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CHECK report for DaMiRseq on merida1

This page was generated on 2019-04-16 12:00:29 -0400 (Tue, 16 Apr 2019).

Package 368/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DaMiRseq 1.6.2
Mattia Chiesa
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/DaMiRseq
Branch: RELEASE_3_8
Last Commit: f5f6030
Last Changed Date: 2019-01-16 09:41:14 -0400 (Wed, 16 Jan 2019)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DaMiRseq
Version: 1.6.2
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DaMiRseq_1.6.2.tar.gz
StartedAt: 2019-04-15 23:21:18 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 23:28:11 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 413.0 seconds
RetCode: 0
Status:  OK 
CheckDir: DaMiRseq.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:DaMiRseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings DaMiRseq_1.6.2.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/DaMiRseq.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.6.2’
* 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.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.EnsembleLearning2cl_Training: no visible binding for global
  variable ‘Classifiers’
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
  variable ‘Accuracy’
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
  variable ‘MCC’
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
  variable ‘Sensitivity’
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
  variable ‘Specificity’
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
  variable ‘PPV’
DaMiR.EnsembleLearning2cl_Training: no visible binding for global
  variable ‘NPV’
DaMiR.EnsembleLearning2cl_Training: 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’
Undefined global functions or variables:
  Accuracy Classifiers MCC NPV PPV Sensitivity Specificity X1 X2 colSds
* 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 sizes of PDF files under ‘inst/doc’ ... 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/DaMiRseq.Rcheck/00check.log’
for details.



Installation output

DaMiRseq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL DaMiRseq
###
##############################################################################
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘DaMiRseq’ ...
** 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
   ‘DaMiRseq.Rnw’ using ‘UTF-8’ 
** testing if installed package can be loaded
* DONE (DaMiRseq)

Tests output

DaMiRseq.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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, colMeans, colSums, colnames,
    dirname, 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

Loading required package: BiocParallel

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

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, divided in:  5 A 6 B 
3 variables: a b class ; 
 'class' included. 
Your dataset has: 
100 Features; 
11 Samples, divided in:  5 A 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' 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: 283 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 35.129   1.596  35.528 

Example timings

DaMiRseq.Rcheck/DaMiRseq-Ex.timings

nameusersystemelapsed
DaMiR.Allplot1.4390.0771.523
DaMiR.Clustplot1.2100.0121.229
DaMiR.EnsembleLearning0.0040.0040.008
DaMiR.EnsembleLearning2cl0.0050.0040.008
DaMiR.EnsembleLearning2cl_Predict0.0040.0040.008
DaMiR.EnsembleLearning2cl_Test0.0040.0040.008
DaMiR.EnsembleLearning2cl_Training0.0040.0040.010
DaMiR.EnsembleLearningNcl0.0050.0040.009
DaMiR.FBest0.0140.0050.019
DaMiR.FReduct0.0250.0030.028
DaMiR.FSelect0.7810.0190.801
DaMiR.FSort0.7860.0240.813
DaMiR.MDSplot0.3250.0160.343
DaMiR.SV0.8310.0450.880
DaMiR.SVadjust0.1630.0130.175
DaMiR.corrplot0.0310.0050.037
DaMiR.goldenDice0.0020.0000.003
DaMiR.makeSE0.0640.0010.067
DaMiR.normalization1.3350.0311.374
DaMiR.sampleFilt0.1690.0190.188
DaMiR.transpose0.0830.0070.092