* using log directory ‘/srv/hornik/tmp/CRAN_pretest/AgriR.Rcheck’
* using R Under development (unstable) (2025-09-04 r88794)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 19.1.7 (3+b1)
    Debian flang-new version 19.1.7 (3+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* checking for file ‘AgriR/DESCRIPTION’ ... OK
* this is package ‘AgriR’ version ‘0.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [3s/3s] NOTE
Maintainer: ‘Cícero Almeida <cicero@arapiraca.ufal.br>’

New submission

The Title field should be in title case. Current version is:
  ‘Experimental design statistics’
In title case that is:
  ‘Experimental Design Statistics’
* 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 whether package ‘AgriR’ can be installed ... [4s/4s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 code files for non-ASCII characters ... WARNING
Found the following file with non-ASCII characters:
  R/reg.poly.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [1s/1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘shiny’
'library' or 'require' call to ‘ggplot2’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s/8s] NOTE
anova.crd: no visible global function definition for ‘aov’
anova.crd: no visible global function definition for ‘shapiro.test’
anova.fat2.crd: no visible global function definition for ‘aov’
anova.fat2.crd: no visible global function definition for
  ‘shapiro.test’
anova.fat2.crd: no visible global function definition for ‘par’
anova.fat2.crd: no visible global function definition for ‘pf’
anova.fat2.rbd: no visible global function definition for ‘aov’
anova.fat2.rbd: no visible global function definition for
  ‘shapiro.test’
anova.fat2.rbd: no visible global function definition for ‘par’
anova.fat2.rbd: no visible binding for global variable ‘cont’
anova.fat2.rbd: no visible global function definition for ‘pf’
anova.rbd: no visible global function definition for ‘aov’
anova.rbd: no visible global function definition for ‘shapiro.test’
anova.rbd: no visible global function definition for ‘par’
anova.sp2.crd: no visible global function definition for ‘aov’
anova.sp2.crd: no visible global function definition for ‘pf’
anova.sp2.crd: no visible global function definition for ‘par’
anova.sp2.crd: no visible binding for global variable ‘sigT’
anova.sp2.rbd: no visible global function definition for ‘aov’
anova.sp2.rbd: no visible global function definition for ‘pf’
anova.sp2.rbd: no visible global function definition for ‘par’
aproximate: no visible global function definition for ‘rnorm’
aproximate: no visible global function definition for ‘hist’
aproximate: no visible global function definition for ‘rgb’
aproximate: no visible global function definition for ‘lines’
aproximate: no visible global function definition for ‘polygon’
aproximate: no visible global function definition for ‘text’
aproximate: no visible global function definition for ‘abline’
barplotb: no visible global function definition for ‘barplot’
barplotb: no visible global function definition for ‘arrows’
barplotb: no visible global function definition for ‘text’
barplotg: no visible global function definition for ‘ggplot’
barplotg: no visible global function definition for ‘geom_bar’
barplotg: no visible global function definition for ‘aes’
barplotg: no visible global function definition for ‘geom_errorbar’
barplotg: no visible global function definition for ‘labs’
barplotg: no visible global function definition for ‘geom_text’
barplotg: no visible global function definition for ‘theme_bw’
boxplotb: no visible global function definition for ‘boxplot’
boxplotb: no visible global function definition for ‘bxp’
boxplotb: no visible global function definition for ‘text’
des.crd: no visible global function definition for ‘colorRampPalette’
des.crd: no visible global function definition for ‘par’
des.crd: no visible global function definition for ‘barplot’
des.crd: no visible global function definition for ‘text’
des.crd: no visible global function definition for ‘dev.copy’
des.crd: no visible binding for global variable ‘tiff’
des.crd: no visible global function definition for ‘dev.off’
des.fat2.crd: no visible global function definition for
  ‘colorRampPalette’
des.fat2.crd: no visible global function definition for ‘par’
des.fat2.crd: no visible global function definition for ‘barplot’
des.fat2.crd: no visible global function definition for ‘text’
des.fat2.crd: no visible global function definition for ‘dev.copy’
des.fat2.crd: no visible binding for global variable ‘tiff’
des.fat2.crd: no visible global function definition for ‘dev.off’
des.fat2.rbd: no visible global function definition for
  ‘colorRampPalette’
des.fat2.rbd: no visible binding for global variable ‘densi’
des.fat2.rbd: no visible global function definition for ‘par’
des.fat2.rbd: no visible global function definition for ‘barplot’
des.fat2.rbd: no visible global function definition for ‘text’
des.fat2.rbd: no visible global function definition for ‘dev.copy’
des.fat2.rbd: no visible binding for global variable ‘tiff’
des.fat2.rbd: no visible global function definition for ‘dev.off’
des.rbd: no visible global function definition for ‘colorRampPalette’
des.rbd: no visible global function definition for ‘par’
des.rbd: no visible global function definition for ‘barplot’
des.rbd: no visible global function definition for ‘text’
des.rbd: no visible global function definition for ‘dev.copy’
des.rbd: no visible binding for global variable ‘tiff’
des.rbd: no visible global function definition for ‘dev.off’
des.sp.crd: no visible global function definition for
  ‘colorRampPalette’
des.sp.crd: no visible global function definition for ‘par’
des.sp.crd: no visible global function definition for ‘barplot’
des.sp.crd: no visible global function definition for ‘text’
des.sp.crd: no visible global function definition for ‘dev.copy’
