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: 2013-03-25 01:52:06 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 01:55:50 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 224.1 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: cn.farms.Rcheck

Warnings: 2

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-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 ... [19s/20s] WARNING
Found the following significant warnings:
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
See '/Users/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck/00install.out' for details.
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [32s/32s] WARNING
Found the following significant warnings:

  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
  Warning: '.find.package' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                 user system elapsed
slSummarization 6.590  0.249   6.887
mlSummarization 5.376  0.390   5.808
* 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

WARNING: There were 2 warnings.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/cn.farms.Rcheck/00check.log'
for details.

* installing *source* package 'cn.farms' ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c R_init_cnfarms.c -o R_init_cnfarms.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks  -c laplace.cpp -o laplace.o
laplace.cpp: In function 'SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)':
laplace.cpp:442: warning: unused variable 'method'
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:199: warning: 'I1right' may be used uninitialized in this function
laplace.cpp:198: warning: 'I1left' may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG  -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic  -c sparse_farms.c -o sparse_farms.o
g++ -arch i386 -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/i386
** R
** demo
** inst
** preparing package for lazy loading
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.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
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
Warning: '.find.package' is deprecated.
Use 'find.package' instead.
See help("Deprecated")
* DONE (cn.farms)

name	user	system	elapsed
combineData	1.969	0.119	2.098
createAnnotation	0.007	0.005	0.013
distributionDistance	0.363	0.070	0.438
dnaCopySf	0.189	0.024	0.216
fragLengCorr	4.411	0.048	4.470
mlSummarization	5.376	0.390	5.808
normalizeAverage	0.010	0.008	0.019
normalizeCels	0.008	0.007	0.015
normalizeNpData	0.007	0.008	0.016
plotDendrogram	0.245	0.079	0.326
plotDensity	0.904	0.081	0.991
plotEvalIc	0.725	0.042	0.778
plotRegions	0.267	0.033	0.309
plotSmoothScatter	1.017	0.085	1.114
plotViolines	0.481	0.024	0.506
slSummarization	6.590	0.249	6.887
sparseFarmsC	0.007	0.007	0.015
summarizeFarmsExact	0.016	0.009	0.025
summarizeFarmsExact2	0.013	0.008	0.021
summarizeFarmsExact3	0.011	0.006	0.017
summarizeFarmsGaussian	0.008	0.005	0.012
summarizeFarmsMethods	0.006	0.004	0.011
summarizeFarmsVariational	0.011	0.007	0.017
summarizeWindowBps	0.023	0.010	0.033
summarizeWindowMethods	0.006	0.004	0.011
summarizeWindowStd	0.011	0.007	0.018