Package: cn.farms

Version: 1.7.4

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch cn.farms_1.7.4.tar.gz

StartedAt: 2013-03-24 03:52:48 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 03:57:11 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 262.9 seconds

RetCode: 0

Status:  OK

CheckDir: cn.farms.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cn.farms.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 'cn.farms/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cn.farms' version '1.7.4'
* 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 ... [23s/24s] 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/37s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
mlSummarization 6.760  0.245   7.040
slSummarization 5.887  0.107   6.073
fragLengCorr    5.689  0.081   5.821
* 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
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 R_init_cnfarms.c -o R_init_cnfarms.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include    -fPIC  -mtune=core2 -g -O2  -c laplace.cpp -o laplace.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 sparse_farms.c -o sparse_farms.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck/cn.farms/libs
** R
** demo
** inst
** preparing package for lazy loading
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
** help
*** installing help indices
** building package indices
** installing vignettes
   'cn.farms.Rnw' using 'UTF-8' 
** testing if installed package can be loaded
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
'.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
* DONE (cn.farms)

name	user	system	elapsed
combineData	2.258	0.082	2.384
createAnnotation	0.012	0.002	0.014
distributionDistance	0.586	0.031	0.621
dnaCopySf	0.253	0.010	0.266
fragLengCorr	5.689	0.081	5.821
mlSummarization	6.760	0.245	7.040
normalizeAverage	0.013	0.002	0.015
normalizeCels	0.011	0.001	0.012
normalizeNpData	0.011	0.005	0.016
plotDendrogram	0.554	0.035	0.593
plotDensity	0.794	0.041	0.927
plotEvalIc	0.956	0.034	1.027
plotRegions	0.244	0.015	0.265
plotSmoothScatter	0.856	0.058	0.936
plotViolines	0.250	0.015	0.267
slSummarization	5.887	0.107	6.073
sparseFarmsC	0.012	0.004	0.016
summarizeFarmsExact	0.015	0.005	0.020
summarizeFarmsExact2	0.018	0.005	0.023
summarizeFarmsExact3	0.019	0.005	0.024
summarizeFarmsGaussian	0.020	0.004	0.024
summarizeFarmsMethods	0.010	0.003	0.013
summarizeFarmsVariational	0.012	0.004	0.016
summarizeWindowBps	0.023	0.005	0.028
summarizeWindowMethods	0.012	0.003	0.014
summarizeWindowStd	0.017	0.003	0.021