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CHECK report for DaMiRseq on tokay2

This page was generated on 2019-04-09 12:30:29 -0400 (Tue, 09 Apr 2019).

Package 381/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DaMiRseq 1.7.3
Mattia Chiesa
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/DaMiRseq
Branch: master
Last Commit: 85e0e73
Last Changed Date: 2019-01-16 09:35:40 -0400 (Wed, 16 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 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
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: DaMiRseq
Version: 1.7.3
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DaMiRseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DaMiRseq_1.7.3.tar.gz
StartedAt: 2019-04-09 02:08:34 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 02:18:23 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 588.3 seconds
RetCode: 0
Status:  OK  
CheckDir: DaMiRseq.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DaMiRseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings DaMiRseq_1.7.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/DaMiRseq.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DaMiRseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DaMiRseq' version '1.7.3'
* 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 whether package 'DaMiRseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/DaMiRseq.Rcheck/00check.log'
for details.



Installation output

DaMiRseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/DaMiRseq_1.7.3.tar.gz && rm -rf DaMiRseq.buildbin-libdir && mkdir DaMiRseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DaMiRseq.buildbin-libdir DaMiRseq_1.7.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL DaMiRseq_1.7.3.zip && rm DaMiRseq_1.7.3.tar.gz DaMiRseq_1.7.3.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2850k  100 2850k    0     0  12.4M      0 --:--:-- --:--:-- --:--:-- 12.8M

install for i386

* installing *source* package 'DaMiRseq' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DaMiRseq'
    finding HTML links ... done
    DaMiR.Allplot                           html  
    DaMiR.Clustplot                         html  
    DaMiR.EnsembleLearning                  html  
    DaMiR.EnsembleLearning2cl               html  
    DaMiR.EnsembleLearning2cl_Predict       html  
    DaMiR.EnsembleLearning2cl_Test          html  
    DaMiR.EnsembleLearning2cl_Training      html  
    DaMiR.EnsembleLearningNcl               html  
    DaMiR.FBest                             html  
    DaMiR.FReduct                           html  
    finding level-2 HTML links ... done

    DaMiR.FSelect                           html  
    DaMiR.FSort                             html  
    DaMiR.MDSplot                           html  
    DaMiR.SV                                html  
    DaMiR.SVadjust                          html  
    DaMiR.corrplot                          html  
    DaMiR.goldenDice                        html  
    DaMiR.makeSE                            html  
    DaMiR.normalization                     html  
    DaMiR.sampleFilt                        html  
    DaMiR.transpose                         html  
    SE                                      html  
    SEtest_norm                             html  
    data_min                                html  
    data_norm                               html  
    data_reduced                            html  
    data_relief                             html  
    df                                      html  
    selected_features                       html  
    sv                                      html  
** building package indices
** installing vignettes
   'DaMiRseq.Rnw' using 'UTF-8' 
** 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

install for x64

* installing *source* package 'DaMiRseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DaMiRseq' as DaMiRseq_1.7.3.zip
* DONE (DaMiRseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'DaMiRseq' successfully unpacked and MD5 sums checked

Tests output

DaMiRseq.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Attaching package: 'IRanges'

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

    windows

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, 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. 
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: 294 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  31.85    2.96   38.60 

DaMiRseq.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

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

    windows

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, 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. 
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: 294 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  34.50    1.21   34.62 

Example timings

DaMiRseq.Rcheck/examples_i386/DaMiRseq-Ex.timings

nameusersystemelapsed
DaMiR.Allplot2.590.162.75
DaMiR.Clustplot0.410.010.42
DaMiR.EnsembleLearning0.000.020.01
DaMiR.EnsembleLearning2cl000
DaMiR.EnsembleLearning2cl_Predict0.010.000.02
DaMiR.EnsembleLearning2cl_Test0.000.010.01
DaMiR.EnsembleLearning2cl_Training0.000.020.02
DaMiR.EnsembleLearningNcl0.020.000.01
DaMiR.FBest0.010.000.02
DaMiR.FReduct0.030.000.03
DaMiR.FSelect0.690.000.69
DaMiR.FSort0.580.050.62
DaMiR.MDSplot0.410.060.47
DaMiR.SV0.680.080.77
DaMiR.SVadjust0.180.000.17
DaMiR.corrplot0.010.000.01
DaMiR.goldenDice000
DaMiR.makeSE0.040.000.05
DaMiR.normalization1.830.011.84
DaMiR.sampleFilt0.170.020.24
DaMiR.transpose0.860.000.85

DaMiRseq.Rcheck/examples_x64/DaMiRseq-Ex.timings

nameusersystemelapsed
DaMiR.Allplot2.510.053.62
DaMiR.Clustplot0.610.031.50
DaMiR.EnsembleLearning0.000.020.02
DaMiR.EnsembleLearning2cl0.020.000.02
DaMiR.EnsembleLearning2cl_Predict0.000.010.01
DaMiR.EnsembleLearning2cl_Test0.020.000.02
DaMiR.EnsembleLearning2cl_Training0.010.030.06
DaMiR.EnsembleLearningNcl0.000.020.22
DaMiR.FBest0.030.000.03
DaMiR.FReduct0.030.000.23
DaMiR.FSelect0.780.011.30
DaMiR.FSort0.720.021.85
DaMiR.MDSplot0.360.020.81
DaMiR.SV0.850.091.45
DaMiR.SVadjust0.170.030.63
DaMiR.corrplot0.030.000.03
DaMiR.goldenDice000
DaMiR.makeSE0.090.000.09
DaMiR.normalization1.470.032.84
DaMiR.sampleFilt0.100.050.15
DaMiR.transpose1.200.052.09