docs: fix absolute urls in vigngette (#320)

Author: mllg

DESCRIPTION

@@ -2,31 +2,30 @@ Package: batchtools
 Title: Tools for Computation on Batch Systems
 Version: 0.9.18
 Authors@R: c(
-    person("Michel", "Lang", NULL, "michellang@gmail.com",
-      role = c("cre", "aut"), comment = c(ORCID = "0000-0001-9754-0393")),
-    person("Bernd", "Bischl", NULL, "bernd_bischl@gmx.net", role = "aut"),
-    person("Dirk", "Surmann", NULL, "surmann@statistik.tu-dortmund.de",
-      role = "ctb", comment = c(ORCID = "0000-0003-0873-137X"))
-    )
-Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
-    this package provides a parallel implementation of the Map function for high
-    performance computing systems managed by schedulers 'IBM Spectrum LSF'
-    (<https://www.ibm.com/products/hpc-workload-management>),
-    'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
-    Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>),
-    'TORQUE/PBS'
+    person("Michel", "Lang", , "michellang@gmail.com", role = c("cre", "aut"),
+           comment = c(ORCID = "0000-0001-9754-0393")),
+    person("Bernd", "Bischl", , "bernd_bischl@gmx.net", role = "aut"),
+    person("Dirk", "Surmann", , "surmann@statistik.tu-dortmund.de", role = "ctb",
+           comment = c(ORCID = "0000-0003-0873-137X"))
+  )
+Description: As a successor of the packages 'BatchJobs' and
+    'BatchExperiments', this package provides a parallel implementation of
+    the Map function for high performance computing systems managed by
+    schedulers 'IBM Spectrum LSF'
+    (<https://www.ibm.com/products/hpc-workload-management>), 'Univa Grid
+    Engine'/'Oracle Grid Engine'
+    (<https://altair.com/hpc-cloud-applications/>), 'Slurm'
+    (<https://slurm.schedmd.com/>), 'TORQUE/PBS'
     (<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>),
-    or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>).
-    A multicore and socket mode allow the parallelization on a local machines,
-    and multiple machines can be hooked up via SSH to create a makeshift
-    cluster. Moreover, the package provides an abstraction mechanism to define
-    large-scale computer experiments in a well-organized and reproducible way.
+    or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>).  A
+    multicore and socket mode allow the parallelization on a local
+    machines, and multiple machines can be hooked up via SSH to create a
+    makeshift cluster. Moreover, the package provides an abstraction
+    mechanism to define large-scale computer experiments in a
+    well-organized and reproducible way.
 License: LGPL-3
 URL: https://github.com/mlr-org/batchtools, https://batchtools.mlr-org.com
 BugReports: https://github.com/mlr-org/batchtools/issues
-NeedsCompilation: yes
-ByteCompile: yes
-Encoding: UTF-8
 Depends:
     R (>= 3.0.0)
 Imports:
@@ -47,8 +46,8 @@ Imports:
     withr (>= 2.0.0)
 Suggests:
     debugme,
-    doParallel,
     doMPI,
+    doParallel,
     e1071,
     foreach,
     future,
@@ -61,6 +60,10 @@ Suggests:
     snow,
     testthat,
     tibble
-VignetteBuilder: knitr
+VignetteBuilder:
+    knitr
+ByteCompile: yes
+Encoding: UTF-8
+NeedsCompilation: yes
 Roxygen: list(r6 = FALSE)
 RoxygenNote: 7.3.2

README.Rmd

@@ -14,7 +14,7 @@ Package website: [release](https://batchtools.mlr-org.com/) | [dev](https://batc
 [![Mattermost](https://img.shields.io/badge/chat-mattermost-orange.svg)](https://lmmisld-lmu-stats-slds.srv.mwn.de/mlr_invite/)
 <!-- badges: end -->
 
