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CHECK report for PWMEnrich on tokay2

This page was generated on 2018-10-17 08:36:21 -0400 (Wed, 17 Oct 2018).

Package 1153/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
PWMEnrich 4.16.0
Robert Stojnic
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/PWMEnrich
Branch: RELEASE_3_7
Last Commit: 43403bb
Last Changed Date: 2018-04-30 10:35:25 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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

Summary

Package: PWMEnrich
Version: 4.16.0
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings PWMEnrich_4.16.0.tar.gz
StartedAt: 2018-10-17 04:08:05 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 04:11:04 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 179.5 seconds
RetCode: 0
Status:  OK  
CheckDir: PWMEnrich.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings PWMEnrich_4.16.0.tar.gz
###
##############################################################################
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/PWMEnrich.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'PWMEnrich/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'PWMEnrich' version '4.16.0'
* 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 'PWMEnrich' 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
'library' or 'require' calls in package code:
  'PWMEnrich.Dmelanogaster.background' 'PWMEnrich.Hsapiens.background'
  'PWMEnrich.Mmusculus.background' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colMedians: no visible binding for global variable 'median'
getPromoters: no visible global function definition for
  'providerVersion'
getPromoters: no visible global function definition for 'data'
gevPerSequence: no visible global function definition for 'predict.lm'
logNormPval: no visible global function definition for 'plnorm'
makePWMGEVBackground : <anonymous>: no visible global function
  definition for 'lm'
makePWMLognBackground : dlnorm.lcen: no visible global function
  definition for 'dlnorm'
makePWMLognBackground : dlnorm.lcen: no visible global function
  definition for 'plnorm'
makePWMLognBackground: no visible global function definition for
  'quantile'
makePWMLognBackground: no visible global function definition for
  'median'
makePWMLognBackground: no visible global function definition for
  'optimize'
makePWMPvalCutoffBackground: no visible global function definition for
  'quantile'
makePWMPvalCutoffBackground: no visible global function definition for
  'ecdf'
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for 'na.omit'
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for 'quantile'
makePWMPvalCutoffBackgroundFromSeq: no visible global function
  definition for 'ecdf'
motifEcdf : <anonymous>: no visible global function definition for
  'na.omit'
motifEcdf: no visible binding for global variable 'ecdf'
motifEnrichment: no visible binding for global variable 'qlnorm'
motifEnrichment : <anonymous>: no visible global function definition
  for 'pchisq'
motifScores: no visible global function definition for 'mclapply'
motifScoresBigMemory: no visible global function definition for
  'mclapply'
plotMotifScores: no visible global function definition for 'palette'
plotMotifScores: no visible global function definition for 'col2rgb'
plotMotifScores: no visible global function definition for 'rgb'
plotMotifScores: no visible global function definition for 'par'
plotMotifScores: no visible global function definition for 'lines'
plotMotifScores: no visible global function definition for 'polygon'
plotMotifScores: no visible global function definition for 'rect'
plotMotifScores: no visible global function definition for 'text'
registerCoresPWMEnrich: no visible global function definition for
  'detectCores'
tryAllMotifAlignments : <anonymous>: no visible global function
  definition for 'cor'
Undefined global functions or variables:
  col2rgb cor data detectCores dlnorm ecdf lines lm mclapply median
  na.omit optimize palette par pchisq plnorm polygon predict.lm
  providerVersion qlnorm quantile rect rgb text
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
  importFrom("graphics", "lines", "par", "polygon", "rect", "text")
  importFrom("stats", "cor", "dlnorm", "ecdf", "lm", "median", "na.omit",
             "optimize", "pchisq", "plnorm", "predict.lm", "qlnorm",
             "quantile")
  importFrom("utils", "data")
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 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 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.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-3.7-bioc/meat/PWMEnrich.Rcheck/00check.log'
for details.



Installation output

PWMEnrich.Rcheck/00install.out

##############################################################################
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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/PWMEnrich_4.16.0.tar.gz && rm -rf PWMEnrich.buildbin-libdir && mkdir PWMEnrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PWMEnrich.buildbin-libdir PWMEnrich_4.16.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL PWMEnrich_4.16.0.zip && rm PWMEnrich_4.16.0.tar.gz PWMEnrich_4.16.0.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 3482k  100 3482k    0     0  31.8M      0 --:--:-- --:--:-- --:--:-- 34.0M

