BioC 3.1: CHECK report for tigre on petty

Package: tigre

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings tigre_1.22.0.tar.gz

StartedAt: 2015-10-09 02:20:58 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:24:04 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 185.4 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_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/tigre.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tigre/DESCRIPTION’ ... OK
* this is package ‘tigre’ version ‘1.22.0’
* 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 ‘tigre’ can be installed ... [14s/14s] 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 ... NOTE
'library' or 'require' calls in package code:
  ‘lumi’ ‘puma’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
processData: no visible global function definition for ‘prcfive’
processData: no visible global function definition for ‘prctwfive’
processData: no visible global function definition for ‘prcfifty’
processData: no visible global function definition for ‘prcsevfive’
processData: no visible global function definition for ‘prcninfive’
processData: no visible global function definition for ‘se.exprs’
updateObject,scoreList: no visible global function definition for
  ‘getObjectSlots’
* 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 ... [16s/16s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
processData 5.078  0.133   5.214
* 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/tigre.Rcheck/00check.log’
for details.

* installing *source* package ‘tigre’ ...
** libs
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2 -Wall  -c miscCFunctions.c -o miscCFunctions.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -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 -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-3.1-bioc/meat/tigre.Rcheck/tigre/libs
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (tigre)

name	user	system	elapsed
ExpressionTimeSeries-class	0.003	0.000	0.003
GPLearn	2.730	0.093	3.108
GPModel-class	0.002	0.001	0.002
GPPlot	0.002	0.000	0.002
GPRankTargets	0.001	0.001	0.001
SCGoptim	0.001	0.000	0.001
expTransform	0.002	0.000	0.001
export	0.002	0.000	0.003
generateModels	0.001	0.000	0.002
gpsimCreate	0.000	0.000	0.001
kernCompute	0.002	0.000	0.002
kernCreate	0.009	0.001	0.009
kernDiagGradX	0.003	0.000	0.003
kernGradient	0.003	0.001	0.003
lnDiffErfs	0.002	0.000	0.001
modelDisplay	0.267	0.002	0.269
modelExpandParam	0.002	0.000	0.001
modelExtractParam	0.259	0.001	0.261
modelGradient	0.358	0.002	0.359
modelTieParam	0.008	0.001	0.008
optimiDefaultConstraint	0.001	0.000	0.002
plotTimeseries	0.501	0.010	0.529
processData	5.078	0.133	5.214
scoreList-class	0.002	0.000	0.003
tigre-package	0.001	0.000	0.001