des.sp.crd: no visible binding for global variable ‘tiff’
des.sp.crd: no visible global function definition for ‘dev.off’
des.sp.rbd: no visible global function definition for
  ‘colorRampPalette’
des.sp.rbd: no visible global function definition for ‘par’
des.sp.rbd: no visible global function definition for ‘barplot’
des.sp.rbd: no visible global function definition for ‘text’
des.sp.rbd: no visible global function definition for ‘dev.copy’
des.sp.rbd: no visible binding for global variable ‘tiff’
des.sp.rbd: no visible global function definition for ‘dev.off’
desc: no visible global function definition for ‘median’
desc: no visible global function definition for ‘sd’
duncan: no visible global function definition for ‘qtukey’
duncan: no visible binding for global variable ‘sd’
histg: no visible global function definition for ‘sd’
histg: no visible global function definition for ‘IQR’
histg: no visible global function definition for ‘hist’
histg: no visible global function definition for ‘ggplot’
histg: no visible global function definition for ‘aes’
histg: no visible global function definition for ‘geom_histogram’
int.confidance: no visible global function definition for ‘sd’
int.confidance: no visible global function definition for ‘rnorm’
int.confidance: no visible global function definition for ‘rgb’
int.confidance: no visible global function definition for ‘lines’
int.confidance: no visible global function definition for ‘polygon’
int.confidance: no visible global function definition for ‘text’
int.confidance: no visible global function definition for ‘abline’
int.confidance: no visible global function definition for
  ‘shapiro.test’
latsd: no visible global function definition for ‘aov’
latsd: no visible global function definition for ‘shapiro.test’
latsd: no visible global function definition for ‘lsdb’
latsd: no visible global function definition for ‘ccboot’
latsd: no visible global function definition for ‘ccF’
lsd: no visible global function definition for ‘combn’
lsd: no visible global function definition for ‘ptukey’
lsd: no visible binding for global variable ‘sd’
means.test: no visible global function definition for ‘rnorm’
means.test: no visible global function definition for ‘sd’
means.test: no visible global function definition for ‘hist’
means.test: no visible global function definition for ‘rgb’
means.test: no visible global function definition for ‘lines’
means.test: no visible global function definition for ‘polygon’
means.test: no visible global function definition for ‘abline’
means.test: no visible global function definition for ‘text’
par.test: no visible global function definition for ‘sd’
par.test: no visible global function definition for ‘var’
par.test: no visible global function definition for ‘hist’
par.test: no visible global function definition for ‘rnorm’
par.test: no visible global function definition for ‘rgb’
par.test: no visible global function definition for ‘lines’
par.test: no visible global function definition for ‘polygon’
par.test: no visible global function definition for ‘abline’
par.test: no visible global function definition for ‘text’
pointplotg: no visible global function definition for ‘ggplot’
pointplotg: no visible global function definition for ‘aes’
pointplotg: no visible global function definition for ‘geom_point’
pointplotg: no visible global function definition for ‘geom_errorbar’
pointplotg: no visible global function definition for ‘labs’
pointplotg: no visible global function definition for ‘geom_text’
pointplotg: no visible global function definition for ‘theme_bw’
reg.poly: no visible global function definition for ‘anova’
reg.poly: no visible global function definition for ‘lm’
reg.poly: no visible global function definition for ‘pf’
reg.poly: no visible global function definition for ‘lines’
reg.poly: no visible global function definition for ‘mtext’
scheffe: no visible global function definition for ‘df.residual’
scheffe: no visible global function definition for ‘deviance’
scheffe: no visible global function definition for ‘anova’
scheffe : <anonymous>: no visible global function definition for
  ‘quantile’
scheffe: no visible global function definition for ‘qf’
scheffe: no visible global function definition for ‘pf’
scheffe: no visible binding for global variable ‘sd’
scottknott : sk: no visible global function definition for ‘pchisq’
scottknott: no visible global function definition for ‘read.table’
scottknott: no visible binding for global variable ‘sd’
snk: no visible global function definition for ‘qtukey’
snk: no visible binding for global variable ‘sd’
tukey: no visible binding for global variable ‘sd’
tukey: no visible global function definition for ‘qtukey’
tukey: no visible global function definition for ‘combn’
tukey: no visible global function definition for ‘ptukey’
Undefined global functions or variables:
  IQR abline aes anova aov arrows barplot boxplot bxp ccF ccboot
  colorRampPalette combn cont densi dev.copy dev.off deviance
  df.residual geom_bar geom_errorbar geom_histogram geom_point
  geom_text ggplot hist labs lines lm lsdb median mtext par pchisq pf
  polygon ptukey qf qtukey quantile read.table rgb rnorm sd
  shapiro.test sigT text theme_bw tiff var
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.copy", "dev.off",
             "rgb", "tiff")
  importFrom("graphics", "abline", "arrows", "barplot", "boxplot", "bxp",
             "hist", "lines", "mtext", "par", "polygon", "text")
  importFrom("stats", "IQR", "anova", "aov", "deviance", "df.residual",
             "lm", "median", "pchisq", "pf", "ptukey", "qf", "qtukey",
             "quantile", "rnorm", "sd", "shapiro.test", "var")
  importFrom("utils", "combn", "read.table")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... WARNING
Missing link(s) in Rd file 'anova.fat2.crd.Rd':
  ‘plotres’ ‘crd’ ‘fat3.crd’ ‘split2.crd’ ‘fat2.ad.crd’ ‘fat3.ad.crd’

