Package: MultiDataSet

Version: 1.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MultiDataSet_1.6.0.tar.gz

StartedAt: 2018-04-12 01:21:23 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:23:40 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 137.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: MultiDataSet.Rcheck

Warnings: 3

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings MultiDataSet_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/MultiDataSet.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 ‘MultiDataSet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MultiDataSet’ version ‘1.6.0’
* 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 ... WARNING
Codoc mismatches from documentation object 'ResultSet':
\S4method{plot}{ResultSet,ANY}
  Code: function(x, y, rid = 1, coef = 2, contrast = NULL, type, tFC =
                 2, tPV = -log10(0.001), show.labels = TRUE,
                 show.effect = FALSE, show.lambda = TRUE, fNames =
                 c("chromosome", "start"), subset, highlight, ...)
  Docs: function(x, y, rid = 1, coef = 2, contrast = NULL, type, tFC =
                 2, tPV = -log10(0.001), show.effect = FALSE,
                 show.lambda = TRUE, fNames = c("chromosome", "start"),
                 subset, highlight, ...)
  Argument names in code not in docs:
    show.labels
  Mismatches in argument names (first 3):
    Position: 9 Code: show.labels Docs: show.effect
    Position: 10 Code: show.effect Docs: show.lambda
    Position: 11 Code: show.lambda Docs: fNames

Codoc mismatches from documentation object 'getAssociation':
getAssociation
  Code: function(object, rid, coef = 2, contrast = NULL, fNames = NULL,
                 ...)
  Docs: function(object, rid, coef = 2, contrast = NULL, fNames =
                 c("chromosome", "start", "end", "genesymbol"), ...)
  Mismatches in argument default values:
    Name: 'fNames' Code: NULL Docs: c("chromosome", "start", "end", "genesymbol")

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'MultiDataSet-class'
  ‘...’ ‘methySet’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
'library' or 'require' call not declared from: ‘BRGEdata’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* 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 ‘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: 3 WARNINGs, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/MultiDataSet.Rcheck/00check.log’
for details.

* installing *source* package ‘MultiDataSet’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing 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
* DONE (MultiDataSet)

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(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, 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")'.

> 
> test_check("MultiDataSet")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 146 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 21.172   0.428  21.630 

name	user	system	elapsed
MultiDataSet-class	0.000	0.000	0.001
ResultSet-class	0.004	0.000	0.001
add_eset	0.148	0.012	0.159
add_genexp	0.472	0.000	0.473
add_methy	0.000	0.000	0.001
add_rnaseq-methods	0.404	0.000	0.405
add_rse	0.168	0.004	0.172
add_se	0.092	0.000	0.095
add_snps	0.052	0.000	0.049
add_table	0.008	0.000	0.009
chrNumToChar	0	0	0
commonIds	0.096	0.000	0.099
commonSamples	0.148	0.000	0.146
getAssociation-methods	0.052	0.000	0.053
lambdaClayton	0.000	0.000	0.002
opt-methods	0.004	0.000	0.002
qq_plot	1.728	0.008	1.737
rowRangesElements	0.092	0.000	0.093
volcano_plot	0.448	0.000	0.448