mode = "wb", ...):
+## downloaded length 359739 != reported length 359739
 

 
 
## [[1]]
@@ -242,15 +251,15 @@ 
Creating a miniCRAN repository

 
makeRepo(pkgList, path=pth, repos=revolution, type="win.binary")
 

 
-
## Created new folder: C:/Users/ANDRIE~1/AppData/Local/Temp/RtmpcRONMK/miniCRAN/bin/windows/contrib/3.2
+
## Created new folder: C:/Users/ANDRIE~1/AppData/Local/Temp/Rtmpm2fNyk/miniCRAN/bin/windows/contrib/3.1
 

 
-
## Warning in utils::download.packages(pkgs, destdir = pkgPath, available =
-## pdb, : no package 'codetools' at the repositories
+
## Warning in download.file(url, destfile, method, mode = "wb", ...):
+## downloaded length 388705 != reported length 388705
 

 
 
## [[1]]
-## [1] 2
+## [1] 3
 

 
 
Investigate the repository file structure:

@@ -259,15 +268,32 @@ 
Creating a miniCRAN repository

 list.files(pth, recursive=TRUE, full.names=FALSE)
 

 
-
## [1] "bin/windows/contrib/3.2/foreach_1.4.2.zip"  
-## [2] "bin/windows/contrib/3.2/iterators_1.0.7.zip"
-## [3] "bin/windows/contrib/3.2/PACKAGES"           
-## [4] "bin/windows/contrib/3.2/PACKAGES.gz"        
-## [5] "src/contrib/codetools_0.2-11.tar.gz"        
-## [6] "src/contrib/foreach_1.4.2.tar.gz"           
-## [7] "src/contrib/iterators_1.0.7.tar.gz"         
-## [8] "src/contrib/PACKAGES"                       
-## [9] "src/contrib/PACKAGES.gz"
+
##  [1] "2015-03-27/bin/macosx/contrib/3.1/adaptivetau_2.2.tgz" 
+##  [2] "2015-03-27/bin/macosx/contrib/3.1/aprof_0.2.4.tgz"     
+##  [3] "2015-03-27/bin/macosx/contrib/3.1/chron_2.3-45.tgz"    
+##  [4] "2015-03-27/bin/macosx/contrib/3.1/PACKAGES"            
+##  [5] "2015-03-27/bin/macosx/contrib/3.1/PACKAGES.gz"         
+##  [6] "2015-03-27/bin/windows/contrib/3.1/adaptivetau_2.2.zip"
+##  [7] "2015-03-27/bin/windows/contrib/3.1/aprof_0.2.4.zip"    
+##  [8] "2015-03-27/bin/windows/contrib/3.1/chron_2.3-45.zip"   
+##  [9] "2015-03-27/bin/windows/contrib/3.1/PACKAGES"           
+## [10] "2015-03-27/bin/windows/contrib/3.1/PACKAGES.gz"        
+## [11] "2015-03-27/src/contrib/adaptivetau_2.2.tar.gz"         
+## [12] "2015-03-27/src/contrib/aprof_0.2.1.tar.gz"             
+## [13] "2015-03-27/src/contrib/aprof_0.2.4.tar.gz"             
+## [14] "2015-03-27/src/contrib/chron_2.3-45.tar.gz"            
+## [15] "2015-03-27/src/contrib/PACKAGES"                       
+## [16] "2015-03-27/src/contrib/PACKAGES.gz"                    
+## [17] "bin/windows/contrib/3.1/codetools_0.2-11.zip"          
+## [18] "bin/windows/contrib/3.1/foreach_1.4.2.zip"             
+## [19] "bin/windows/contrib/3.1/iterators_1.0.7.zip"           
+## [20] "bin/windows/contrib/3.1/PACKAGES"                      
+## [21] "bin/windows/contrib/3.1/PACKAGES.gz"                   
+## [22] "src/contrib/codetools_0.2-11.tar.gz"                   
+## [23] "src/contrib/foreach_1.4.2.tar.gz"                      
+## [24] "src/contrib/iterators_1.0.7.tar.gz"                    
+## [25] "src/contrib/PACKAGES"                                  
+## [26] "src/contrib/PACKAGES.gz"
 

