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CHECK report for rcellminerData on malbec2

This page was generated on 2021-01-18 15:58:39 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE rcellminerData PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 288/385HostnameOS / ArchINSTALLBUILDCHECK
rcellminerData 2.13.0
Augustin Luna , Vinodh Rajapakse
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/rcellminerData
Branch: master
Last Commit: cda0aed
Last Changed Date: 2020-10-27 10:11:59 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS 

Summary

Package: rcellminerData
Version: 2.13.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rcellminerData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rcellminerData_2.13.0.tar.gz
StartedAt: 2021-01-18 12:33:48 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 12:37:21 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 213.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: rcellminerData.Rcheck
Warnings: 2

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:rcellminerData.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings rcellminerData_2.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-data-experiment/meat/rcellminerData.Rcheck’
* using R Under development (unstable) (2021-01-05 r79797)
* 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 ‘2.13.0’
* package encoding: UTF-8
* 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:
  .BBSoptions
  .git_fetch_output.txt
  .git_merge_output.txt
  .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 451.5Mb
  sub-directories of 1Mb or more:
    data      37.0Mb
    extdata  414.5Mb
* 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 ... WARNING
  Warning: found non-ASCII strings
  '(sp-4-2)-mu4-[n,n<c3><b8>-bis(3-aminopropyl)butane-1,4-diamine]...' in object 'drugData'
  '1,3-bis(trifluoromethyl)-2,4-diaza-butadientylamido,n,n<c3><b8>...' in object 'drugData'
* 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    6.8Mb    4.2Mb       xz
  molData.RData    30.3Mb   19.3Mb       xz
* 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: 2 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-data-experiment/meat/rcellminerData.Rcheck/00check.log’
for details.



Installation output

rcellminerData.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL rcellminerData
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘rcellminerData’ ...
** using staged installation
** data
*** moving datasets to lazyload DB
** 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 (rcellminerData)

Tests output

rcellminerData.Rcheck/tests/testthat.Rout


R Under development (unstable) (2021-01-05 r79797) -- "Unsuffered Consequences"
Copyright (C) 2021 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, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, 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: 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")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 92 ]
> 
> proc.time()
   user  system elapsed 
  3.912   0.302   4.199 

Example timings