REVDEP: Adding revdep checks [ci skip]

Author: HenrikBengtsson

revdep/README.md

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+# Platform
+
+|field    |value                        |
+|:--------|:----------------------------|
+|version  |R version 3.4.1 (2017-06-30) |
+|os       |Ubuntu 16.04.3 LTS           |
+|system   |x86_64, linux-gnu            |
+|ui       |X11                          |
+|language |en                           |
+|collate  |en_US.UTF-8                  |
+|tz       |America/Los_Angeles          |
+|date     |2017-09-08                   |
+
+# Dependencies
+
+|package           |old    |new        |Δ  |
+|:-----------------|:------|:----------|:--|
+|future.batchtools |0.5.0  |0.5.0-9000 |*  |
+|assertthat        |0.2.0  |0.2.0      |   |
+|backports         |1.1.0  |1.1.0      |   |
+|base64url         |1.2    |1.2        |   |
+|batchtools        |0.9.6  |0.9.6      |   |
+|brew              |1.0-6  |1.0-6      |   |
+|checkmate         |1.8.3  |1.8.3      |   |
+|data.table        |1.10.4 |1.10.4     |   |
+|digest            |0.6.12 |0.6.12     |   |
+|future            |1.6.0  |1.6.0      |   |
+|globals           |0.10.2 |0.10.2     |   |
+|listenv           |0.6.0  |0.6.0      |   |
+|magrittr          |1.5    |1.5        |   |
+|prettyunits       |1.0.2  |1.0.2      |   |
+|progress          |1.1.2  |1.1.2      |   |
+|R6                |2.2.2  |2.2.2      |   |
+|rappdirs          |0.3.1  |0.3.1      |   |
+|stringi           |1.1.5  |1.1.5      |   |
+|withr             |2.0.0  |2.0.0      |   |
+
+# Revdeps
+
+## All (1)
+
+|package                        |version |error |warning |note |
+|:------------------------------|:-------|:-----|:-------|:----|
+|[origami](problems.md#origami) |0.8.0   |      |2       |1    |
+

revdep/problems.md

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+# origami
+
+Version: 0.8.0
+
+## In both
+
+*   checking CRAN incoming feasibility ... WARNING
+    ```
+    Maintainer: ‘Jeremy Coyle <[email protected]>’
+    
+    Insufficient package version (submitted: 0.8.0, existing: 0.8.0)
+    
+    This build time stamp is over a month old.
+    ```
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error in re-building vignettes:
+      ...
+    sh: 1: /home/hb/bin/pandoc: not found
+    Error: processing vignette 'generalizedCV.Rmd' failed with diagnostics:
+    error in running command
+    Execution halted
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespace in Imports field not imported from: ‘methods’
+      All declared Imports should be used.
+    ```
+

revdep/run.R

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+options(warn = 1)
+
+availableCores <- function() {
+  getenv <- function(name) {
+    as.integer(Sys.getenv(name, NA_character_))
+  }
+  getopt <- function(name) {
+    as.integer(getOption(name, NA_integer_))
+  }
+  if (is.finite(n <- getopt("mc.cores") + 1L)) return(n)
+  if (is.finite(n <- getopt("Ncpus") + 1L)) return(n)
+  if (is.finite(n <- getenv("PBS_NUM_PPN"))) return(n)
+  if (is.finite(n <- getenv("SLURM_CPUS_PER_TASK"))) return(n)
+  if (is.finite(n <- getenv("NSLOTS"))) return(n)
+  1L
+}
+
+reset <- isTRUE(as.logical(toupper(Sys.getenv("_R_CHECK_REVDEP_RESET_", "FALSE"))))
+revdep_framework <- Sys.getenv("_R_CHECK_REVDEP_", "revdepcheck")
+if (revdep_framework == "devtools") {
+  library("devtools")
+  if (reset) revdep_check_reset()
+  revdep_check(bioconductor = TRUE, recursive = FALSE, threads = availableCores(), reset = FALSE)
+  revdep_check_save_summary()
+  revdep_check_print_problems()
+} else if (revdep_framework == "revdepcheck") {
+  library("revdepcheck")
+  if (reset) revdep_reset()
+  revdep_check(bioc = TRUE, num_workers = availableCores(),
+               timeout = as.difftime(30, units = "mins"), quiet = FALSE)
+} else {
+  stop("Unknown revdep framework: ", revdep_framework)
+}