Missing link(s) in Rd file 'anova.fat2.rbd.Rd':
  ‘plotres’ ‘fat2.rbd’ ‘fat3.rbd’ ‘split2.rbd’ ‘strip’ ‘fat2.ad.rbd’
  ‘fat3.ad.rbd’

Missing link(s) in Rd file 'anova.rbd.Rd':
  ‘fat2.crd’ ‘fat3.crd’ ‘split2.crd’ ‘fat2.ad.crd’ ‘fat3.ad.crd’

Missing link(s) in Rd file 'anova.sp2.crd.Rd':
  ‘plotres’ ‘split2.rbd’ ‘strip’

Missing link(s) in Rd file 'anova.sp2.rbd.Rd':
  ‘plotres’ ‘split2.rbd’ ‘strip’

Missing link(s) in Rd file 'latsd.Rd':
  ‘plotres’ ‘crd’ ‘rbd’

Missing link(s) in Rd file 'lsd.Rd':
  ‘ccboot’ ‘lsdb’ ‘ccF’

Missing link(s) in Rd file 'scottknott.Rd':
  ‘lsdb’ ‘ccboot’ ‘ccF’

Missing link(s) in Rd file 'snk.Rd':
  ‘lsdb’ ‘ccboot’ ‘ccF’

Missing link(s) in Rd file 'tukey.Rd':
  ‘lsdb’ ‘ccboot’ ‘ccF’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  anova.fat2.crd.Rd: plotres, crd, fat3.crd, split2.crd, fat2.ad.crd,
    fat3.ad.crd
  anova.fat2.rbd.Rd: plotres, fat2.rbd, fat3.rbd, split2.rbd, strip,
    fat2.ad.rbd, fat3.ad.rbd
  anova.rbd.Rd: fat2.crd, fat3.crd, split2.crd, fat2.ad.crd,
    fat3.ad.crd
  anova.sp2.crd.Rd: plotres, split2.rbd, strip
  anova.sp2.rbd.Rd: plotres, split2.rbd, strip
  latsd.Rd: plotres, crd, rbd
  lsd.Rd: ccboot, lsdb, ccF
  scottknott.Rd: lsdb, ccboot, ccF
  snk.Rd: lsdb, ccboot, ccF
  tukey.Rd: lsdb, ccboot, ccF
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘aproximate’ ‘barplotb’ ‘barplotg’ ‘boxplotb’ ‘des.fat2.crd’
  ‘des.fat2.rbd’ ‘des.rbd’ ‘des.sp.crd’ ‘des.sp.rbd’ ‘int.confidance’
  ‘means.test’ ‘orderPvalue’ ‘par.test’ ‘pointplotg’ ‘scheffe’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'anova.crd.Rd'
  ‘graph’ ‘graph.type’ ‘graph.col’ ‘xlab’ ‘ylab’ ‘main’ ‘graph.den’
  ‘best.fit’

