BioC 2.13: CHECK report for tigre on zin1

Package: tigre

Version: 1.16.1

Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings tigre_1.16.1.tar.gz

StartedAt: 2014-04-05 04:21:05 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 04:23:10 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 125.0 seconds

RetCode: 0

Status:  OK

CheckDir: tigre.Rcheck

Warnings: 0

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/tigre.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘tigre/DESCRIPTION’ ... OK
* this is package ‘tigre’ version ‘1.16.1’
* 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 ... [9s/9s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BiocGenerics’ ‘Biobase’ ‘puma’ ‘annotate’
A package should be listed in only one of these fields.
* 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 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 ... OK
* 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 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 ... [8s/8s] OK
* 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

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/tigre.Rcheck/00check.log’
for details.

* installing *source* package ‘tigre’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c miscCFunctions.c -o miscCFunctions.o
gcc -std=gnu99 -shared -L/usr/local/lib -o tigre.so miscCFunctions.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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	0.116	0.004	0.122
GPLearn	1.600	0.032	1.709
GPModel-class	0.016	0.000	0.015
GPPlot	0.032	0.004	0.038
GPRankTargets	0.028	0.000	0.027
SCGoptim	0.020	0.000	0.021
expTransform	0.024	0.000	0.021
export	0.044	0.000	0.044
generateModels	0.036	0.000	0.035
gpsimCreate	0.012	0.000	0.014
kernCompute	0.024	0.000	0.022
kernCreate	0.024	0.000	0.027
kernDiagGradX	0.016	0.000	0.015
kernGradient	0.024	0.000	0.022
lnDiffErfs	0.008	0.000	0.010
modelDisplay	0.220	0.000	0.219
modelExpandParam	0.020	0.000	0.022
modelExtractParam	0.236	0.000	0.237
modelGradient	0.448	0.000	0.447
modelTieParam	0.020	0.004	0.026
optimiDefaultConstraint	0.004	0.004	0.009
plotTimeseries	0.204	0.016	0.220
processData	0.368	0.008	0.376
scoreList-class	0.02	0.00	0.02
tigre-package	0.028	0.000	0.028