Package: MultiDataSet

Version: 1.11.0

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_1.11.0.tar.gz

StartedAt: 2019-04-09 02:14:50 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 02:18:26 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 216.5 seconds

RetCode: 0

Status:  OK

CheckDir: MultiDataSet.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.11.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/MultiDataSet.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘1.11.0’
* 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 : <anonymous>: 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 16.019  0.721  18.067
* 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.

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

R Under development (unstable) (2019-03-18 r76245) -- "Unsuffered Consequences"
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, colMeans, colSums, 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, 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")'.

> 
> 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: 205 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 34.040   0.914  35.671 

name	user	system	elapsed
MultiDataSet-class	0.001	0.000	0.001
ResultSet-class	0.002	0.000	0.002
add_eset	0.117	0.000	0.118
add_genexp	0.148	0.000	0.149
add_methy	16.019	0.721	18.067
add_rnaseq-methods	0.078	0.008	0.085
add_rse	0.206	0.004	0.210
add_se	0.244	0.000	0.243
add_snps	0.045	0.000	0.045
add_table	0.013	0.000	0.013
chrNumToChar	0	0	0
commonIds	0.116	0.000	0.116
commonSamples	0.138	0.000	0.137
getAssociation-methods	0.027	0.004	0.030
lambdaClayton	0.002	0.000	0.003
opt-methods	0.000	0.002	0.002
qq_plot	0.872	0.005	0.876
rowRangesElements	0.124	0.004	0.129
volcano_plot	0.26	0.00	0.26