BioC 3.3: CHECK report for contiBAIT on zin2

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings contiBAIT_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/contiBAIT.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.0.0’
* 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 ... 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
* 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’
strandSeqFreqTable : overlapStrand: no visible binding for global
  variable ‘rname’
clusterContigs,StrandStateMatrix : runOnce: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  rname runif
Consider adding
  importFrom("stats", "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 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
           user system elapsed
contiBAIT 6.821  0.083   7.041
* 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 NOTE
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/contiBAIT.Rcheck/00check.log’
for details.

* installing *source* package ‘contiBAIT’ ...
** libs
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c computeSim.cpp -o computeSim.o
g++ -I/home/biocbuild/bbs-3.3-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.3-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.3-bioc/R/library/BH/include"   -fpic  -g -O2  -Wall -c orderContigsGreedy.cpp -o orderContigsGreedy.o
g++ -shared -L/home/biocbuild/bbs-3.3-bioc/R/lib -L/usr/local/lib -o contiBAIT.so computeSim.o orderContigsGreedy.o -lm -L/home/biocbuild/bbs-3.3-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.3-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	0.001	0.000	0.000
ContigOrdering	0.001	0.000	0.001
LinkageGroupList	0.002	0.000	0.003
OrientationFrame	0.005	0.000	0.005
StrandFreqMatrix	0.039	0.012	0.050
StrandReadMatrix	0.009	0.000	0.009
StrandStateMatrix	0.003	0.000	0.002
barplotLinkageGroupCalls-LinkageGroupList-ChrTable-method	0.352	0.000	0.355
clusterContigs-StrandStateMatrix-method	1.930	0.000	2.018
contiBAIT	6.821	0.083	7.041
ideogramPlot-StrandReadMatrix-StrandReadMatrix-ChrTable-method	1.861	0.000	2.250
makeBoxPlot	0.037	0.000	0.057
makeChrTable	0.573	0.000	0.739
mergeLinkageGroups	1.757	0.000	1.835
orderAllLinkageGroups	0.212	0.004	0.231
plotContigOrder	0.446	0.000	0.504
plotLGDistances-LinkageGroupList-StrandStateMatrix-method	0.193	0.000	0.199
plotWCdistribution-StrandFreqMatrix-method	0.121	0.004	0.130
preprocessStrandTable-StrandFreqMatrix-method	0.160	0.000	0.163
reorientLinkageGroups	1.609	0.012	1.648
strandSeqFreqTable	3.733	0.008	3.845
writeBed	0.000	0.000	0.001

BioC 3.3: CHECK report for contiBAIT on zin2

Summary

Command output