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CHECK report for traseR on tokay1

This page was generated on 2018-04-12 13:26:37 -0400 (Thu, 12 Apr 2018).

Package 1417/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
traseR 1.8.0
li chen
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/traseR
Branch: RELEASE_3_6
Last Commit: ecd8054
Last Changed Date: 2017-10-30 12:40:53 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: traseR
Version: 1.8.0
Command: rm -rf traseR.buildbin-libdir traseR.Rcheck && mkdir traseR.buildbin-libdir traseR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=traseR.buildbin-libdir traseR_1.8.0.tar.gz >traseR.Rcheck\00install.out 2>&1 && cp traseR.Rcheck\00install.out traseR-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=traseR.buildbin-libdir --install="check:traseR-install.out" --force-multiarch --no-vignettes --timings traseR_1.8.0.tar.gz
StartedAt: 2018-04-12 03:39:30 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 03:45:17 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 347.2 seconds
RetCode: 0
Status:  OK  
CheckDir: traseR.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf traseR.buildbin-libdir traseR.Rcheck && mkdir traseR.buildbin-libdir traseR.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=traseR.buildbin-libdir traseR_1.8.0.tar.gz >traseR.Rcheck\00install.out 2>&1 && cp traseR.Rcheck\00install.out traseR-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=traseR.buildbin-libdir --install="check:traseR-install.out" --force-multiarch --no-vignettes --timings traseR_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/traseR.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 'traseR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'traseR' version '1.8.0'
* 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 'traseR' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
* 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 ... NOTE
enrichTest: no visible global function definition for 'chisq.test'
enrichTest: no visible global function definition for 'binom.test'
enrichTest: no visible global function definition for 'phyper'
plotContext: no visible global function definition for 'subjectHits'
plotContext: no visible global function definition for 'pie'
plotContext: no visible global function definition for 'rainbow'
plotGene: no visible global function definition for 'plot'
plotGene: no visible global function definition for 'mtext'
plotGene: no visible global function definition for 'axis'
plotGene: no visible global function definition for 'box'
plotGene: no visible global function definition for 'points'
plotGene: no visible global function definition for 'text'
plotGene: no visible global function definition for 'arrows'
plotGene: no visible global function definition for 'segments'
plotInterval: no visible global function definition for 'subjectHits'
plotInterval: no visible global function definition for 'plot'
plotInterval: no visible global function definition for 'mtext'
plotInterval: no visible global function definition for 'axis'
plotInterval: no visible global function definition for 'box'
plotInterval: no visible global function definition for 'points'
plotInterval: no visible global function definition for 'text'
plotInterval: no visible global function definition for 'arrows'
plotInterval: no visible global function definition for 'segments'
plotPvalue: no visible global function definition for 'boxplot'
plotPvalue: no visible global function definition for 'density'
plotPvalue: no visible global function definition for 'plot'
plotPvalue: no visible global function definition for 'lines'
plotPvalue: no visible global function definition for 'legend'
plotPvalue: no visible global function definition for 'subjectHits'
plotSNP: no visible global function definition for 'plot'
plotSNP: no visible global function definition for 'mtext'
plotSNP: no visible global function definition for 'axis'
plotSNP: no visible global function definition for 'box'
plotSNP: no visible global function definition for 'points'
plotSNP: no visible global function definition for 'text'
plotSNP: no visible global function definition for 'arrows'
plotSNP: no visible global function definition for 'segments'
queryKeyword: no visible global function definition for 'subjectHits'
querySNP: no visible global function definition for 'subjectHits'
traseR: no visible global function definition for 'seqlengths'
traseR: no visible global function definition for 'subjectHits'
traseR: no visible global function definition for 'runif'
traseR: no visible global function definition for 'Rle'
traseR: no visible global function definition for 'queryHits'
traseR: no visible global function definition for 'p.adjust'
Undefined global functions or variables:
  Rle arrows axis binom.test box boxplot chisq.test density legend
  lines mtext p.adjust phyper pie plot points queryHits rainbow runif
  segments seqlengths subjectHits text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "arrows", "axis", "box", "boxplot", "legend",
             "lines", "mtext", "pie", "plot", "points", "segments",
             "text")
  importFrom("stats", "binom.test", "chisq.test", "density", "p.adjust",
             "phyper", "runif")
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 installed files from 'inst/doc' ... 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 '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: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/traseR.Rcheck/00check.log'
for details.



Installation output

traseR.Rcheck/00install.out


install for i386

* installing *source* package 'traseR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'traseR'
    finding HTML links ... done
    CEU                                     html  
    Tcell                                   html  
    plots                                   html  
    print.traseR                            html  
    querys                                  html  
    taSNP                                   html  
    taSNPLD                                 html  
    traseR-package                          html  
    traseR                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'traseR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'traseR' as traseR_1.8.0.zip
* DONE (traseR)
In R CMD INSTALL
In R CMD INSTALL

Tests output

traseR.Rcheck/tests_i386/runTests.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.

> BiocGenerics:::testPackage("traseR")

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, 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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'Biostrings'

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

    strsplit

There are  128094211 bp in the query region, accounting for  0.0421875469310327  of the genome.
There are  573 traits in the analysis.
There are  33 trait class in the analysis.
100 traits have been tested!
200 traits have been tested!
300 traits have been tested!
400 traits have been tested!
500 traits have been tested!
10 trait class have been tested!
20 trait class have been tested!
30 trait class have been tested!


RUNIT TEST PROTOCOL -- Thu Apr 12 03:44:52 2018 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
traseR RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  19.21    0.34   19.56 

traseR.Rcheck/tests_x64/runTests.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.

> BiocGenerics:::testPackage("traseR")

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, 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


Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'Biostrings'

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

    strsplit

There are  128094211 bp in the query region, accounting for  0.0421875469310327  of the genome.
There are  573 traits in the analysis.
There are  33 trait class in the analysis.
100 traits have been tested!
200 traits have been tested!
300 traits have been tested!
400 traits have been tested!
500 traits have been tested!
10 trait class have been tested!
20 trait class have been tested!
30 trait class have been tested!


RUNIT TEST PROTOCOL -- Thu Apr 12 03:45:13 2018 
*********************************************** 
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
traseR RUnit Tests - 4 test functions, 0 errors, 0 failures
Number of test functions: 4 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  20.40    0.29   20.70 

Example timings

traseR.Rcheck/examples_i386/traseR-Ex.timings

nameusersystemelapsed
plots1.970.092.07
print.traseR3.060.063.13
querys1.750.001.75
traseR3.380.033.41

traseR.Rcheck/examples_x64/traseR-Ex.timings

nameusersystemelapsed
plots3.280.123.40
print.traseR4.410.094.50
querys1.910.081.98
traseR4.260.034.30