Package: DaMiRseq

Version: 1.2.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DaMiRseq_1.2.0.tar.gz

StartedAt: 2018-04-11 22:43:05 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:49:33 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 387.7 seconds

RetCode: 0

Status:  OK

CheckDir: DaMiRseq.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings DaMiRseq_1.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/DaMiRseq.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 ‘DaMiRseq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘DaMiRseq’ version ‘1.2.0’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DaMiRseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
* 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 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
DaMiR.Allplot: warning in pheatmap(sampleDistMatrix,
  clustering_distance_rows = mydist, clustering_distance_cols = mydist,
  col = colors, breaks = seque, annotation_col = df): partial argument
  match of 'col' to 'color'
DaMiR.Clustplot: warning in pheatmap(count_data,
  clustering_distance_rows = d_r, clustering_distance_cols = d_c, scale
  = "row", col = colors, annotation_col = df): partial argument match
  of 'col' to 'color'
DaMiR.Allplot: no visible binding for global variable ‘X1’
DaMiR.Allplot: no visible binding for global variable ‘X2’
DaMiR.EnsembleLearning: no visible binding for global variable
  ‘Classifiers’
DaMiR.EnsembleLearning: no visible binding for global variable
  ‘Accuracy’
DaMiR.MDSplot: no visible binding for global variable ‘X1’
DaMiR.MDSplot: no visible binding for global variable ‘X2’
Undefined global functions or variables:
  Accuracy Classifiers X1 X2
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
DaMiR.FSort            18.824  0.028  18.861
DaMiR.EnsembleLearning 11.488  0.024  11.510
DaMiR.Allplot           4.992  0.136   5.106
* 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-3.6-bioc/meat/DaMiRseq.Rcheck/00check.log’
for details.

* installing *source* package ‘DaMiRseq’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DaMiRseq)

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(DaMiRseq)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
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

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

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

    apply

Loading required package: ggplot2
> 
> test_check("DaMiRseq")
10 Predictors have been selected for classification 
3 Predictors have been selected for classification 
100 Highly correlated features have been discarded for classification. 
 0 Features remained. 
100 Highly correlated features have been discarded for classification. 
 0 Features remained. 
15 Genes have been discarded for classification 985 Genes remained. 
All the genes have been discarded!!!
        th.VIP argument is too high. Please choose a lower level of th.VIPPlease wait. This operation will take about 21 seconds (i.e. about 0 minutes).Your dataset has: 
100 Features; 
11 Samples: 5 A and 6 B 
3 variables: a b class ; 
 'class' included.Your dataset has: 
100 Features; 
11 Samples: 5 A and 6 B 
3 variables: a b class ; 
 'class' included.0 Features have been filtered out by espression. 100 Features remained. 
0 'Hypervariant' Features have been filtered out. 100 Features remained. 
Performing Normalization by 'vst' 
0 Samples have been excluded by averaged Sample-per-Sample correlation. 
 40 Samples remained. 
The number of SVs identified, which explain 95 % of Variance, is: 4 
All the sv have been used to adjust the dataAll the sv have been used to adjust the data══ testthat results  ═══════════════════════════════════════════════════════════
OK: 294 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 32.756   0.736  32.580 

name	user	system	elapsed
DaMiR.Allplot	4.992	0.136	5.106
DaMiR.Clustplot	0.868	0.004	0.874
DaMiR.EnsembleLearning	11.488	0.024	11.510
DaMiR.FBest	0.072	0.000	0.070
DaMiR.FReduct	0.028	0.000	0.027
DaMiR.FSelect	4.428	0.044	4.472
DaMiR.FSort	18.824	0.028	18.861
DaMiR.MDSplot	0.268	0.000	0.268
DaMiR.SV	0.928	0.000	0.930
DaMiR.SVadjust	0.140	0.000	0.142
DaMiR.corrplot	0.080	0.000	0.081
DaMiR.goldenDice	0.004	0.000	0.003