install for i386

* installing *source* package 'PWMEnrich' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'PWMEnrich'
    finding HTML links ... done
    MotifEnrichmentReport                   html  
    MotifEnrichmentResults                  html  
    PFMtoPWM                                html  
    PWM                                     html  
    PWMCutoffBackground                     html  
    PWMEmpiricalBackground                  html  
    PWMGEVBackground                        html  
    PWMLognBackground                       html  
    PWMUnscaled                             html  
    as.data.frame-commaMotifEnrichmentReport-method
                                            html  
    getBackgroundFrequencies                html  
    groupReport-commaMotifEnrichmentResults-method
                                            html  
    makeBackground                          html  
    makePWMCutoffBackground                 html  
    makePWMEmpiricalBackground              html  
    makePWMGEVBackground                    html  
    makePWMLognBackground                   html  
    makePWMPvalCutoffBackground             html  
    makePWMPvalCutoffBackgroundFromSeq      html  
    makePriors                              html  
    motifDiffEnrichment                     html  
    motifEcdf                               html  
    motifEnrichment                         html  
    motifIC                                 html  
    motifRankingForGroup-commaMotifEnrichmentResults-method
                                            html  
    motifRankingForSequence-commaMotifEnrichmentResults-method
                                            html  
    motifScores                             html  
    motifSimilarity                         html  
    operators-MotifEnrichmentReport         html  
    operators-MotifEnrichmentResults        html  
    operators-PWM                           html  
    operators-PWMCutoffBackground           html  
    operators-PWMEmpiricalBackground        html  
    operators-PWMGEVBackground              html  
    operators-PWMLognBackground             html  
    plot                                    html  
    plotMotifScores                         html  
    plotMultipleMotifs                      html  
    plotTopMotifsGroup-commaMotifEnrichmentResults-method
                                            html  
    plotTopMotifsSequence-commaMotifEnrichmentResults-method
                                            html  
    readMotifs                              html  
    registerCoresPWMEnrich                  html  
    reverseComplement                       html  
    scanWithPWM                             html  
    seqLogoGrid                             html  
    sequenceReport-commaMotifEnrichmentResults-method
                                            html  
    subsetting-PWMCutoffBackground          html  
    subsetting-PWMEmpiricalBackground       html  
    subsetting-PWMGEVBackground             html  
    subsetting-PWMLognBackground            html  
    toPWM                                   html  
    useBigMemoryPWMEnrich                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'PWMEnrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PWMEnrich' as PWMEnrich_4.16.0.zip
* DONE (PWMEnrich)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'PWMEnrich' successfully unpacked and MD5 sums checked
In R CMD INSTALL

Tests output

PWMEnrich.Rcheck/tests_i386/test-all.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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(PWMEnrich)
Loading required package: grid
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, 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: 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

> 
> test_package("PWMEnrich")
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
NOTE: Using the 'default' algorithm to infer background parameters,
      appropriate for all organisms except human.
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
NOTE: Using the 'default' algorithm to infer background parameters,
      appropriate for all organisms except human.
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
== testthat results  ===========================================================
OK: 48 SKIPPED: 0 FAILED: 0
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
> 
> 
> proc.time()
   user  system elapsed 
   4.31    0.20    5.21 

PWMEnrich.Rcheck/tests_x64/test-all.Rout


R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
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(PWMEnrich)
Loading required package: grid
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, 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: 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

> 
> test_package("PWMEnrich")
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
NOTE: Using the 'default' algorithm to infer background parameters,
      appropriate for all organisms except human.
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
NOTE: Using the 'default' algorithm to infer background parameters,
      appropriate for all organisms except human.
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
== testthat results  ===========================================================
OK: 48 SKIPPED: 0 FAILED: 0
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
> 
> 
> proc.time()
   user  system elapsed 
   5.85    0.21    6.06 

Example timings

PWMEnrich.Rcheck/examples_i386/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM2.220.332.89
PWMUnscaled0.370.030.41
getBackgroundFrequencies000
groupReport-commaMotifEnrichmentResults-method2.280.222.57
makeBackground0.000.000.07
makePWMCutoffBackground000
makePWMEmpiricalBackground000
makePWMGEVBackground000
makePWMLognBackground000
makePWMPvalCutoffBackground000
makePWMPvalCutoffBackgroundFromSeq000
makePriors0.010.000.01
motifDiffEnrichment2.360.002.36
motifEnrichment3.750.003.82
motifIC0.070.010.23
motifRankingForGroup-commaMotifEnrichmentResults-method2.090.022.11
motifRankingForSequence-commaMotifEnrichmentResults-method2.670.012.69
motifScores4.950.024.97
motifSimilarity0.080.000.08
plot0.230.000.23
plotMotifScores0.130.000.13
plotTopMotifsGroup-commaMotifEnrichmentResults-method2.730.002.73
plotTopMotifsSequence-commaMotifEnrichmentResults-method2.800.032.83
readMotifs0.120.000.14
registerCoresPWMEnrich000
reverseComplement0.030.020.05
scanWithPWM0.080.000.08
sequenceReport-commaMotifEnrichmentResults-method3.970.003.97
toPWM1.940.202.14
useBigMemoryPWMEnrich000

PWMEnrich.Rcheck/examples_x64/PWMEnrich-Ex.timings

nameusersystemelapsed
PFMtoPWM1.80.22.0
PWMUnscaled0.240.020.25
getBackgroundFrequencies000
groupReport-commaMotifEnrichmentResults-method2.410.032.44
makeBackground000
makePWMCutoffBackground000
makePWMEmpiricalBackground000
makePWMGEVBackground000
makePWMLognBackground000
makePWMPvalCutoffBackground000
makePWMPvalCutoffBackgroundFromSeq000
makePriors000
motifDiffEnrichment2.390.002.39
motifEnrichment3.580.013.59
motifIC0.030.020.05
motifRankingForGroup-commaMotifEnrichmentResults-method1.970.021.98
motifRankingForSequence-commaMotifEnrichmentResults-method1.970.001.97
motifScores4.020.014.03
motifSimilarity0.080.000.08
plot0.210.000.22
plotMotifScores0.070.000.06
plotTopMotifsGroup-commaMotifEnrichmentResults-method2.460.032.48
plotTopMotifsSequence-commaMotifEnrichmentResults-method2.290.022.31
readMotifs0.080.000.08
registerCoresPWMEnrich000
reverseComplement0.030.000.03
scanWithPWM0.030.000.03
sequenceReport-commaMotifEnrichmentResults-method3.320.033.35
toPWM1.960.222.19
useBigMemoryPWMEnrich000