Package: VanillaICE

Version: 1.18.0

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings VanillaICE_1.18.0.tar.gz

StartedAt: 2012-09-24 04:07:02 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 04:10:52 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 229.9 seconds

RetCode: 0

Status:  OK

CheckDir: VanillaICE.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/VanillaICE.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 ‘VanillaICE/DESCRIPTION’ ... OK
* this is package ‘VanillaICE’ version ‘1.18.0’
* 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 ‘VanillaICE’ 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 ... 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 ... OK
* 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 compilation flags in Makevars ... 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 ... OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘doRUnit.R’
 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

* installing *source* package ‘VanillaICE’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -Wall -c viterbi.c -o viterbi.o
viterbi.c: In function ‘viterbi’:
viterbi.c:107:34: warning: unused variable ‘tp’
viterbi.c: At top level:
viterbi.c:243:27: warning: "/*" within comment
viterbi.c: In function ‘viterbi2’:
viterbi.c:256:3: warning: "/*" within comment
viterbi.c:261:13: warning: unused variable ‘tt’
viterbi.c:259:34: warning: unused variable ‘tp’
gcc -std=gnu99 -shared -L/usr/local/lib64 -o VanillaICE.so viterbi.o -lm -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/VanillaICE.Rcheck/VanillaICE/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘VanillaICE.Rnw’ 
   ‘crlmmDownstream.Rnw’ 
** testing if installed package can be loaded

* DONE (VanillaICE)

name	user	system	elapsed
BeadStudioSet	20.013	0.364	20.447
BeadStudioSetList-class	0.012	0.000	0.014
BeadStudioSetList	0.012	0.000	0.009
hmmResults	5.945	0.092	6.132
icePlatforms	0.000	0.000	0.001
read.bsfiles	0.016	0.008	0.027
robustSds	0.064	0.000	0.088
sd-methods	0.116	0.000	0.120