Package: aCGH

Version: 1.31.0

Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings aCGH_1.31.0.tar.gz

StartedAt: 2011-05-09 12:03:58 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 12:05:29 -0700 (Mon, 09 May 2011)

EllapsedTime: 90.9 seconds

RetCode: 0

Status:  OK

CheckDir: aCGH.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/aCGH.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-04-17 r55484)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.31.0'
* 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 installed package size ... NOTE
  installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data       4.4Mb
    doc        3.7Mb
    examples   1.2Mb
* checking package directory ... OK
* checking for portable file names ... 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 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 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

* installing *source* package 'aCGH' ...
** libs
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include" -g3         -O2 -Wall  -c hmm.cpp -o hmm.o
g++ -shared -s -static-libgcc -o aCGH.dll tmp.def hmm.o -lm -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/aCGH.Rcheck/aCGH/libs/i386
** 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
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'aCGH.Rnw' 
** testing if installed package can be loaded

* DONE (aCGH)

name	user	system	elapsed
aCGH	4.00	0.01	4.06
aCGH.process	0.11	0.00	0.11
aCGH.read.Sprocs	0.45	0.00	0.45
clusterGenome	2.85	0.03	2.89
colorectal	0.90	0.00	0.91
fga.func	0.91	0.04	0.94
find.hmm.states	1.06	0.01	1.09
gainLoss	1.84	0.05	1.92
heatmap	0.99	0.00	0.99
impute.HMM	1.59	0.00	1.59
impute.lowess	0.16	0.00	0.17
mergeLevels	0.12	0.00	0.13
plotFreqStat	7.88	0.00	7.89
plotGenome	2.14	0.06	2.31
plotHmmStates	0.75	0.02	0.77
plotSummaryProfile	2.30	0.01	2.31
summarize.clones	0.84	0.02	0.86
threshold.func	0.66	0.00	0.67