-As a successor of the packages [BatchJobs](https://github.com/tudo-r/BatchJobs) and [BatchExperiments](https://github.com/tudo-r/Batchexperiments), batchtools provides a parallel implementation of Map for high performance computing systems managed by schedulers like Slurm, Sun Grid Engine, OpenLava, TORQUE/OpenPBS, Load Sharing Facility (LSF) or Docker Swarm (see the setup section in the [vignette](https://batchtools.mlr-org.com/batchtools/articles/batchtools.html)).
+As a successor of the packages [BatchJobs](https://github.com/tudo-r/BatchJobs) and [BatchExperiments](https://github.com/tudo-r/Batchexperiments), batchtools provides a parallel implementation of Map for high performance computing systems managed by schedulers like Slurm, Sun Grid Engine, OpenLava, TORQUE/OpenPBS, Load Sharing Facility (LSF) or Docker Swarm (see the setup section in the [vignette](https://batchtools.mlr-org.com/articles/batchtools.html)).
 
 Main features:
 
@@ -37,7 +37,7 @@ devtools::install_github("mlr-org/batchtools")
 ```
 
 Next, you need to setup `batchtools` for your HPC (it will run sequentially otherwise).
-See the [vignette](https://mlr-org.github.io/batchtools/articles/batchtools.html#setup) for instructions.
+See the [vignette](https://batchtools.mlr-org.com/articles/batchtools.html) for instructions.
 
 ## Why batchtools?
 The development of [BatchJobs](https://github.com/tudo-r/BatchJobs/) and [BatchExperiments](https://github.com/tudo-r/Batchexperiments) is discontinued for the following reasons:
@@ -46,15 +46,14 @@ The development of [BatchJobs](https://github.com/tudo-r/BatchJobs/) and [BatchE
 * Data base issues: Although we invested weeks to mitigate issues with locks of the SQLite data base or file system (staged queries, file system timeouts, ...), `BatchJobs` kept working unreliable on some systems with high latency under certain conditions. This made `BatchJobs` unusable for many users.
 
 [BatchJobs](https://github.com/tudo-r/BatchJobs/) and [BatchExperiments](https://github.com/tudo-r/Batchexperiments) will remain on CRAN, but new features are unlikely to be ported back.
-The [vignette](https://batchtools.mlr-org.com/batchtools/articles/batchtools.html#migration) contains a section comparing the packages.
+The [vignette](https://batchtools.mlr-org.com/articles/batchtools.html) contains a section comparing the packages.
 
 
 ## Resources
-* [NEWS](https://batchtools.mlr-org.com/batchtools/news/)
-* [Function reference](https://batchtools.mlr-org.com/batchtools/reference/)
-* [Vignette](https://batchtools.mlr-org.com/batchtools/articles/batchtools.html)
+* [Function reference](https://batchtools.mlr-org.com/reference/)
+* [Vignette](https://batchtools.mlr-org.com/articles/batchtools.html)
 * [JOSS Paper](https://doi.org/10.21105/joss.00135): Short paper on batchtools. Please cite this if you use batchtools.
-* [Paper on BatchJobs/BatchExperiments](https://www.jstatsoft.org/v64/i11): The described concept still holds for batchtools and most examples work analogously (see the [vignette](https://batchtools.mlr-org.com/batchtools/articles/batchtools.html#migration) for differences between the packages).
+* [Paper on BatchJobs/BatchExperiments](https://www.jstatsoft.org/v64/i11): The described concept still holds for batchtools and most examples work analogously (see the [vignette](https://batchtools.mlr-org.com/articles/batchtools.html) for differences between the packages).
 
 ## Citation
 Please cite the [JOSS paper](https://doi.org/10.21105/joss.00135) using the following BibTeX entry:

_pkgdown.yml

@@ -16,7 +16,7 @@ toc:
 
 navbar:
   structure:
-    left:  [reference, news, book]
+    left:  [reference, news, articles, book]
     right: [search, github, mattermost, stackoverflow, rss, lightswitch]
   components:
     home: ~