 
 
Use pkgAvail to list available packages in your repository:

@@ -276,9 +302,10 @@ 
Creating a miniCRAN repository

 pkgAvail(repos=pth, type="win.binary")[, c(1:3, 5)]
 

 
-
##           Package     Version Priority Imports                      
-## foreach   "foreach"   "1.4.2" NA       "codetools, utils, iterators"
-## iterators "iterators" "1.0.7" NA       NA
+
##           Package     Version  Priority      Imports                      
+## codetools "codetools" "0.2-11" "recommended" NA                           
+## foreach   "foreach"   "1.4.2"  NA            "codetools, utils, iterators"
+## iterators "iterators" "1.0.7"  NA            NA
 

 
 
Install packages from your local repository

@@ -317,6 +344,10 @@ 
Adding an older version of a package from CRAN

 addOldPackage(pkgList, path=pth, vers=oldVers$version, repos=revolution, type="source")
 

 
+
## Warning in download.file(x, destfile = file.path(pkgPath, basename(x)), :
+## downloaded length 359222 != reported length 359222
+

+
 
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.

@@ -343,7 +374,7 @@ 
Adding an older version of a package from CRAN

 
basename(pkgVersionsBin)
 

 
-
## [1] "foreach_1.4.2.zip"   "iterators_1.0.7.zip"
+
## [1] "foreach_1.4.2.zip"    "codetools_0.2-11.zip" "iterators_1.0.7.zip"
 

 
 
file.remove(pkgVersionsSrc[c(2,4,6)])
@@ -360,7 +391,7 @@ 
Adding an older version of a package from CRAN

 ## [1] 7
 ## 
 ## [[2]]
-## [1] 2
+## [1] 3
 

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

@@ -389,9 +420,10 @@ 
Adding an older version of a package from CRAN

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

 
-
##           Package     Version Priority Imports                      
-## foreach   "foreach"   "1.4.2" NA       "codetools, utils, iterators"
-## iterators "iterators" "1.0.7" NA       NA
+
##           Package     Version  Priority      Imports                      
+## codetools "codetools" "0.2-11" "recommended" NA                           
+## foreach   "foreach"   "1.4.2"  NA            "codetools, utils, iterators"
+## iterators "iterators" "1.0.7"  NA            NA
 

 
 
Adding packages from other sources

diff --git a/inst/doc/miniCRAN-non-CRAN-repos.R b/inst/doc/miniCRAN-non-CRAN-repos.R
index b333244..f8f0834 100644
--- a/inst/doc/miniCRAN-non-CRAN-repos.R
+++ b/inst/doc/miniCRAN-non-CRAN-repos.R
@@ -8,8 +8,13 @@ index <- function(url, type="source", filters=NULL, head=5, cols=c("Package", "V
 }
  
 
-## ----CRAN----------------------------------------------------------------
-CRAN <- "http://cran.r-project.org"
+## ----CRAN, eval=FALSE----------------------------------------------------
+#  CRAN <- "http://cran.r-project.org"
+#  index(CRAN)
+
+## ----CRAN-mock, echo=FALSE-----------------------------------------------
+# One has to assume CRAN master is not available, hence mock the behaviour using a different mirror
+CRAN <- "http://cran.revolutionanalytics.com"
 index(CRAN)
 
 ## ----revo----------------------------------------------------------------
diff --git a/inst/doc/miniCRAN-non-CRAN-repos.html b/inst/doc/miniCRAN-non-CRAN-repos.html
index eca34c7..9ad2689 100644
--- a/inst/doc/miniCRAN-non-CRAN-repos.html
+++ b/inst/doc/miniCRAN-non-CRAN-repos.html
@@ -290,20 +290,20 @@ 
Using BioConductor

 })
 

 
-
## Bioconductor version 3.1 (BiocInstaller 1.17.6), ?biocLite for help
+
## Bioconductor version 3.0 (BiocInstaller 1.16.1), ?biocLite for help
 

 
 
bioc
 

 
 
