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CHECK report for GRridge on tokay1

This page was generated on 2018-04-12 13:29:05 -0400 (Thu, 12 Apr 2018).

Package 621/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GRridge 1.2.0
Mark A. van de Wiel
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/GRridge
Branch: RELEASE_3_6
Last Commit: 1b5e901
Last Changed Date: 2017-10-30 12:41:23 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: GRridge
Version: 1.2.0
Command: rm -rf GRridge.buildbin-libdir GRridge.Rcheck && mkdir GRridge.buildbin-libdir GRridge.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GRridge.buildbin-libdir GRridge_1.2.0.tar.gz >GRridge.Rcheck\00install.out 2>&1 && cp GRridge.Rcheck\00install.out GRridge-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GRridge.buildbin-libdir --install="check:GRridge-install.out" --force-multiarch --no-vignettes --timings GRridge_1.2.0.tar.gz
StartedAt: 2018-04-12 00:34:10 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 00:48:09 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 838.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GRridge.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf GRridge.buildbin-libdir GRridge.Rcheck && mkdir GRridge.buildbin-libdir GRridge.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=GRridge.buildbin-libdir GRridge_1.2.0.tar.gz >GRridge.Rcheck\00install.out 2>&1 && cp GRridge.Rcheck\00install.out GRridge-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=GRridge.buildbin-libdir --install="check:GRridge-install.out" --force-multiarch --no-vignettes --timings GRridge_1.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GRridge.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GRridge/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'GRridge' version '1.2.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'penalized' 'Iso' 'survival' 'GSEABase' 'BiocGenerics' 'Biobase'
  'annotate' 'graph'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'GRridge' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GSEABase::setdiff' by 'BiocGenerics::setdiff' when loading 'GRridge'
  Warning: replacing previous import 'stats::xtabs' by 'BiocGenerics::xtabs' when loading 'GRridge'
  Warning: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when loading 'GRridge'
  Warning: replacing previous import 'GSEABase::intersect' by 'BiocGenerics::intersect' when loading 'GRridge'
  Warning: replacing previous import 'stats::IQR' by 'BiocGenerics::IQR' when loading 'GRridge'
  Warning: replacing previous import 'penalized::as.data.frame' by 'BiocGenerics::as.data.frame' when loading 'GRridge'
  Warning: replacing previous import 'stats::mad' by 'BiocGenerics::mad' when loading 'GRridge'
  Warning: replacing previous import 'stats::var' by 'BiocGenerics::var' when loading 'GRridge'
See 'C:/Users/biocbuild/bbs-3.6-bioc/meat/GRridge.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
* 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
** checking loading without being on the library search path ... 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 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 ... OK
* 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 ... WARNING
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                    old_size new_size compress
  dataFarkas.rda       3.4Mb    2.5Mb    bzip2
  dataWurdinger.rda    1.9Mb    1.2Mb       xz
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
predict.grridge 219.92   3.29  223.42
grridgeCV        82.28   1.28   83.57
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
predict.grridge 205.32   3.67  209.08
grridgeCV        90.19   1.48   91.68
* 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 WARNINGs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/GRridge.Rcheck/00check.log'
for details.

Installation output

GRridge.Rcheck/00install.out


install for i386

* installing *source* package 'GRridge' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'GSEABase::setdiff' by 'BiocGenerics::setdiff' when loading 'GRridge'
Warning: replacing previous import 'stats::xtabs' by 'BiocGenerics::xtabs' when loading 'GRridge'
Warning: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when loading 'GRridge'
Warning: replacing previous import 'GSEABase::intersect' by 'BiocGenerics::intersect' when loading 'GRridge'
Warning: replacing previous import 'stats::IQR' by 'BiocGenerics::IQR' when loading 'GRridge'
Warning: replacing previous import 'penalized::as.data.frame' by 'BiocGenerics::as.data.frame' when loading 'GRridge'
Warning: replacing previous import 'stats::mad' by 'BiocGenerics::mad' when loading 'GRridge'
Warning: replacing previous import 'stats::var' by 'BiocGenerics::var' when loading 'GRridge'
** help
*** installing help indices
  converting help for package 'GRridge'
    finding HTML links ... done
    CreatePartition                         html  
    GRridge-package                         html  
    PartitionsSelection                     html  
    auc                                     html  
    dataFarkas                              html  
    dataVerlaat                             html  
    dataWurdinger                           html  
    grridge                                 html  
    grridgeCV                               html  
    hello                                   html  
    matchGeneSets                           html  
    mergeGroups                             html  
    predict.grridge                         html  
    roc                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'GSEABase::setdiff' by 'BiocGenerics::setdiff' when loading 'GRridge'
Warning: replacing previous import 'stats::xtabs' by 'BiocGenerics::xtabs' when loading 'GRridge'
Warning: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when loading 'GRridge'
Warning: replacing previous import 'GSEABase::intersect' by 'BiocGenerics::intersect' when loading 'GRridge'
Warning: replacing previous import 'stats::IQR' by 'BiocGenerics::IQR' when loading 'GRridge'
Warning: replacing previous import 'penalized::as.data.frame' by 'BiocGenerics::as.data.frame' when loading 'GRridge'
Warning: replacing previous import 'stats::mad' by 'BiocGenerics::mad' when loading 'GRridge'
Warning: replacing previous import 'stats::var' by 'BiocGenerics::var' when loading 'GRridge'
In R CMD INSTALL

