BioC 2.12: CHECK report for puma on petty

Package: puma

Version: 3.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch puma_3.2.1.tar.gz

StartedAt: 2013-10-08 23:32:22 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 23:42:46 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 624.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: puma.Rcheck

Warnings: 1

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/puma.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '3.2.1'
* 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 ... [18s/18s] 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 ... 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 ... 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 sizes of PDF files under 'inst/doc' ... NOTE
  'qpdf' made some significant size reductions:
     compacted 'puma.pdf' from 236Kb to 136Kb
  consider running tools::compactPDF() on these files
* checking installed files from 'inst/doc' ... OK
* checking examples ... [489s/497s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
puma-package     103.450  9.114 113.699
hcomb             66.708 12.538  80.035
pumaDE            62.342  7.337  71.712
pumaCombImproved  36.179  6.163  42.919
pumaClustii       39.642  0.467  40.503
DEResult-class    27.355  1.400  29.251
pumaComb          26.596  1.217  28.032
pumaPCA           22.692  1.001  24.077
plot-methods      21.929  1.015  23.327
calculateFC       11.737  0.237  12.129
calculateLimma     6.017  0.176   6.453
* 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 -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
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (puma)

name	user	system	elapsed
DEResult-class	27.355	1.400	29.251
PMmmgmos	0.009	0.003	0.014
bcomb	0.452	0.107	0.562
calcAUC	0.872	0.093	0.979
calculateFC	11.737	0.237	12.129
calculateLimma	6.017	0.176	6.453
calculateTtest	0.319	0.007	0.334
clusterNormE	0.132	0.008	0.143
clusterNormVar	0.182	0.021	0.206
createContrastMatrix	4.238	0.141	4.530
createDesignMatrix	2.932	0.102	3.150
erfc	0.011	0.005	0.018
exprReslt-class	1.811	0.094	2.687
gmoExon	0.013	0.008	0.022
hcomb	66.708	12.538	80.035
legend2	0.020	0.007	0.028
license.puma	0.015	0.005	0.021
matrixDistance	0.010	0.004	0.014
mgmos	0.012	0.006	0.017
mmgmos	0.012	0.006	0.017
normalisation.gs	0.038	0.011	0.050
numFP	0.011	0.006	0.018
numOfFactorsToUse	0.513	0.033	0.548
numTP	0.029	0.011	0.041
orig_pplr	0.406	0.080	0.492
plot-methods	21.929	1.015	23.327
plotErrorBars	0.834	0.074	0.948
plotHistTwoClasses	0.022	0.008	0.030
plotROC	0.675	0.061	0.743
pplr	0.405	0.083	0.492
puma-package	103.450	9.114	113.699
pumaClustii	39.642	0.467	40.503
pumaComb	26.596	1.217	28.032
pumaCombImproved	36.179	6.163	42.919
pumaDE	62.342	7.337	71.712
pumaFull	0.003	0.004	0.007
pumaNormalize	1.174	0.155	1.343
pumaPCA	22.692	1.001	24.077
pumaclust	3.692	0.029	3.833
removeUninformativeFactors	0.138	0.008	0.147