BioC 3.4: CHECK report for tigre on malbec1

Package: tigre

Version: 1.28.1

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings tigre_1.28.1.tar.gz

StartedAt: 2017-04-15 01:37:15 -0400 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:39:08 -0400 (Sat, 15 Apr 2017)

EllapsedTime: 113.1 seconds

RetCode: 0

Status:  OK

CheckDir: tigre.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings tigre_1.28.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/tigre.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tigre/DESCRIPTION’ ... OK
* this is package ‘tigre’ version ‘1.28.1’
* 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 ‘tigre’ 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
GPPlot: no visible global function definition for ‘polygon’
export.scores: no visible global function definition for ‘png’
export.scores: no visible global function definition for ‘dev.off’
gpdisimLogLikeGradients: no visible global function definition for
  ‘tail’
[,scoreList: no visible global function definition for ‘slotNames’
c,scoreList: no visible global function definition for ‘slotNames’
Undefined global functions or variables:
  dev.off png polygon slotNames tail
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "polygon")
  importFrom("methods", "slotNames")
  importFrom("utils", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 compiled code ... 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
processData 5.228  0.092   5.881
* 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-3.4-bioc/meat/tigre.Rcheck/00check.log’
for details.

* installing *source* package ‘tigre’ ...
** libs
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c miscCFunctions.c -o miscCFunctions.o
gcc -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o tigre.so miscCFunctions.o -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/meat/tigre.Rcheck/tigre/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 (tigre)

name	user	system	elapsed
ExpressionTimeSeries-class	0.000	0.000	0.003
GPLearn	1.500	0.024	1.656
GPModel-class	0.000	0.000	0.001
GPPlot	0	0	0
GPRankTargets	0.000	0.000	0.001
SCGoptim	0	0	0
expTransform	0	0	0
export	0.000	0.000	0.001
generateModels	0	0	0
gpsimCreate	0	0	0
kernCompute	0.000	0.000	0.001
kernCreate	0.004	0.000	0.003
kernDiagGradX	0.000	0.000	0.001
kernGradient	0.000	0.000	0.001
lnDiffErfs	0.004	0.000	0.000
modelDisplay	0.156	0.000	0.156
modelExpandParam	0	0	0
modelExtractParam	0.128	0.000	0.128
modelGradient	0.184	0.000	0.181
modelTieParam	0.004	0.000	0.003
optimiDefaultConstraint	0	0	0
plotTimeseries	0.120	0.000	0.119
processData	5.228	0.092	5.881
scoreList-class	0.000	0.000	0.001
tigre-package	0	0	0