Multiple platform build/check report for BioC 3.11 - CHECK report for PAPi on tokay2

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PAPi.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings PAPi_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/PAPi.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'PAPi' can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'PAPi' is deprecated and will be removed from Bioconductor
See 'C:/Users/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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... 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
** running examples for arch 'x64' ... 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: 2 ERRORs, 1 WARNING, 1 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/PAPi.Rcheck/00check.log'
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/PAPi_1.28.0.tar.gz && rm -rf PAPi.buildbin-libdir && mkdir PAPi.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PAPi.buildbin-libdir PAPi_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL PAPi_1.28.0.zip && rm PAPi_1.28.0.tar.gz PAPi_1.28.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  517k  100  517k    0     0  8232k      0 --:--:-- --:--:-- --:--:-- 9244k

install for i386

* installing *source* package 'PAPi' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PAPi'
    finding HTML links ... done
    PAPi-package                            html  
    addKeggCodes                            html  
    buildDatabase                           html  
    keggLibrary                             html  
    metabolomicsData                        html  
    papi                                    html  
    papiData                                html  
    papiHtest                               html  
    papiLine                                html  
    papiResults                             html  
** 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

install for x64

* installing *source* package 'PAPi' ...
** testing if installed package can be loaded
Warning: Package 'PAPi' is deprecated and will be removed from Bioconductor
  version 3.12
* MD5 sums
packaged installation of 'PAPi' as PAPi_1.28.0.zip
* DONE (PAPi)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'PAPi' successfully unpacked and MD5 sums checked

CHECK report for PAPi on tokay2

Summary

Command output

Installation output

Tests output

Example timings