BioC 2.12: CHECK report for tigre on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/tigre.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'tigre/DESCRIPTION' ... OK
* this is package 'tigre' version '1.14.0'
* 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 ... [17s/19s] OK
* checking installed package size ... OK
* checking package 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 for unstated 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 ... NOTE
  No methods found in "Biobase" for requests: geneNames
* 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 examples ... [16s/16s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-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    -fPIC  -mtune=native -g -O2 -Wall -pedantic -Wconversion -c miscCFunctions.c -o miscCFunctions.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -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-2.12-bioc/meat/tigre.Rcheck/tigre/libs
** R
** data
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: geneNames
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: geneNames
* DONE (tigre)

name	user	system	elapsed
ExpressionTimeSeries-class	0.007	0.002	0.010
GPLearn	3.984	0.150	4.432
GPModel-class	0.035	0.002	0.037
GPPlot	0.065	0.004	0.093
GPRankTargets	0.051	0.003	0.055
SCGoptim	0.034	0.002	0.037
expTransform	0.030	0.002	0.032
export	0.087	0.005	0.095
generateModels	0.052	0.003	0.056
gpsimCreate	0.016	0.001	0.018
kernCompute	0.051	0.003	0.053
kernCreate	0.072	0.004	0.076
kernDiagGradX	0.034	0.001	0.036
kernGradient	0.035	0.002	0.037
lnDiffErfs	0.034	0.002	0.036
modelDisplay	0.663	0.010	0.672
modelExpandParam	0.053	0.005	0.058
modelExtractParam	0.355	0.013	0.370
modelGradient	0.483	0.008	0.493
modelTieParam	0.057	0.005	0.063
optimiDefaultConstraint	0.038	0.002	0.040
plotTimeseries	0.339	0.020	0.363
processData	0.747	0.030	0.789
scoreList-class	0.055	0.006	0.060
tigre-package	0.065	0.004	0.077

Summary

Command output