BioC 2.12: CHECK report for puma on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/puma.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 'puma/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'puma' version '3.1.1'
* 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 'puma' can be installed ... [15s/16s] 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 ... WARNING
File '/Users/biocbuild/bbs-2.12-bioc/meat/puma.Rcheck/puma/libs/puma.so':
  Found '___stderrp', possibly from 'stderr' (C)
    Objects: 'donlp2.o', 'user_eval.o'
  Found '___stdoutp', possibly from 'stdout' (C)
    Object: 'donlp2.o'
  Found '_exit', possibly from 'exit' (C)
    Objects: 'donlp2.o', 'user_eval.o'
  Found '_printf', possibly from 'printf' (C)
    Object: 'donlp2.o'
  Found '_putchar', possibly from 'putchar' (C)
    Object: 'donlp2.o'
  Found '_puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'donlp2.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [444s/450s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
puma-package     99.010  5.155 104.951
pumaDE           59.877  4.361  64.372
hcomb            58.160  4.787  64.862
pumaClustii      41.214  0.350  42.306
pumaCombImproved 31.103  1.913  33.173
DEResult-class   28.274  1.401  29.919
pumaComb         26.925  0.732  28.099
plot-methods     20.538  0.899  21.526
pumaPCA          19.375  0.701  20.138
calculateFC      10.751  0.297  11.103
calculateLimma    5.415  0.161   5.676
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/puma.Rcheck/00check.log'
for details.

* installing *source* package 'puma' ...
** 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 PMmultimgmos.c -o PMmultimgmos.o
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 cregistration.c -o cregistration.o
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 donlp2.c -o donlp2.o
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 gme.c -o gme.o
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 ipplr_c.c -o ipplr_c.o
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 multimgmos.c -o multimgmos.o
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 newx.c -o newx.o
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 pplr_c.c -o pplr_c.o
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 pumaclust_c.c -o pumaclust_c.o
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 pumaclustii_c.c -o pumaclustii_c.o
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 user_eval.c -o user_eval.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 puma.so PMmultimgmos.o cregistration.o donlp2.o gme.o ipplr_c.o multimgmos.o newx.o pplr_c.o pumaclust_c.o pumaclustii_c.o user_eval.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/puma.Rcheck/puma/libs
** R
** data
** demo
** 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 (puma)

name	user	system	elapsed
DEResult-class	28.274	1.401	29.919
PMmmgmos	0.007	0.004	0.011
bcomb	0.450	0.106	0.556
calcAUC	0.659	0.098	0.777
calculateFC	10.751	0.297	11.103
calculateLimma	5.415	0.161	5.676
calculateTtest	0.259	0.007	0.284
clusterNormE	0.108	0.009	0.124
clusterNormVar	0.113	0.014	0.143
createContrastMatrix	3.164	0.121	3.404
createDesignMatrix	2.325	0.115	2.446
erfc	0.003	0.005	0.008
exprReslt-class	1.445	0.083	1.654
gmoExon	0.015	0.009	0.027
hcomb	58.160	4.787	64.862
legend2	0.023	0.010	0.033
license.puma	0.016	0.007	0.024
matrixDistance	0.013	0.005	0.019
mgmos	0.304	0.020	0.325
mmgmos	0.004	0.006	0.010
normalisation.gs	0.029	0.012	0.041
numFP	0.011	0.009	0.021
numOfFactorsToUse	0.437	0.030	0.470
numTP	0.026	0.011	0.038
orig_pplr	0.418	0.082	0.502
plot-methods	20.538	0.899	21.526
plotErrorBars	1.035	0.079	1.118
plotHistTwoClasses	0.031	0.011	0.043
plotROC	0.611	0.065	0.686
pplr	0.355	0.019	0.375
puma-package	99.010	5.155	104.951
pumaClustii	41.214	0.350	42.306
pumaComb	26.925	0.732	28.099
pumaCombImproved	31.103	1.913	33.173
pumaDE	59.877	4.361	64.372
pumaFull	0.336	0.010	0.347
pumaNormalize	2.114	0.163	2.338
pumaPCA	19.375	0.701	20.138
pumaclust	4.062	0.028	4.101
removeUninformativeFactors	0.099	0.009	0.108

Summary

Command output