Merge branch 'master' into mxkin

Merge DESCRIPTION manually to combine dependencies and rerun check to
update check.log

1 files changed, 115 insertions, 8 deletions

diff --git a/check.log b/check.log
index 4c481fe8..3bf43d07 100644
--- a/check.log
+++ b/check.log
@@ -7,19 +7,126 @@
 * checking extension type ... Package
 * this is package ‘mkin’ version ‘0.9.49.9’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... NOTE
+* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
-
-The Date field is over a month old.
 * checking package namespace information ... OK
-* checking package dependencies ... ERROR
-Namespace dependencies not required: 'nlme', 'purrr'
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking serialization versions ... OK
+* checking whether package ‘mkin’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* 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 for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking use of S3 registration ... OK
+* checking dependencies in R code ... OK
+* checking S3 generic/method consistency ... OK
+* checking replacement functions ... OK
+* checking foreign function calls ... OK
+* 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 cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* 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:
 
-See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
-manual.
+> 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 for unstated dependencies in ‘tests’ ... OK
+* checking tests ... SKIPPED
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking re-building of vignette outputs ... OK
+* checking PDF version of manual ... OK
+* checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 1 ERROR, 1 NOTE
+Status: 1 ERROR, 1 WARNING, 1 NOTE
 See
   ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’
 for details.