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CHECK report for MultiDataSet on tokay2

This page was generated on 2019-01-10 15:37:22 -0500 (Thu, 10 Jan 2019).

Package 1021/1651HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MultiDataSet 1.11.0
Carlos Ruiz-Arenas
Snapshot Date: 2019-01-09 16:46:14 -0500 (Wed, 09 Jan 2019)
URL: https://git.bioconductor.org/packages/MultiDataSet
Branch: master
Last Commit: bafaaa3
Last Changed Date: 2018-10-30 11:54:36 -0500 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  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 

Summary

Package: MultiDataSet
Version: 1.11.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MultiDataSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MultiDataSet_1.11.0.tar.gz
StartedAt: 2019-01-10 05:24:17 -0500 (Thu, 10 Jan 2019)
EndedAt: 2019-01-10 05:29:47 -0500 (Thu, 10 Jan 2019)
EllapsedTime: 329.8 seconds
RetCode: 0
Status:  OK  
CheckDir: MultiDataSet.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:MultiDataSet.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MultiDataSet_1.11.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MultiDataSet.Rcheck'
* using R Under development (unstable) (2018-11-18 r75627)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MultiDataSet/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MultiDataSet' version '1.11.0'
* 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 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
* 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 ... 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 ... 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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
add_methy 13.58   2.19   26.41
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
add_methy 16.52   1.06   17.72
* 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/MultiDataSet.Rcheck/00check.log'
for details.



Installation output

MultiDataSet.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MultiDataSet_1.11.0.tar.gz && rm -rf MultiDataSet.buildbin-libdir && mkdir MultiDataSet.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MultiDataSet.buildbin-libdir MultiDataSet_1.11.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MultiDataSet_1.11.0.zip && rm MultiDataSet_1.11.0.tar.gz MultiDataSet_1.11.0.zip
###
##############################################################################
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  % 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 70188  100 70188    0     0   971k      0 --:--:-- --:--:-- --:--:-- 1087k

install for i386

* installing *source* package 'MultiDataSet' ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
in method for 'add_methy' with signature '"MultiDataSet","GenomicRatioSet"': no definition for class "GenomicRatioSet"
** help
*** installing help indices
  converting help for package 'MultiDataSet'
    finding HTML links ... done
    MultiDataSet-class                      html  
    MultiDataSet                            html  
    ResultSet-class                         html  
    add_eset                                html  
    add_genexp                              html  
    add_methy                               html  
    add_rnaseq-methods                      html  
    add_rse                                 html  
    add_se                                  html  
    add_snps                                html  
    add_table                               html  
    chrNumToChar                            html  
    commonIds                               html  
    commonSamples                           html  
    getAssociation-methods                  html  
    lambdaClayton                           html  
    mae2mds                                 html  
    mds2mae                                 html  
    opt-methods                             html  
    qq_plot                                 html  
    rowRangesElements                       html  
    rset                                    html  
    volcano_plot                            html  
    w_iclusterplus                          html  
    w_mcia                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'MultiDataSet' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MultiDataSet' as MultiDataSet_1.11.0.zip
* DONE (MultiDataSet)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MultiDataSet' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

MultiDataSet.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2018-11-18 r75627) -- "Unsuffered Consequences"
Copyright (C) 2018 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(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, 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

Welcome to Bioconductor

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

> 
> test_check("MultiDataSet")
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: NO
 . phenoData:
    . rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: YES
 . phenoData:
    . rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: NO
 . phenoData:
    . rnaseq: 2 samples, 2 cols (id, sex)
Object of class 'ResultSet'
 . created with: test 
 . sva:   
 . #results: 1 ( error: 1 )
 . featureData:  0 
Object of class 'ResultSet'
 . created with: association 
    . via: a and b 
 . sva:   
 . #results: 1 ( error: 1 )
 . featureData: 10 probes x 2 variables
Object of class 'ResultSet'
 . created with: crossomics 
 . sva:   
    . method: met  ( metpac )
 . #results: 2 ( error: 1 )
 . featureData:  2 
    . pac: 10x2
    . cot: 10x2
== testthat results  ===========================================================
OK: 205 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  28.12    2.68   30.86 

MultiDataSet.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2018-11-18 r75627) -- "Unsuffered Consequences"
Copyright (C) 2018 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(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, 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

Welcome to Bioconductor

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

> 
> test_check("MultiDataSet")
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: NO
 . phenoData:
    . rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: YES
 . phenoData:
    . rnaseq: 2 samples, 1 cols (id)
Object of class 'MultiDataSet'
 . assayData: 1 elements
    . rnaseq: 3 features, 2 samples 
 . featureData:
    . rnaseq: 3 rows, 5 cols (chromosome, ..., status)
 . rowRanges:
    . rnaseq: NO
 . phenoData:
    . rnaseq: 2 samples, 2 cols (id, sex)
Object of class 'ResultSet'
 . created with: test 
 . sva:   
 . #results: 1 ( error: 1 )
 . featureData:  0 
Object of class 'ResultSet'
 . created with: association 
    . via: a and b 
 . sva:   
 . #results: 1 ( error: 1 )
 . featureData: 10 probes x 2 variables
Object of class 'ResultSet'
 . created with: crossomics 
 . sva:   
    . method: met  ( metpac )
 . #results: 2 ( error: 1 )
 . featureData:  2 
    . pac: 10x2
    . cot: 10x2
== testthat results  ===========================================================
OK: 205 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  31.20    1.59   32.92 

Example timings

MultiDataSet.Rcheck/examples_i386/MultiDataSet-Ex.timings

nameusersystemelapsed
MultiDataSet-class000
ResultSet-class000
add_eset0.080.030.11
add_genexp0.080.060.14
add_methy13.58 2.1926.41
add_rnaseq-methods0.140.000.15
add_rse0.330.020.34
add_se0.120.000.12
add_snps0.080.000.08
add_table0.020.000.02
chrNumToChar000
commonIds0.360.010.37
commonSamples0.150.000.16
getAssociation-methods0.050.000.05
lambdaClayton000
opt-methods000
qq_plot0.670.020.69
rowRangesElements0.110.000.11
volcano_plot0.280.010.30

MultiDataSet.Rcheck/examples_x64/MultiDataSet-Ex.timings

nameusersystemelapsed
MultiDataSet-class000
ResultSet-class000
add_eset0.090.000.09
add_genexp0.120.000.12
add_methy16.52 1.0617.72
add_rnaseq-methods0.260.000.26
add_rse0.610.010.63
add_se0.120.000.12
add_snps0.070.000.07
add_table0.020.000.02
chrNumToChar000
commonIds0.170.000.17
commonSamples0.830.000.83
getAssociation-methods0.020.040.05
lambdaClayton000
opt-methods0.000.010.01
qq_plot2.310.002.31
rowRangesElements0.140.000.15
volcano_plot0.330.020.34