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 beta (2013-03-21 r62346)
* 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 '1.13.2'
* 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 ... [19s/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 ... [15s/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
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  -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/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
'.path.package' is deprecated.
Use 'path.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'tigre.Rnw' 
   'tigre_quick.Rnw' 
** 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	0.009
GPLearn	2.979	0.140	3.271
GPModel-class	0.033	0.001	0.035
GPPlot	0.050	0.004	0.054
GPRankTargets	0.071	0.004	0.074
SCGoptim	0.034	0.002	0.036
expTransform	0.033	0.002	0.035
export	0.080	0.004	0.085
generateModels	0.324	0.004	0.328
gpsimCreate	0.019	0.003	0.021
kernCompute	0.039	0.004	0.044
kernCreate	0.063	0.006	0.069
kernDiagGradX	0.037	0.003	0.053
kernGradient	0.036	0.002	0.038
lnDiffErfs	0.036	0.002	0.046
modelDisplay	0.356	0.012	0.378
modelExpandParam	0.068	0.001	0.078
modelExtractParam	0.355	0.024	0.390
modelGradient	0.506	0.014	0.535
modelTieParam	0.060	0.004	0.064
optimiDefaultConstraint	0.040	0.003	0.043
plotTimeseries	0.371	0.018	0.393
processData	0.763	0.023	0.789
scoreList-class	0.053	0.008	0.061
tigre-package	0.057	0.007	0.065

Summary

Command output