* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’ * using R version 3.6.3 (2020-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘mkin’ version ‘0.9.49.10’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ * checking package namespace information ... OK * 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 ... OK * 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 ... NOTE nlme.mmkin: no visible binding for global variable ‘na.fail’ nlme.mmkin: no visible binding for global variable ‘f’ Undefined global functions or variables: f na.fail Consider adding importFrom("stats", "na.fail") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd line widths ... OK * 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: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: nlme_function > ### Title: Estimation of parameter distributions from mmkin row objects > ### Aliases: nlme_function mean_degparms nlme_data > > ### ** 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, cores = 1, quiet = TRUE) > mean_dp <- mean_degparms(f) > grouped_data <- nlme_data(f) > nlme_f <- nlme_function(f) > # These assignments are necessary for these objects to be > # visible to nlme and augPred when evaluation is done by > # pkgdown to generated the html docs. > assign("nlme_f", nlme_f, globalenv()) > assign("grouped_data", grouped_data, globalenv()) > > library(nlme) > m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink), + data = grouped_data, + fixed = parent_0 + log_k_parent_sink ~ 1, + random = pdDiag(parent_0 + log_k_parent_sink ~ 1), + start = mean_dp) > summary(m_nlme) Nonlinear mixed-effects model fit by maximum likelihood Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) Data: grouped_data AIC BIC logLik 253.6377 262.9937 -121.8188 Random effects: Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) Level: ds Structure: Diagonal parent_0 log_k_parent_sink Residual StdDev: 2.486822 0.6481355 2.368137 Fixed effects: parent_0 + log_k_parent_sink ~ 1 Value Std.Error DF t-value p-value parent_0 101.43096 1.5960157 44 63.55261 0 log_k_parent_sink -3.07614 0.3827294 44 -8.03737 0 Correlation: prnt_0 log_k_parent_sink 0.011 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -1.9643731 -0.5430765 0.1659516 0.6160408 1.8082871 Number of Observations: 48 Number of Groups: 3 > plot(augPred(m_nlme, level = 0:1), layout = c(3, 1)) > > m_nlme <- nlme(nlme_formula, + data = grouped_data, + fixed = parent_0 + log_k_parent_sink ~ 1, + random = pdDiag(parent_0 + log_k_parent_sink ~ 1), + start = mean_dp) Error in nlme(nlme_formula, data = grouped_data, fixed = parent_0 + log_k_parent_sink ~ : object 'nlme_formula' not found 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 See ‘/home/jranke/git/mkin/mkin.Rcheck/00check.log’ for details.