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Sleuth3 log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2019-01-24-06-46/RF_PKG_CHECK/PKGS/Sleuth3.Rcheck'
* using R version 3.5.2 Patched (2019-01-14 r75999)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'Sleuth3/DESCRIPTION' ... OK
* this is package 'Sleuth3' version '1.0-3'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Berwin A Turlach '

Days since last update: 1

New maintainer:
  Berwin A Turlach 
Old maintainer(s):
  ORPHANED

CRAN repository db overrides:
  X-CRAN-Comment: Orphaned on 2019-01-23 as no response to request to
    fix check issues.
  Maintainer: ORPHANED
CRAN repository db conflicts: 'Maintainer'
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'Sleuth3' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
* checking package directory ... 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 ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'Sleuth3-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: case0501
> ### Title: Diet Restriction and Longevity
> ### Aliases: case0501
> ### Keywords: datasets
> 
> ### ** Examples
> 
> str(case0501)
'data.frame':	349 obs. of  2 variables:
 $ Lifetime: num  35.5 35.4 34.9 34.8 33.8 33.5 32.6 32.4 31.8 31.6 ...
 $ Diet    : Factor w/ 6 levels "N/N85","N/R40",..: 4 4 4 4 4 4 4 4 4 4 ...
> attach(case0501)
> 
> # Re-order levels for better boxplot organization: 
> myDiet  <- factor(Diet, levels=c("NP","N/N85","N/R50","R/R50","lopro","N/R40") ) 
>  
> myNames <- c("NP(49)","N/N85(57)","N/R50(71)","R/R50(56)","lopro(56)",
+   "N/R40(60)")   # Make these for boxplot labeling.
> boxplot(Lifetime ~ myDiet, ylab= "Lifetime (months)", names=myNames, 
+   xlab="Treatment (and sample size)") 
> myAov1   <- aov(Lifetime ~ Diet) # One-way analysis of variance
> plot(myAov1, which=1) # Plot residuals versus estimated means.
> summary(myAov1) 
             Df Sum Sq Mean Sq F value Pr(>F)    
Diet          5  12734  2546.8    57.1 <2e-16 ***
Residuals   343  15297    44.6                   
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
> pairwise.t.test(Lifetime,Diet, pool.SD=TRUE, p.adj="none") # All t-tests

	Pairwise comparisons using t tests with pooled SD 

data:  Lifetime and Diet 

      N/N85   N/R40   N/R50   NP      R/R50
N/R40 < 2e-16 -       -       -       -    
N/R50 1.1e-14 0.017   -       -       -    
NP    5.9e-05 < 2e-16 < 2e-16 -       -    
R/R50 8.9e-15 0.073   0.622   < 2e-16 -    
lopro 5.2e-08 1.6e-05 0.029   < 2e-16 0.012

P value adjustment method: none 
> 
> ## p-VALUES AND CONFIDENCE INTERVALS FOR SPECIFIED COMPARISONS OF MEANS
> if(require(multcomp)){
+   diet    <- factor(Diet,labels=c("NN85", "NR40", "NR50", "NP", "RR50", "lopro")) 
+   myAov2  <- aov(Lifetime ~ diet - 1) 
+   myComparisons <- glht(myAov2,
+           linfct=c("dietNR50 - dietNN85 = 0", 
+           "dietRR50  - dietNR50 = 0",
+           "dietNR40  - dietNR50 = 0",
+           "dietlopro - dietNR50 = 0",
+           "dietNN85  - dietNP   = 0")   ) 
+   summary(myComparisons,test=adjusted("none")) # No multiple comparison adjust.
+   confint(myComparisons, calpha = univariate_calpha()) # No adjustment
+ }
Loading required package: multcomp
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

The following object is masked from 'package:MASS':

    geyser

Error in qmvt(conf.level, df = df, corr = matrix(1), tail = tail, ...) : 
  object 'arg' not found
Calls: confint -> confint.glht -> calpha ->  -> qmvt
Execution halted
** found \donttest examples: check also with --run-donttest
* 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
* DONE

Status: 1 ERROR, 2 NOTEs
See
  'R:/run/building/build_2019-01-24-06-46/RF_PKG_CHECK/PKGS/Sleuth3.Rcheck/00check.log'
for details.

Run time: 255.89 seconds.

Additional Logs:   00install.out
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