##                                               BioCsoft 
-##            "http://bioconductor.org/packages/3.1/bioc" 
+##            "http://bioconductor.org/packages/3.0/bioc" 
 ##                                                BioCann 
-## "http://bioconductor.org/packages/3.1/data/annotation" 
+## "http://bioconductor.org/packages/3.0/data/annotation" 
 ##                                                BioCexp 
-## "http://bioconductor.org/packages/3.1/data/experiment" 
+## "http://bioconductor.org/packages/3.0/data/experiment" 
 ##                                              BioCextra 
-##           "http://bioconductor.org/packages/3.1/extra" 
+##           "http://bioconductor.org/packages/3.0/extra" 
 ##                                                   CRAN 
 ##                  "http://cran.revolutionanalytics.com" 
 ##                                              CRANextra 
@@ -314,24 +314,24 @@ 
Using BioConductor

 

 
 
##                                               BioCsoft 
-##            "http://bioconductor.org/packages/3.1/bioc" 
+##            "http://bioconductor.org/packages/3.0/bioc" 
 ##                                                BioCann 
-## "http://bioconductor.org/packages/3.1/data/annotation" 
+## "http://bioconductor.org/packages/3.0/data/annotation" 
 ##                                                BioCexp 
-## "http://bioconductor.org/packages/3.1/data/experiment" 
+## "http://bioconductor.org/packages/3.0/data/experiment" 
 ##                                              BioCextra 
-##           "http://bioconductor.org/packages/3.1/extra"
+##           "http://bioconductor.org/packages/3.0/extra"
 

 
 
index(bioc["BioCsoft"])
 

 
 
##           Package     Version 
-## a4        "a4"        "1.15.0"
-## a4Base    "a4Base"    "1.15.0"
-## a4Classif "a4Classif" "1.15.0"
-## a4Core    "a4Core"    "1.15.0"
-## a4Preproc "a4Preproc" "1.15.0"
+## a4        "a4"        "1.14.0"
+## a4Base    "a4Base"    "1.14.0"
+## a4Classif "a4Classif" "1.14.0"
+## a4Core    "a4Core"    "1.14.0"
+## a4Preproc "a4Preproc" "1.14.0"
 

 
 
diff --git a/inst/doc/miniCRAN-non-CRAN-repos.rmd b/inst/doc/miniCRAN-non-CRAN-repos.rmd
index be133ff..700a38c 100644
--- a/inst/doc/miniCRAN-non-CRAN-repos.rmd
+++ b/inst/doc/miniCRAN-non-CRAN-repos.rmd
@@ -38,11 +38,17 @@ index <- function(url, type="source", filters=NULL, head=5, cols=c("Package", "V
 
 The URL for the master mirror in Austria:
 
-```{r CRAN}
+```{r CRAN, eval=FALSE}
 CRAN <- "http://cran.r-project.org"
 index(CRAN)
 ```
 
+```{r CRAN-mock, echo=FALSE}
+# One has to assume CRAN master is not available, hence mock the behaviour using a different mirror
+CRAN <- "http://cran.revolutionanalytics.com"
+index(CRAN)
+```
+
 
 ## Using a different mirror
 
diff --git a/vignettes/miniCRAN-non-CRAN-repos.rmd b/vignettes/miniCRAN-non-CRAN-repos.rmd
index be133ff..700a38c 100644
--- a/vignettes/miniCRAN-non-CRAN-repos.rmd
+++ b/vignettes/miniCRAN-non-CRAN-repos.rmd
@@ -38,11 +38,17 @@ index <- function(url, type="source", filters=NULL, head=5, cols=c("Package", "V
 
 The URL for the master mirror in Austria:
 
-```{r CRAN}
+```{r CRAN, eval=FALSE}
 CRAN <- "http://cran.r-project.org"
 index(CRAN)
 ```
 
+```{r CRAN-mock, echo=FALSE}
+# One has to assume CRAN master is not available, hence mock the behaviour using a different mirror
+CRAN <- "http://cran.revolutionanalytics.com"
+index(CRAN)
+```
+
 
 ## Using a different mirror