Package: aCGH

Version: 1.26.0

Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings aCGH_1.26.0.tar.gz

StartedAt: 2010-10-04 15:30:02 -0700 (Mon, 04 Oct 2010)

EndedAt: 2010-10-04 15:31:12 -0700 (Mon, 04 Oct 2010)

EllapsedTime: 70.6 seconds

RetCode: 0

Status:  OK

CheckDir: aCGH.Rcheck

Warnings: 0

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/aCGH.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.26.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aCGH' can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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
plotSummaryProfile: no visible binding for global variable
  'numchromgain'
plotSummaryProfile: no visible binding for global variable
  'numchromloss'
plotSummaryProfile: no visible binding for global variable 'numtrans'
plotSummaryProfile: no visible binding for global variable
  'numtrans.binary'
plotSummaryProfile: no visible binding for global variable 'numaber'
plotSummaryProfile: no visible binding for global variable 'numamplif'
plotSummaryProfile: no visible binding for global variable
  'numamplif.binary'
plotSummaryProfile: no visible binding for global variable
  'numamplicon'
plotSummaryProfile: no visible binding for global variable
  'sizeamplicon'
* 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 data for non-ASCII characters ... 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

* install options are ' --no-html'

* installing *source* package 'aCGH' ...
** libs
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include -g3 -I/usr/local/include    -fpic  -g -O2 -c hmm.cpp -o hmm.o
g++ -shared -L/usr/local/lib64 -o aCGH.so hmm.o -lm -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/aCGH.Rcheck/aCGH/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: splines
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (aCGH)

name	user	system	elapsed
aCGH	3.980	0.084	4.066
aCGH.process	0.120	0.004	0.124
aCGH.read.Sprocs	0.740	0.004	0.745
clusterGenome	1.716	0.052	1.765
colorectal	0.580	0.012	0.607
fga.func	0.676	0.004	0.681
find.hmm.states	1.032	0.016	1.048
gainLoss	1.804	0.028	1.835
heatmap	0.740	0.012	0.756
impute.HMM	0.892	0.004	0.968
impute.lowess	0.244	0.004	0.247
mergeLevels	0.128	0.000	0.128
plotFreqStat	8.225	0.020	8.244
plotGenome	1.304	0.048	1.353
plotHmmStates	0.440	0.020	0.983
plotSummaryProfile	2.064	0.000	2.063
summarize.clones	0.684	0.008	0.690
threshold.func	0.424	0.012	0.438