##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:CCl4.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings CCl4_1.46.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/CCl4.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘CCl4/DESCRIPTION’ ... OK
* this is package ‘CCl4’ version ‘1.46.0’
* 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 ‘CCl4’ can be installed ... OK
* checking installed package size ... INFO
  installed size is 183.5Mb
  sub-directories of 1Mb or more:
    data      10.9Mb
    extdata  172.4Mb
* 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 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 Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'CCl4.Rd':
  ‘[limma:rglist]{RGList}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  CCl4.RData           9.1Mb    2.1Mb       xz
  CCl4_RGList.RData    2.9Mb    2.0Mb       xz
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘validDataFiles.R’
  Comparing ‘validDataFiles.Rout’ to ‘validDataFiles.Rout.save’ ...5,27d4
< Attaching package: 'generics'
< 
< The following objects are masked from 'package:base':
< 
<     as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
<     setequal, union
< 
< 
< Attaching package: 'BiocGenerics'
< 
< The following objects are masked from 'package:stats':
< 
<     IQR, mad, sd, var, xtabs
< 
< The following objects are masked from 'package:base':
< 
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
<     mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
<     rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
<     unsplit, which.max, which.min
< 
30,39c7,9
<     Vignettes contain introductory material; view with
<     'browseVignettes()'. To cite Bioconductor, see
<     'citation("Biobase")', and for packages 'citation("pkgname")'.
< 
< 
< Attaching package: 'limma'
< 
< The following object is masked from 'package:BiocGenerics':
< 
<     plotMA
---
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
 NOTE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.21-data-experiment/meat/CCl4.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL CCl4
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘CCl4’ ...
** this is package ‘CCl4’ version ‘1.46.0’
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CCl4)

R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("CCl4")
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: limma

Attaching package: 'limma'

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

    plotMA

> dataPath = system.file("extdata", package="CCl4")
> if(setequal(dir(dataPath),
+             c("251316214319_auto_479-628.gpr", "251316214320_auto_478-629.gpr",
+               "251316214321_auto_410-592.gpr", "251316214329_auto_429-673.gpr",
+               "251316214330_auto_457-658.gpr", "251316214331_auto_431-588.gpr",
+               "251316214332_auto_492-625.gpr", "251316214333_auto_487-712.gpr",
+               "251316214379_auto_443-617.gpr", "251316214380_auto_493-682.gpr",
+               "251316214381_auto_497-602.gpr", "251316214382_auto_481-674.gpr",
+               "251316214384_auto_450-642.gpr", "251316214389_auto_456-694.gpr",
+               "251316214390_auto_456-718.gpr", "251316214391_auto_475-599.gpr",
+               "251316214393_auto_460-575.gpr", "251316214394_auto_463-521.gpr",
+               "samplesInfo.txt", "013162_D_SequenceList_20060815.txt"))) {
+   cat("Fine.\n")
+ } else {
+   cat(sprintf("Contents of %s differs from expectation.\n", dataPath))
+ }
Fine.
> 
> proc.time()
   user  system elapsed 
  0.670   0.066   0.724 

R version 2.9.0 Under development (unstable) (2009-03-06 r48061)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library("CCl4")
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: limma
> dataPath = system.file("extdata", package="CCl4")
> if(setequal(dir(dataPath),
+             c("251316214319_auto_479-628.gpr", "251316214320_auto_478-629.gpr",
+               "251316214321_auto_410-592.gpr", "251316214329_auto_429-673.gpr",
+               "251316214330_auto_457-658.gpr", "251316214331_auto_431-588.gpr",
+               "251316214332_auto_492-625.gpr", "251316214333_auto_487-712.gpr",
+               "251316214379_auto_443-617.gpr", "251316214380_auto_493-682.gpr",
+               "251316214381_auto_497-602.gpr", "251316214382_auto_481-674.gpr",
+               "251316214384_auto_450-642.gpr", "251316214389_auto_456-694.gpr",
+               "251316214390_auto_456-718.gpr", "251316214391_auto_475-599.gpr",
+               "251316214393_auto_460-575.gpr", "251316214394_auto_463-521.gpr",
+               "samplesInfo.txt", "013162_D_SequenceList_20060815.txt"))) {
+   cat("Fine.\n")
+ } else {
+   cat(sprintf("Contents of %s differs from expectation.\n", dataPath))
+ }
Fine.
>