Package: contiBAIT

Version: 1.6.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings contiBAIT_1.6.0.tar.gz

StartedAt: 2018-04-11 22:31:26 -0400 (Wed, 11 Apr 2018)

EndedAt: 2018-04-11 22:35:39 -0400 (Wed, 11 Apr 2018)

EllapsedTime: 253.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: contiBAIT.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings contiBAIT_1.6.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/contiBAIT.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘contiBAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘contiBAIT’ version ‘1.6.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘contiBAIT’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.4Mb
* 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
* 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
clusterContigs.func : runOnce: no visible global function definition
  for ‘runif’
locateMisorients.func: no visible global function definition for
  ‘unstrand’
makeBoxPlot.func: no visible global function definition for ‘boxplot’
makeChrTable: no visible global function definition for ‘queryHits’
makeChrTable: no visible global function definition for ‘subjectHits’
mergeFlankedLGs.func: no visible binding for global variable ‘head’
mergeFlankedLGs.func : <anonymous>: no visible global function
  definition for ‘head’
mergeFlankedLGs.func : <anonymous>: no visible global function
  definition for ‘tail’
plotContigOrder.func: no visible global function definition for ‘lm’
plotLGDistances.func: no visible global function definition for
  ‘legend’
plotWCdistribution.func : <anonymous>: no visible global function
  definition for ‘hist’
plotWCdistribution.func: no visible global function definition for
  ‘rbinom’
plotWCdistribution.func: no visible global function definition for
  ‘boxplot’
plotWCdistribution.func: no visible global function definition for
  ‘lines’
plotWCdistribution.func: no visible global function definition for
  ‘text’
clusterContigs,StrandStateMatrix : runOnce: no visible global function
  definition for ‘runif’
locateMisorients,GRanges: no visible global function definition for
  ‘unstrand’
makeBoxPlot,ChrTable-LinkageGroupList: no visible global function
  definition for ‘boxplot’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix: no visible binding
  for global variable ‘head’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix : <anonymous>: no
  visible global function definition for ‘head’
mergeFlankedLGs,LinkageGroupList-StrandStateMatrix : <anonymous>: no
  visible global function definition for ‘tail’
plotContigOrder,ContigOrdering: no visible global function definition
  for ‘lm’
plotLGDistances,LinkageGroupList-StrandStateMatrix: no visible global
  function definition for ‘legend’
plotWCdistribution,StrandFreqMatrix : <anonymous>: no visible global
  function definition for ‘hist’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘rbinom’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘boxplot’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘lines’
plotWCdistribution,StrandFreqMatrix: no visible global function
  definition for ‘text’
show,ContigOrdering: no visible global function definition for ‘head’
show,ContigOrdering: no visible global function definition for ‘tail’
show,LibraryGroupList: no visible global function definition for ‘head’
show,LibraryGroupList: no visible global function definition for ‘tail’
show,LinkageGroupList: no visible global function definition for ‘head’
show,LinkageGroupList: no visible global function definition for ‘tail’
show,StrandStateList: no visible global function definition for ‘head’
show,StrandStateList: no visible global function definition for ‘tail’
Undefined global functions or variables:
  boxplot head hist legend lines lm queryHits rbinom runif subjectHits
  tail text unstrand
Consider adding
  importFrom("graphics", "boxplot", "hist", "legend", "lines", "text")
  importFrom("stats", "lm", "rbinom", "runif")
  importFrom("utils", "head", "tail")
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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... WARNING
Found the following significant warnings:

  Warning: 'switch' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
           user system elapsed
contiBAIT 7.368  0.132   7.505
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.

* installing *source* package ‘contiBAIT’ ...
** libs
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c computeSim.cpp -o computeSim.o
g++  -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.6-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.6-bioc/R/library/BH/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c orderContigsGreedy.cpp -o orderContigsGreedy.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o contiBAIT.so computeSim.o orderContigsGreedy.o -lm -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.6-bioc/meat/contiBAIT.Rcheck/contiBAIT/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (contiBAIT)

name	user	system	elapsed
BAIT	0	0	0
ContigOrdering	0.000	0.000	0.002
LibraryGroupList	0.008	0.000	0.007
LinkageGroupList	0	0	0
OrientationFrame	0.004	0.000	0.008
StrandFreqMatrix	0.028	0.004	0.035
StrandReadMatrix	0.012	0.000	0.011
StrandStateMatrix	0.000	0.000	0.001
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method	1.100	0.000	1.102
clusterContigs-StrandStateMatrix-method	1.200	0.000	1.203
contiBAIT	7.368	0.132	7.505
findSimilarLibraries	1.924	0.236	2.187
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method	2.680	0.008	2.692
makeBoxPlot	0.028	0.000	0.027
makeChrTable	1.316	0.048	1.364
orderAllLinkageGroups	0.336	0.004	0.340
plotContigOrder	0.608	0.004	0.614
plotLGDistances-LinkageGroupList-StrandStateMatrix-method	0.824	0.000	0.824
plotWCdistribution-StrandFreqMatrix-method	0.092	0.000	0.090
preprocessStrandTable-StrandFreqMatrix-method	0.2	0.0	0.2
reorientAndMergeLGs	1.084	0.000	1.086
strandSeqFreqTable	3.092	0.020	3.115
thoroughBed	0.032	0.000	0.033
writeBed	0	0	0