Add three functions to facilitate the use of nlme

1 files changed, 4 insertions, 67 deletions

diff --git a/check.log b/check.log
index 3bf43d07..0a75a713 100644
--- a/check.log
+++ b/check.log
@@ -24,27 +24,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
 * checking for future file timestamps ... OK
 * checking ‘build’ directory ... OK
 * checking DESCRIPTION meta-information ... OK
-* checking top-level files ... WARNING
-Conversion of ‘README.md’ failed:
-[WARNING] This document format requires a nonempty <title> element.
-  Please specify either ‘title’ or ‘pagetitle’ in the metadata.
-  Falling back to ‘README’
-Could not fetch https://codecov.io/github/jranke/mkin/branch/master/graphs/badge.svg
-HttpExceptionRequest Request {
-  host                 = "codecov.io"
-  port                 = 443
-  secure               = True
-  requestHeaders       = []
-  path                 = "/github/jranke/mkin/branch/master/graphs/badge.svg"
-  queryString          = ""
-  method               = "GET"
-  proxy                = Nothing
-  rawBody              = False
-  redirectCount        = 10
-  responseTimeout      = ResponseTimeoutDefault
-  requestVersion       = HTTP/1.1
-}
- ConnectionTimeout
+* checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK
 * checking package subdirectories ... OK
@@ -64,13 +44,7 @@ HttpExceptionRequest Request {
 * checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
-* checking Rd line widths ... NOTE
-Rd file 'memkin.Rd':
-  \examples lines wider than 100 characters:
-     f_nlme_sfo_sfo_2 <- memkin(f_2[1, ], "pdDiag(parent_0 + log_k_parent_sink + log_k_parent_A1 + log_k_A1_sink ~ 1)") # explicit
-     f_nlme_sfo_sfo_3 <- memkin(f_2[1, ], "pdDiag(parent_0 + log_k_parent_sink + log_k_parent_A1 ~ 1)") # reduced
-
-These lines will be truncated in the PDF manual.
+* checking Rd line widths ... OK
 * checking Rd cross-references ... OK
 * checking for missing documentation entries ... OK
 * checking for code/documentation mismatches ... OK
@@ -82,41 +56,7 @@ These lines will be truncated in the PDF manual.
 * checking data for ASCII and uncompressed saves ... OK
 * checking installed files from ‘inst/doc’ ... OK
 * checking files in ‘vignettes’ ... OK
-* checking examples ... ERROR
-Running examples in ‘mkin-Ex.R’ failed
-The error most likely occurred in:
-
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
-> ### Name: memkin
-> ### Title: Estimation of parameter distributions from mmkin row objects
-> ### Aliases: memkin
-> 
-> ### ** Examples
-> 
-> sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-> m_SFO <- mkinmod(parent = mkinsub("SFO"))
-> d_SFO_1 <- mkinpredict(m_SFO,
-+   c(k_parent_sink = 0.1),
-+   c(parent = 98), sampling_times)
-> d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
-> d_SFO_2 <- mkinpredict(m_SFO,
-+   c(k_parent_sink = 0.05),
-+   c(parent = 102), sampling_times)
-> d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
-> d_SFO_3 <- mkinpredict(m_SFO,
-+   c(k_parent_sink = 0.02),
-+   c(parent = 103), sampling_times)
-> d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
-> 
-> d1 <- add_err(d_SFO_1, function(value) 3, n = 1)
-> d2 <- add_err(d_SFO_2, function(value) 2, n = 1)
-> d3 <- add_err(d_SFO_3, function(value) 4, n = 1)
-> ds <- c(d1 = d1, d2 = d2, d3 = d3)
-> 
-> f <- mmkin("SFO", ds)
-Error in .check_ncores(cores) : 8 simultaneous processes spawned
-Calls: mmkin -> mclapply -> .check_ncores
-Execution halted
+* checking examples ... OK
 * checking for unstated dependencies in ‘tests’ ... OK
 * checking tests ... SKIPPED
 * checking for unstated dependencies in vignettes ... OK
@@ -126,8 +66,5 @@ Execution halted
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 1 ERROR, 1 WARNING, 1 NOTE
-See
-  ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
-for details.
+Status: OK