install for x64

* installing *source* package 'GRridge' ...
** testing if installed package can be loaded
Warning: replacing previous import 'stats::xtabs' by 'BiocGenerics::xtabs' when loading 'GRridge'
Warning: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when loading 'GRridge'
Warning: replacing previous import 'stats::mad' by 'BiocGenerics::mad' when loading 'GRridge'
Warning: replacing previous import 'stats::IQR' by 'BiocGenerics::IQR' when loading 'GRridge'
Warning: replacing previous import 'GSEABase::intersect' by 'BiocGenerics::intersect' when loading 'GRridge'
Warning: replacing previous import 'penalized::as.data.frame' by 'BiocGenerics::as.data.frame' when loading 'GRridge'
Warning: replacing previous import 'GSEABase::setdiff' by 'BiocGenerics::setdiff' when loading 'GRridge'
Warning: replacing previous import 'stats::var' by 'BiocGenerics::var' when loading 'GRridge'
* MD5 sums
packaged installation of 'GRridge' as GRridge_1.2.0.zip
* DONE (GRridge)
In R CMD INSTALL
In R CMD INSTALL

Tests output

GRridge.Rcheck/tests_i386/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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("GRridge")
Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: Iso
Iso 0.0-17
Loading required package: GSEABase
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 object is masked from 'package:penalized':

    as.data.frame

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: 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: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

Warning messages:
1: replacing previous import 'GSEABase::setdiff' by 'BiocGenerics::setdiff' when loading 'GRridge' 
2: replacing previous import 'stats::xtabs' by 'BiocGenerics::xtabs' when loading 'GRridge' 
3: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when loading 'GRridge' 
4: replacing previous import 'GSEABase::intersect' by 'BiocGenerics::intersect' when loading 'GRridge' 
5: replacing previous import 'stats::IQR' by 'BiocGenerics::IQR' when loading 'GRridge' 
6: replacing previous import 'penalized::as.data.frame' by 'BiocGenerics::as.data.frame' when loading 'GRridge' 
7: replacing previous import 'stats::mad' by 'BiocGenerics::mad' when loading 'GRridge' 
8: replacing previous import 'stats::var' by 'BiocGenerics::var' when loading 'GRridge' 
> 
> testthat::test_check("GRridge")
[1] "Summary of group sizes:"
 VarIn VarOut 
    50     50 
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   4.40    0.15    4.56

GRridge.Rcheck/tests_x64/testthat.Rout


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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("GRridge")
Loading required package: penalized
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").
Loading required package: Iso
Iso 0.0-17
Loading required package: GSEABase
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 object is masked from 'package:penalized':

    as.data.frame

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: 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: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

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

    addNode

Warning messages:
1: replacing previous import 'stats::xtabs' by 'BiocGenerics::xtabs' when loading 'GRridge' 
2: replacing previous import 'stats::sd' by 'BiocGenerics::sd' when loading 'GRridge' 
3: replacing previous import 'stats::mad' by 'BiocGenerics::mad' when loading 'GRridge' 
4: replacing previous import 'stats::IQR' by 'BiocGenerics::IQR' when loading 'GRridge' 
5: replacing previous import 'GSEABase::intersect' by 'BiocGenerics::intersect' when loading 'GRridge' 
6: replacing previous import 'penalized::as.data.frame' by 'BiocGenerics::as.data.frame' when loading 'GRridge' 
7: replacing previous import 'GSEABase::setdiff' by 'BiocGenerics::setdiff' when loading 'GRridge' 
8: replacing previous import 'stats::var' by 'BiocGenerics::var' when loading 'GRridge' 
> 
> testthat::test_check("GRridge")
[1] "Summary of group sizes:"
 VarIn VarOut 
    50     50 
== testthat results  ===========================================================
OK: 1 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
   5.45    0.09    5.53

Example timings

GRridge.Rcheck/examples_i386/GRridge-Ex.timings

nameusersystemelapsed
CreatePartition0.090.000.09
PartitionsSelection0.020.000.02
auc0.340.030.37
dataFarkas0.310.020.33
dataVerlaat0.050.000.05
dataWurdinger2.110.102.21
grridge0.110.040.14
grridgeCV82.28 1.2883.57
hello000
matchGeneSets2.270.142.40
mergeGroups1.950.112.07
predict.grridge219.92 3.29223.42
roc1.310.041.35

GRridge.Rcheck/examples_x64/GRridge-Ex.timings

nameusersystemelapsed
CreatePartition0.130.000.13
PartitionsSelection000
auc0.420.020.44
dataFarkas0.330.010.34
dataVerlaat0.050.000.05
dataWurdinger2.980.023.00
grridge0.130.000.12
grridgeCV90.19 1.4891.68
hello000
matchGeneSets1.760.051.81
mergeGroups1.450.061.52
predict.grridge205.32 3.67209.08
roc1.760.021.78