BioC 2.12: CHECK report for puma on lamb2

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/puma.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘puma/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘puma’ version ‘3.1.0’
* 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 ‘puma’ can be installed ... 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 ... WARNING
Foreign function call with ‘PACKAGE’ argument in a different package:
  .Call("ReadHeader", ..., PACKAGE = "affyio")
Undeclared package in foreign function calls:
   ‘affyio’
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* 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 ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/puma.Rcheck/puma/libs/puma.so’:
  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’
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Objects: ‘donlp2.o’, ‘user_eval.o’
  Found ‘stdout’, possibly from ‘stdout’ (C)
    Object: ‘donlp2.o’

Compiled code should not call functions 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 ... OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
puma-package     83.969  0.080  84.070
hcomb            54.404  0.060  54.481
pumaDE           52.244  0.052  52.305
pumaClustii      32.270  0.008  32.291
pumaCombImproved 29.185  0.036  29.315
pumaComb         21.966  0.016  21.987
DEResult-class   21.141  0.040  21.197
pumaPCA          15.853  0.004  15.859
plot-methods     15.521  0.012  15.538
calculateFC       9.949  0.144  10.105
calculateLimma    5.972  0.072   6.050
* checking PDF version of manual ... OK

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/puma.Rcheck/00check.log’
for details.

* installing *source* package ‘puma’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c PMmultimgmos.c -o PMmultimgmos.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c cregistration.c -o cregistration.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c donlp2.c -o donlp2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c gme.c -o gme.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c ipplr_c.c -o ipplr_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c multimgmos.c -o multimgmos.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c newx.c -o newx.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pplr_c.c -o pplr_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pumaclust_c.c -o pumaclust_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c pumaclustii_c.c -o pumaclustii_c.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c user_eval.c -o user_eval.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -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 -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/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	21.141	0.040	21.197
PMmmgmos	0.012	0.000	0.011
bcomb	0.140	0.008	0.147
calcAUC	0.460	0.076	0.552
calculateFC	9.949	0.144	10.105
calculateLimma	5.972	0.072	6.050
calculateTtest	0.212	0.000	0.210
clusterNormE	0.084	0.000	0.086
clusterNormVar	0.084	0.004	0.090
createContrastMatrix	2.516	0.004	2.522
createDesignMatrix	2.596	0.028	2.626
erfc	0.000	0.000	0.003
exprReslt-class	0.748	0.008	0.760
gmoExon	0.004	0.000	0.006
hcomb	54.404	0.060	54.481
legend2	0.012	0.000	0.014
license.puma	0.016	0.000	0.013
matrixDistance	0.008	0.000	0.007
mgmos	0.004	0.000	0.004
mmgmos	0.012	0.000	0.012
normalisation.gs	0.028	0.000	0.028
numFP	0.012	0.000	0.011
numOfFactorsToUse	0.300	0.008	0.308
numTP	0.028	0.000	0.028
orig_pplr	0.328	0.000	0.325
plot-methods	15.521	0.012	15.538
plotErrorBars	0.564	0.016	0.578
plotHistTwoClasses	0.032	0.000	0.030
plotROC	0.468	0.088	0.564
pplr	0.376	0.000	0.375
puma-package	83.969	0.080	84.070
pumaClustii	32.270	0.008	32.291
pumaComb	21.966	0.016	21.987
pumaCombImproved	29.185	0.036	29.315
pumaDE	52.244	0.052	52.305
pumaFull	0.000	0.000	0.004
pumaNormalize	1.040	0.004	1.045
pumaPCA	15.853	0.004	15.859
pumaclust	3.168	0.000	3.171
removeUninformativeFactors	0.084	0.000	0.085

Summary

Command output