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### Running command:
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###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:PAPi.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings PAPi_1.28.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/PAPi.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PAPi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PAPi’ version ‘1.28.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘PAPi’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'PAPi' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.11-bioc/meat/PAPi.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* 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 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
addKeggCodes: no visible global function definition for ‘read.csv’
addKeggCodes: no visible global function definition for ‘select.list’
addKeggCodes: no visible global function definition for ‘write.csv’
buildDatabase : apply_pb: no visible global function definition for
  ‘txtProgressBar’
buildDatabase : apply_pb : wrapper: no visible global function
  definition for ‘setTxtProgressBar’
buildDatabase: no visible global function definition for ‘write.csv’
papi: no visible global function definition for ‘read.csv’
papi: no visible global function definition for ‘select.list’
papi: no visible global function definition for ‘txtProgressBar’
papi: no visible global function definition for ‘setTxtProgressBar’
papi: no visible global function definition for ‘write.csv’
papiHtest : test.t : <anonymous>: no visible global function definition
  for ‘t.test’
papiHtest : anova.t : <anonymous>: no visible global function
  definition for ‘lm’
papiHtest : anova.t: no visible binding for global variable ‘anova’
papiHtest: no visible global function definition for ‘read.csv’
papiHtest: no visible global function definition for ‘p.adjust’
papiHtest: no visible global function definition for ‘write.csv’
papiLine: no visible global function definition for ‘read.csv’
papiLine: no visible global function definition for ‘colors’
papiLine: no visible global function definition for ‘png’
papiLine: no visible global function definition for ‘par’
papiLine: no visible global function definition for ‘points’
papiLine: no visible global function definition for ‘lines’
papiLine: no visible global function definition for ‘axis’
papiLine: no visible global function definition for ‘text’
papiLine: no visible global function definition for ‘legend’
papiLine: no visible global function definition for ‘graphics.off’
Undefined global functions or variables:
  anova axis colors graphics.off legend lines lm p.adjust par png
  points read.csv select.list setTxtProgressBar t.test text
  txtProgressBar write.csv
Consider adding
  importFrom("grDevices", "colors", "graphics.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "par", "points",
             "text")
  importFrom("stats", "anova", "lm", "p.adjust", "t.test")
  importFrom("utils", "read.csv", "select.list", "setTxtProgressBar",
             "txtProgressBar", "write.csv")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... 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 ‘PAPi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: papiHtest
> ### Title: Apply ANOVA or t-test to results produced by 'papi'.
> ### Aliases: papiHtest
> 
> ### ** Examples
> 
> ### Building input data ####
> Names <- c("Replicates", "Galactose metabolism", "Glycerolipid metabolism", 
+ "Carbon fixation in photosynthetic organisms", "Fatty acid biosynthesis", 
+ "D-Alanine metabolism")
> Sample1 <- c("cond1", 200, 77, 99, 42, 29)
> Sample2 <- c("cond1", 236, 72, 80, 39, 14)
> Sample3 <- c("cond1", 269, 83, 89, 45, 31)
> Sample4 <- c("cond2", 68, 12, NA, 6, 0.006)
> Sample5 <- c("cond2", 57, 10, NA, 7, 0.1)
> Sample6 <- c("cond2", 58, 13, NA, 8, 0.05) 
> 
> dataInput <- data.frame(cbind(Names, Sample1, Sample2, Sample3, Sample4, 
+ Sample5, Sample6), stringsAsFactors = FALSE)
> 
> ### Applying papiHtest ####
> papiHtestResults <- papiHtest(dataInput, save = FALSE)
Data frame loaded...
t-test is in progress.. 

Error in t.test.default(x = c(0.602059991327962, 0.602059991327962, 0.602059991327962 : 
  data are essentially constant
Calls: papiHtest ... t.test.formula -> do.call -> t.test -> t.test.default
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.11-bioc/meat/PAPi.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL PAPi
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘PAPi’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘PAPiPackage.Rnw’ 
** testing if installed package can be loaded from temporary location
Warning: Package 'PAPi' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'PAPi' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (PAPi)