Package: cn.farms

Version: 1.4.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings cn.farms_1.4.0.tar.gz

StartedAt: 2012-09-24 00:11:03 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 00:13:54 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 171.2 seconds

RetCode: 0

Status:  OK

CheckDir: cn.farms.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/cn.farms.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.4.0’
* 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 whether package ‘cn.farms’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 ... NOTE
plotEvalIc: warning in rgb(130, 0, 139, max = 255): partial argument
  match of 'max' to 'maxColorValue'
* 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 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’ ... NOTE
The following files should probably not be installed:
  ‘bioinf.cls’, ‘cnFarmsDefs.sty’, ‘natbib.bst’, ‘natbib.sty’
The following directories should probably not be installed:
  ‘figures’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
* checking examples ... OK
* 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

NOTE: There were 2 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/cn.farms.Rcheck/00check.log’
for details.

* installing *source* package ‘cn.farms’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-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-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c laplace.cpp -o laplace.o
laplace.cpp: In function ‘SEXPREC* momentsGauss(SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*, SEXPREC*)’:
laplace.cpp:442:6: 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:198:9: warning: ‘I1left’ may be used uninitialized in this function
laplace.cpp:199:9: warning: ‘I1right’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-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/lib64 -o cn.farms.so R_init_cnfarms.o laplace.o sparse_farms.o -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-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
   ‘cn.farms.Rnw’ 
** testing if installed package can be loaded

* DONE (cn.farms)

name	user	system	elapsed
combineData	1.832	0.036	1.905
createAnnotation	0	0	0
distributionDistance	0.456	0.004	0.460
dnaCopySf	0.144	0.000	0.149
fragLengCorr	3.948	0.008	3.960
mlSummarization	5.161	0.128	5.290
normalizeAverage	0.000	0.004	0.001
normalizeCels	0	0	0
normalizeNpData	0	0	0
plotDendrogram	0.172	0.004	0.178
plotDensity	0.964	0.012	0.976
plotEvalIc	0.384	0.012	0.400
plotRegions	0.176	0.000	0.177
plotSmoothScatter	0.648	0.020	0.665
plotViolines	0.172	0.000	0.171
slSummarization	4.280	0.028	4.318
sparseFarmsC	0.000	0.000	0.001
summarizeFarmsExact	0.004	0.004	0.007
summarizeFarmsExact2	0.004	0.004	0.007
summarizeFarmsExact3	0.008	0.000	0.008
summarizeFarmsGaussian	0.004	0.000	0.003
summarizeFarmsMethods	0.000	0.000	0.003
summarizeFarmsVariational	0.004	0.000	0.004
summarizeWindowBps	0.008	0.000	0.010
summarizeWindowMethods	0.004	0.000	0.002
summarizeWindowStd	0.004	0.000	0.003