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CHECK report for MultiDataSet on malbec2

This page was generated on 2019-10-16 12:08:52 -0400 (Wed, 16 Oct 2019).

Package 1066/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiDataSet 1.12.0
Carlos Ruiz-Arenas
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/MultiDataSet
Branch: RELEASE_3_9
Last Commit: 27b08a0
Last Changed Date: 2019-05-02 11:54:01 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: MultiDataSet
Version: 1.12.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MultiDataSet_1.12.0.tar.gz
StartedAt: 2019-10-16 03:25:59 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 03:29:38 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 219.9 seconds
RetCode: 0
Status:  OK 
CheckDir: MultiDataSet.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:MultiDataSet.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings MultiDataSet_1.12.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MultiDataSet.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MultiDataSet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiDataSet’ version ‘1.12.0’
* 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 ‘MultiDataSet’ can be installed ... OK
* 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
* 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 ... NOTE
Unexported objects imported by ':::' calls:
  ‘Biobase:::assayDataEnvLock’ ‘Biobase:::assayDataStorageMode’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
downloadGEO : : no visible global function definition for
  ‘methylationSet’
lambdaClayton: no visible global function definition for ‘qnorm’
lambdaClayton: no visible global function definition for ‘qchisq’
qq_plot: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  methylationSet qbeta qchisq qnorm
Consider adding
  importFrom("stats", "qbeta", "qchisq", "qnorm")
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
add_methy 15.634  0.896  18.268
* 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 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.



Installation output

MultiDataSet.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL MultiDataSet
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘MultiDataSet’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for ‘add_methy’ with signature ‘"MultiDataSet","GenomicRatioSet"’: no definition for class “GenomicRatioSet”
** 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 (MultiDataSet)

Tests output

MultiDataSet.Rcheck/tests/testthat.Rout


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(MultiDataSet)
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, 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")'.

> 
> test_check("MultiDataSet")
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: NO
 . phenoData:
    . rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: YES
 . phenoData:
    . rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: NO
 . phenoData:
    . rnaseq: 2 samples, 2 cols (id, sex)
Object of class 'ResultSet'
 . created with: test 
 . sva:   
 . #results: 1 ( error: 1 )
 . featureData:  0 
Object of class 'ResultSet'
 . created with: association 
    . via: a and b 
 . sva:   
 . #results: 1 ( error: 1 )
 . featureData: 10 probes x 2 variables
Object of class 'ResultSet'
 . created with: crossomics 
 . sva:   
    . method: met  ( metpac )
 . #results: 2 ( error: 1 )
 . featureData:  2 
    . pac: 10x2
    . cot: 10x2
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 178 | SKIPPED: 0 | WARNINGS: 27 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 31.805   0.987  32.789 

Example timings

MultiDataSet.Rcheck/MultiDataSet-Ex.timings

nameusersystemelapsed
MultiDataSet-class0.0000.0010.001
ResultSet-class0.0000.0010.001
add_eset0.0740.0160.090
add_genexp0.0920.0160.108
add_methy15.634 0.89618.268
add_rnaseq-methods0.1340.0000.135
add_rse0.4280.0040.431
add_se0.0680.0000.068
add_snps0.0410.0000.041
add_table0.0080.0000.009
chrNumToChar000
commonIds0.0900.0000.091
commonSamples0.1080.0000.109
getAssociation-methods0.0300.0120.042
lambdaClayton0.0020.0000.002
opt-methods0.0020.0000.002
qq_plot0.5750.0080.583
rowRangesElements0.1130.0000.113
volcano_plot0.2350.0000.236