BioC 2.12: CHECK report for cn.farms on george2

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck’
* using R version 3.0.1 (2013-05-16)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cn.farms/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cn.farms’ version ‘1.8.0’
* 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 ‘cn.farms’ can be installed ... [28s/32s] 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 R/sysdata.rda ... 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 ... [37s/39s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mlSummarization 7.224  0.168   7.629
slSummarization 5.993  0.056   6.132
fragLengCorr    5.085  0.012   5.397
* 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

* installing *source* package ‘cn.farms’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)’:
laplace.cpp:442:6: warning: unused variable ‘method’ [-Wunused-variable]
laplace.cpp: In function ‘void computeParameters(double, double, double, double, double, double, int&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&, double&)’:
laplace.cpp:368:57: warning: ‘I1right’ may be used uninitialized in this function [-Wuninitialized]
laplace.cpp:367:53: warning: ‘I1left’ may be used uninitialized in this function [-Wuninitialized]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c sparse_farms.c -o sparse_farms.o
g++ -shared -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (cn.farms)

name	user	system	elapsed
combineData	2.356	0.080	2.467
createAnnotation	0.008	0.004	0.010
distributionDistance	0.728	0.008	0.737
dnaCopySf	0.204	0.004	0.227
fragLengCorr	5.085	0.012	5.397
mlSummarization	7.224	0.168	7.629
normalizeAverage	0.020	0.000	0.019
normalizeCels	0.020	0.000	0.017
normalizeNpData	0.028	0.000	0.028
plotDendrogram	0.216	0.008	0.225
plotDensity	0.820	0.016	0.833
plotEvalIc	1.036	0.012	1.050
plotRegions	0.232	0.004	0.236
plotSmoothScatter	0.948	0.012	0.959
plotViolines	0.224	0.000	0.223
slSummarization	5.993	0.056	6.132
sparseFarmsC	0.012	0.000	0.012
summarizeFarmsExact	0.020	0.000	0.019
summarizeFarmsExact2	0.012	0.008	0.020
summarizeFarmsExact3	0.016	0.004	0.020
summarizeFarmsGaussian	0.016	0.000	0.014
summarizeFarmsMethods	0.012	0.000	0.014
summarizeFarmsVariational	0.016	0.000	0.015
summarizeWindowBps	0.024	0.000	0.024
summarizeWindowMethods	0.016	0.000	0.015
summarizeWindowStd	0.024	0.004	0.029

BioC 2.12: CHECK report for cn.farms on george2

Summary

Command output