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CHECK report for DaMiRseq on malbec2

This page was generated on 2020-10-17 11:54:38 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE DaMiRseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 420/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DaMiRseq 2.0.0
Mattia Chiesa
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/DaMiRseq
Branch: RELEASE_3_11
Last Commit: 43c49ad
Last Changed Date: 2020-04-27 15:06:15 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 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
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: DaMiRseq
Version: 2.0.0
Command: /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings DaMiRseq_2.0.0.tar.gz
StartedAt: 2020-10-17 00:27:28 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 00:35:46 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 498.4 seconds
RetCode: 0
Status:  OK 
CheckDir: DaMiRseq.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings DaMiRseq_2.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/DaMiRseq.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.0.0’
* 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  5.9Mb
  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 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.Allplot: no visible binding for global variable ‘value’
DaMiR.Allplot: no visible binding for global variable ‘variable’
DaMiR.EnsembleLearning2cl: no visible binding for global variable
  ‘Classifiers’
DaMiR.EnsembleLearning2cl: no visible binding for global variable
  ‘Accuracy’
DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘MCC’
DaMiR.EnsembleLearning2cl: no visible binding for global variable
  ‘Specificity’
DaMiR.EnsembleLearning2cl: no visible binding for global variable
  ‘Sensitivity’
DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘PPV’
DaMiR.EnsembleLearning2cl: no visible binding for global variable ‘NPV’
DaMiR.EnsembleLearning2cl: no visible global function definition for
  ‘colSds’
DaMiR.EnsembleLearningNcl: no visible binding for global variable
  ‘Classifiers’
DaMiR.EnsembleLearningNcl: no visible binding for global variable
  ‘Accuracy’
DaMiR.EnsembleLearningNcl: no visible global function definition for
  ‘colSds’
DaMiR.MDSplot: no visible binding for global variable ‘X1’
DaMiR.MDSplot: no visible binding for global variable ‘X2’
DaMiR.ModelSelect: no visible binding for global variable ‘Accuracy’
DaMiR.ModelSelect: no visible binding for global variable
  ‘N.predictors’
DaMiR.ModelSelect: no visible binding for global variable ‘counts’
DaMiR.iTSadjust: no visible binding for global variable ‘value’
DaMiR.iTSadjust: no visible binding for global variable ‘variable’
DaMiR.iTSnorm: no visible binding for global variable ‘value’
DaMiR.iTSnorm: no visible binding for global variable ‘variable’
Undefined global functions or variables:
  Accuracy Classifiers MCC N.predictors NPV PPV Sensitivity Specificity
  X1 X2 colSds counts value variable
* 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 (user + system) or elapsed time > 5s
               user system elapsed
DaMiR.Allplot 7.065  0.319   7.383
* 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-3.11-bioc/meat/DaMiRseq.Rcheck/00check.log’
for details.



Installation output

DaMiRseq.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL DaMiRseq
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘DaMiRseq’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** 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 (DaMiRseq)

Tests output

DaMiRseq.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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

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 objects are masked from 'package:base':

    aperm, apply, rowsum

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. 
Your dataset has: 
100 Features; 
11 Samples, divided in:  
3 variables: a b class ; 
 'class' included. 
Your dataset has: 
100 Features; 
11 Samples, divided in:  
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' with dispersion parameter:  parametric 
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: 111 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 26.778   1.253  29.760 

Example timings

DaMiRseq.Rcheck/DaMiRseq-Ex.timings

nameusersystemelapsed
DaMiR.Allplot7.0650.3197.383
DaMiR.Clustplot0.3650.0050.368
DaMiR.EnsL_Predict0.0030.0000.003
DaMiR.EnsL_Test0.0040.0000.004
DaMiR.EnsL_Train0.0020.0010.003
DaMiR.EnsembleLearning0.0020.0020.004
DaMiR.EnsembleLearning2cl0.0030.0000.003
DaMiR.EnsembleLearningNcl0.0010.0030.004
DaMiR.FBest0.0160.0000.016
DaMiR.FReduct0.0260.0000.026
DaMiR.FSelect0.8420.0080.849
DaMiR.FSort0.7330.0000.733
DaMiR.MDSplot0.2410.0040.244
DaMiR.ModelSelect0.0000.0000.001
DaMiR.SV1.9130.0081.920
DaMiR.SVadjust0.1700.0040.174
DaMiR.corrplot0.0270.0040.030
DaMiR.goldenDice0.0010.0000.001
DaMiR.iTSadjust0.0020.0000.002
DaMiR.iTSnorm0.0020.0000.002
DaMiR.makeSE0.0370.0000.045
DaMiR.normalization2.1300.0082.137
DaMiR.sampleFilt0.1640.0000.164
DaMiR.transpose0.0880.0080.095