Undocumented arguments in Rd file 'anova.fat2.crd.Rd'
  ‘fac.fix’ ‘graph’ ‘graph.type’ ‘graph.col’ ‘xlab’ ‘ylab’ ‘main’
  ‘graph.den’ ‘best.fit’
Documented arguments not in \usage in Rd file 'anova.fat2.crd.Rd':
  ‘sigT’

Undocumented arguments in Rd file 'anova.fat2.rbd.Rd'
  ‘fac.fix’ ‘graph’ ‘graph.type’ ‘graph.col’ ‘xlab’ ‘ylab’ ‘main’
  ‘graph.den’ ‘best.fit’
Documented arguments not in \usage in Rd file 'anova.fat2.rbd.Rd':
  ‘sigT’

Undocumented arguments in Rd file 'anova.rbd.Rd'
  ‘graph’ ‘graph.type’ ‘graph.col’ ‘xlab’ ‘ylab’ ‘main’ ‘graph.den’
  ‘best.fit’

Undocumented arguments in Rd file 'anova.sp2.crd.Rd'
  ‘fac.fix’ ‘graph’ ‘graph.type’ ‘graph.col’ ‘xlab’ ‘ylab’ ‘graph.den’
Documented arguments not in \usage in Rd file 'anova.sp2.crd.Rd':
  ‘sigT’

Undocumented arguments in Rd file 'anova.sp2.rbd.Rd'
  ‘block’ ‘fac.fix’ ‘graph’ ‘graph.type’ ‘graph.col’ ‘xlab’ ‘ylab’
  ‘graph.den’ ‘nl’ ‘hvar’
Documented arguments not in \usage in Rd file 'anova.sp2.rbd.Rd':
  ‘repet’

Undocumented arguments in Rd file 'ari_mean.Rd'
  ‘x’ ‘na.rm’

Undocumented arguments in Rd file 'desc.Rd'
  ‘y’ ‘x’ ‘boxplot’ ‘xlab’ ‘ylab’ ‘graph.col’

Undocumented arguments in Rd file 'duncan.Rd'
  ‘graph’ ‘graph.col’ ‘graph.den’ ‘graph.type’ ‘xlab’ ‘ylab’

Undocumented arguments in Rd file 'freqtable.Rd'
  ‘y’ ‘bins’

Undocumented arguments in Rd file 'geo_mean.Rd'
  ‘x’ ‘na.rm’

Undocumented arguments in Rd file 'har_mean.Rd'
  ‘x’ ‘na.rm’

Undocumented arguments in Rd file 'histg.Rd'
  ‘y’ ‘xlab’ ‘ylab’ ‘graph.col’ ‘scores’ ‘border’ ‘freq’ ‘graph.type’
  ‘main’

Undocumented arguments in Rd file 'lsd.Rd'
  ‘graph’ ‘graph.col’ ‘graph.den’ ‘graph.type’ ‘xlab’ ‘ylab’

Undocumented arguments in Rd file 'pon_mean.Rd'
  ‘x’ ‘w’ ‘na.rm’

Undocumented arguments in Rd file 'reg.poly.Rd'
  ‘main’ ‘xlab’ ‘ylab’ ‘graph’ ‘best.fit’

Undocumented arguments in Rd file 'scottknott.Rd'
  ‘graph’ ‘graph.col’ ‘graph.den’ ‘graph.type’ ‘xlab’ ‘ylab’

Undocumented arguments in Rd file 'snk.Rd'
  ‘graph’ ‘graph.col’ ‘graph.den’ ‘graph.type’ ‘xlab’ ‘ylab’

Undocumented arguments in Rd file 'tukey.Rd'
  ‘graph’ ‘graph.col’ ‘graph.den’ ‘graph.type’ ‘xlab’ ‘ylab’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [1s/1s] ERROR
Running examples in ‘AgriR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anova.crd
> ### Title: One factor Completely Randomized Design
> ### Aliases: anova.crd
> 
> ### ** Examples
> 
> dados=read.table("R/data.crd.csv", sep=";", header=T, dec=",")
Warning in file(file, "rt") :
  cannot open file 'R/data.crd.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: read.table -> file
Execution halted
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 5 WARNINGs, 2 NOTEs