BioC 3.4: CHECK report for tigre on morelia

Package: tigre

Version: 1.28.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tigre_1.28.1.tar.gz

StartedAt: 2017-04-15 08:51:17 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 08:53:48 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 150.8 seconds

RetCode: 0

Status:  OK

CheckDir: tigre.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tigre_1.28.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/tigre.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 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
processData 5.251  0.153   5.727
* 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
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/tigre.Rcheck/00check.log’
for details.

* installing *source* package ‘tigre’ ...
** libs
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2  -c miscCFunctions.c -o miscCFunctions.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o tigre.so miscCFunctions.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/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	0.002	0.000	0.002
GPLearn	1.563	0.074	2.526
GPModel-class	0.001	0.000	0.001
GPPlot	0.000	0.001	0.001
GPRankTargets	0.001	0.000	0.001
SCGoptim	0.000	0.000	0.001
expTransform	0.001	0.000	0.001
export	0.002	0.001	0.002
generateModels	0.001	0.000	0.002
gpsimCreate	0.000	0.000	0.001
kernCompute	0.002	0.000	0.002
kernCreate	0.005	0.000	0.006
kernDiagGradX	0.002	0.000	0.002
kernGradient	0.002	0.000	0.002
lnDiffErfs	0.001	0.000	0.001
modelDisplay	0.153	0.005	0.157
modelExpandParam	0.001	0.000	0.001
modelExtractParam	0.150	0.005	0.154
modelGradient	0.191	0.003	0.194
modelTieParam	0.003	0.000	0.004
optimiDefaultConstraint	0.001	0.000	0.001
plotTimeseries	0.144	0.005	0.149
processData	5.251	0.153	5.727
scoreList-class	0.002	0.001	0.003
tigre-package	0.001	0.000	0.001