diff options
Diffstat (limited to 'check.log')
| -rw-r--r-- | check.log | 123 |
1 files changed, 115 insertions, 8 deletions
@@ -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. |