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CHECK report for coseq on tokay2

This page was generated on 2019-03-11 11:30:00 -0400 (Mon, 11 Mar 2019).

Package 341/1676HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
coseq 1.7.2
Andrea Rau
Snapshot Date: 2019-03-10 17:02:02 -0400 (Sun, 10 Mar 2019)
URL: https://git.bioconductor.org/packages/coseq
Branch: master
Last Commit: 51da8dc
Last Changed Date: 2019-02-12 21:38:18 -0400 (Tue, 12 Feb 2019)
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: coseq
Version: 1.7.2
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings coseq_1.7.2.tar.gz
StartedAt: 2019-03-11 02:19:26 -0400 (Mon, 11 Mar 2019)
EndedAt: 2019-03-11 02:25:34 -0400 (Mon, 11 Mar 2019)
EllapsedTime: 368.3 seconds
RetCode: 0
Status:  OK  
CheckDir: coseq.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:coseq.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings coseq_1.7.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/coseq.Rcheck'
* using R Under development (unstable) (2019-01-10 r75962)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'coseq/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'coseq' version '1.7.2'
* 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 whether package 'coseq' 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 ... 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 ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
plot    5.66   0.00    5.66
summary 5.26   0.02    5.28
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
              user system elapsed
plot          5.83   0.01    5.84
compareARI    5.81   0.02    5.82
coseqHelpers  5.40   0.02    5.42
compareICL    5.17   0.01    5.19
coseq-package 5.03   0.00    5.03
* 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: OK

Installation output

coseq.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/coseq_1.7.2.tar.gz && rm -rf coseq.buildbin-libdir && mkdir coseq.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=coseq.buildbin-libdir coseq_1.7.2.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL coseq_1.7.2.zip && rm coseq_1.7.2.tar.gz coseq_1.7.2.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  226k  100  226k    0     0  3483k      0 --:--:-- --:--:-- --:--:-- 3965k

install for i386

* installing *source* package 'coseq' ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for 'plot' in package 'coseq'
** help
*** installing help indices
  converting help for package 'coseq'
    finding HTML links ... done
    NormMixClus                             html  
    NormMixClusK                            html  
    NormMixParam                            html  
    clusterEntropy                          html  
    clusterInertia                          html  
    compareARI                              html  
    compareICL                              html  
    convertLegacyCoseq                      html  
    coseq-package                           html  
    coseq                                   html  
    coseqHelpers                            html  
    coseqResults                            html  
    coseqRun                                html  
    fietz                                   html  
    kmeansProbaPost                         html  
    logclr                                  html  
    matchContTable                          html  
    plot                                    html  
    summary                                 html  
    transformRNAseq                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'coseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'coseq' as coseq_1.7.2.zip
* DONE (coseq)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'coseq' successfully unpacked and MD5 sums checked

Tests output

coseq.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2019-01-10 r75962) -- "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("coseq")
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


Attaching package: 'coseq'

The following object is masked from 'package:stats4':

    plot

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

    plot

> test_check("coseq")
****************************************
coseq analysis: kmeans approach & logclr transformation
K = 0 to 3 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: Gamma approach & logclr transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: Normal approach & none transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: Normal approach & logMedianRef transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
== testthat results  ===========================================================
OK: 30 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  13.67    1.06   15.34

coseq.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2019-01-10 r75962) -- "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("coseq")
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


Attaching package: 'coseq'

The following object is masked from 'package:stats4':

    plot

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

    plot

> test_check("coseq")
****************************************
coseq analysis: kmeans approach & logclr transformation
K = 0 to 3 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: Gamma approach & logclr transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: kmeans approach & other transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: Normal approach & none transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
****************************************
coseq analysis: Normal approach & logMedianRef transformation
K = 2 to 4 
Use set.seed() prior to running coseq for reproducible results.
****************************************
== testthat results  ===========================================================
OK: 30 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  10.34    0.56   10.90

Example timings

coseq.Rcheck/examples_i386/coseq-Ex.timings

nameusersystemelapsed
NormMixClus0.620.050.67
NormMixClusK0.270.000.26
NormMixParam0.160.000.16
clusterEntropy000
clusterInertia0.490.030.52
compareARI3.860.053.91
compareICL4.200.034.23
coseq-package3.580.063.64
coseq3.430.003.42
coseqHelpers3.610.033.64
coseqRun1.030.001.03
kmeansProbaPost000
matchContTable0.010.000.02
plot5.660.005.66
summary5.260.025.28
transformRNAseq0.020.000.01

coseq.Rcheck/examples_x64/coseq-Ex.timings

nameusersystemelapsed
NormMixClus0.890.000.89
NormMixClusK0.480.000.48
NormMixParam0.280.000.28
clusterEntropy000
clusterInertia0.720.000.72
compareARI5.810.025.82
compareICL5.170.015.19
coseq-package5.030.005.03
coseq4.570.004.57
coseqHelpers5.400.025.42
coseqRun1.600.001.59
kmeansProbaPost000
matchContTable0.010.000.02
plot5.830.015.84
summary4.450.114.56
transformRNAseq0.020.000.02