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CHECK report for rcellminerData on malbec1

This page was generated on 2018-04-12 12:49:55 -0400 (Thu, 12 Apr 2018).

Package 249/326HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rcellminerData 2.0.0
Augustin Luna , Vinodh Rajapakse
Snapshot Date: 2018-04-12 07:35:06 -0400 (Thu, 12 Apr 2018)
URL: https://git.bioconductor.org/packages/rcellminerData
Branch: RELEASE_3_6
Last Commit: 1e5915f
Last Changed Date: 2017-11-21 11:18:17 -0400 (Tue, 21 Nov 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository

Summary

Package: rcellminerData
Version: 2.0.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rcellminerData_2.0.0.tar.gz
StartedAt: 2018-04-12 10:27:27 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 10:31:15 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 228.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rcellminerData.Rcheck
Warnings: 1

Command output

##############################################################################
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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rcellminerData_2.0.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.6-data-experiment/meat/rcellminerData.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 ‘rcellminerData/DESCRIPTION’ ... OK
* this is package ‘rcellminerData’ version ‘2.0.0’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rcellminerData’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 431.6Mb
  sub-directories of 1Mb or more:
    data      29.2Mb
    extdata  401.6Mb
* 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 ... NOTE
  Note: found 2 marked UTF-8 strings
* 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
  drugData.RData    7.1Mb    4.3Mb       xz
  molData.RData    22.3Mb   13.0Mb       xz
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-data-experiment/meat/rcellminerData.Rcheck/00check.log’
for details.



Installation output

rcellminerData.Rcheck/00install.out

* installing *source* package ‘rcellminerData’ ...
** data
*** moving datasets to lazyload DB
** inst
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rcellminerData)

Tests output

rcellminerData.Rcheck/tests/testthat.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(testthat)
> library(rcellminer)
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: rcdk
Loading required package: rcdklibs
Loading required package: rJava

Attaching package: 'rcdk'

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

    matches

Loading required package: fingerprint
Loading required package: rcellminerData
Consider citing this package: Luna A, et al. rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. PMID: 26635141; citation("rcellminer")
> library(rcellminerData)
> 
> test_check("rcellminerData")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 89 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  4.872   0.360   6.188 

Example timings