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CHECK report for motifStack on tokay2

This page was generated on 2019-04-09 12:01:09 -0400 (Tue, 09 Apr 2019).

Package 1026/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
motifStack 1.27.4
Jianhong Ou
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/motifStack
Branch: master
Last Commit: 9de080a
Last Changed Date: 2019-04-03 09:26:48 -0400 (Wed, 03 Apr 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: motifStack
Version: 1.27.4
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:motifStack.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings motifStack_1.27.4.tar.gz
StartedAt: 2019-04-09 04:23:58 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:29:21 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 323.5 seconds
RetCode: 0
Status:  OK  
CheckDir: motifStack.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:motifStack.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings motifStack_1.27.4.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/motifStack.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 'motifStack/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'motifStack' version '1.27.4'
* 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 'motifStack' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
browseMotifs 3.84   0.83     5.5
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  Running 'runTests.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

motifStack.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/motifStack_1.27.4.tar.gz && rm -rf motifStack.buildbin-libdir && mkdir motifStack.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=motifStack.buildbin-libdir motifStack_1.27.4.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL motifStack_1.27.4.zip && rm motifStack_1.27.4.tar.gz motifStack_1.27.4.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  150k  100  150k    0     0  2240k      0 --:--:-- --:--:-- --:--:-- 2506k

install for i386

* installing *source* package 'motifStack' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'motifStack'
    finding HTML links ... done
    DNAmotifAlignment                       html  
    browseMotifs-shiny                      html  
    browseMotifs                            html  
    colorset                                html  
    getRankedUniqueMotifs                   html  
    highlightCol                            html  
    importMatrix                            html  
    mergeMotifs                             html  
    motifCircos                             html  
    motifCloud                              html  
    motifPiles                              html  
    motifSig-class                          html  
    motifSig-methods                        html  
    motifSignature                          html  
    motifStack-package                      html  
    motifStack                              html  
    ouNode-class                            html  
    pcm-class                               html  
    pcm-methods                             html  
    pfm-class                               html  
    pfm-methods                             html  
    pfm2pwm                                 html  
    plotAffinityLogo                        html  
    plotMotifLogo                           html  
    plotMotifLogoA                          html  
    plotMotifLogoStack                      html  
    plotMotifLogoStackWithTree              html  
    plotMotifOverMotif                      html  
    plotMotifStackWithPhylog                html  
    plotMotifStackWithRadialPhylog          html  
    plotXaxis                               html  
    plotYaxis                               html  
    psam-class                              html  
    psam-methods                            html  
    readPCM                                 html  
    reorderUPGMAtree                        html  
** building package indices
** installing vignettes
** 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 'motifStack' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'motifStack' as motifStack_1.27.4.zip
* DONE (motifStack)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'motifStack' successfully unpacked and MD5 sums checked

Tests output

motifStack.Rcheck/tests_i386/runTests.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.

> require("motifStack") || stop("unable to load Package:motifStack")
Loading required package: motifStack
Loading required package: grImport2
Loading required package: grid
Loading required package: MotIV
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


Attaching package: 'MotIV'

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

    filter

Loading required package: ade4

Attaching package: 'ade4'

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

    score

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

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: XVector

Attaching package: 'Biostrings'

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

    strsplit

[1] TRUE
> #require("MotifDb") || stop("unalble to load Package::motifDb")
> BiocGenerics:::testPackage("motifStack")


RUNIT TEST PROTOCOL -- Tue Apr 09 04:29:03 2019 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
motifStack RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   9.37    0.48   10.06 

motifStack.Rcheck/tests_x64/runTests.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.

> require("motifStack") || stop("unable to load Package:motifStack")
Loading required package: motifStack
Loading required package: grImport2
Loading required package: grid
Loading required package: MotIV
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


Attaching package: 'MotIV'

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

    filter

Loading required package: ade4

Attaching package: 'ade4'

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

    score

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

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: XVector

Attaching package: 'Biostrings'

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

    strsplit

[1] TRUE
> #require("MotifDb") || stop("unalble to load Package::motifDb")
> BiocGenerics:::testPackage("motifStack")


RUNIT TEST PROTOCOL -- Tue Apr 09 04:29:15 2019 
*********************************************** 
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
motifStack RUnit Tests - 10 test functions, 0 errors, 0 failures
Number of test functions: 10 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  11.57    0.50   12.06 

Example timings

motifStack.Rcheck/examples_i386/motifStack-Ex.timings

nameusersystemelapsed
DNAmotifAlignment1.160.001.16
browseMotifs3.840.835.50
colorset000
getRankedUniqueMotifs000
highlightCol000
importMatrix0.030.000.03
mergeMotifs0.170.000.18
motifCircos000
motifCloud000
motifPiles0.010.000.01
motifSignature000
motifStack000
ouNode-class0.020.000.02
pcm-class0.580.020.59
pcm-methods000
pfm-class0.100.040.14
pfm-methods0.010.000.01
pfm2pwm0.160.000.16
plotAffinityLogo0.970.051.08
plotMotifLogo0.320.000.31
plotMotifLogoA0.290.000.30
plotMotifLogoStack0.280.170.45
plotMotifLogoStackWithTree2.680.052.72
plotMotifOverMotif0.400.000.41
plotMotifStackWithPhylog000
plotMotifStackWithRadialPhylog000
psam-class1.080.001.07
psam-methods0.010.000.02
readPCM0.020.000.01
reorderUPGMAtree000

motifStack.Rcheck/examples_x64/motifStack-Ex.timings

nameusersystemelapsed
DNAmotifAlignment0.190.020.20
browseMotifs4.560.144.77
colorset000
getRankedUniqueMotifs000
highlightCol000
importMatrix0.020.000.01
mergeMotifs0.140.000.14
motifCircos000
motifCloud000
motifPiles000
motifSignature0.010.000.01
motifStack000
ouNode-class000
pcm-class0.660.000.66
pcm-methods0.020.000.01
pfm-class0.180.020.21
pfm-methods0.020.000.01
pfm2pwm0.200.010.22
plotAffinityLogo1.100.021.11
plotMotifLogo0.480.000.48
plotMotifLogoA0.390.000.40
plotMotifLogoStack0.360.010.37
plotMotifLogoStackWithTree303
plotMotifOverMotif0.580.020.59
plotMotifStackWithPhylog0.010.000.02
plotMotifStackWithRadialPhylog000
psam-class0.800.010.81
psam-methods0.000.020.02
readPCM0.020.000.01
reorderUPGMAtree000