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CHECK report for CCl4 on malbec1

This page was generated on 2018-04-12 12:49:03 -0400 (Thu, 12 Apr 2018).

Package 38/326HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CCl4 1.16.0
Audrey Kauffmann
Snapshot Date: 2018-04-12 07:35:06 -0400 (Thu, 12 Apr 2018)
URL: https://git.bioconductor.org/packages/CCl4
Branch: RELEASE_3_6
Last Commit: 72cd46a
Last Changed Date: 2017-10-30 11:58:22 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: CCl4
Version: 1.16.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CCl4_1.16.0.tar.gz
StartedAt: 2018-04-12 09:44:06 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 09:46:03 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 117.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: CCl4.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings CCl4_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/CCl4.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CCl4/DESCRIPTION’ ... OK
* this is package ‘CCl4’ version ‘1.16.0’
* 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 ... NOTE
  installed size is 304.4Mb
  sub-directories of 1Mb or more:
    data      12.0Mb
    extdata  292.2Mb
* 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 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 ... 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 installed files from ‘inst/doc’ ... OK
* 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’ ...5,26d4
< Attaching package: 'BiocGenerics'
< 
< The following objects are masked from 'package:parallel':
< 
<     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
<     clusterExport, clusterMap, parApply, parCapply, parLapply,
<     parLapplyLB, parRapply, parSapply, parSapplyLB
< 
< 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, append,
<     as.data.frame, cbind, colMeans, colSums, colnames, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
<     pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
<     setdiff, sort, table, tapply, union, unique, unsplit, which,
<     which.max, which.min
< 
29,38c7,9
<     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)'.
 OK
* 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.6-data-experiment/meat/CCl4.Rcheck/00check.log’
for details.



Installation output

CCl4.Rcheck/00install.out

* installing *source* package ‘CCl4’ ...
** data
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (CCl4)

Tests output

CCl4.Rcheck/tests/validDataFiles.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    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 
  0.648   0.032   0.675 

CCl4.Rcheck/tests/validDataFiles.Rout.save


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.
> 

Example timings

CCl4.Rcheck/CCl4-Ex.timings

nameusersystemelapsed
CCl40.9480.0280.978