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Package 2/419HostnameOS / ArchBUILDCHECKBUILD BIN
aCGH 1.28.0
Peter Dimitrov
Snapshot Date: 2011-03-30 23:22:56 -0700 (Wed, 30 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_7/madman/Rpacks/aCGH
Last Changed Rev: 50293 / Revision: 54281
Last Changed Date: 2010-10-17 22:34:23 -0700 (Sun, 17 Oct 2010)
lamb2 Linux (openSUSE 11.2) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: aCGH
Version: 1.28.0
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings aCGH_1.28.0.tar.gz
StartedAt: 2011-03-31 04:59:41 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 05:01:45 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 123.7 seconds
RetCode: 0
Status:  OK  
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/aCGH.Rcheck'
* using R version 2.12.2 (2011-02-25)
* 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 '1.28.0'
* 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 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 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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

aCGH.Rcheck/00install.out:

* installing *source* package 'aCGH' ...
** libs
g++ -I"E:/biocbld/BBS-2˜1.7-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˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-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
  '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)

aCGH.Rcheck/aCGH-Ex.timings:

nameusersystemelapsed
aCGH6.340.066.45
aCGH.process0.140.000.14
aCGH.read.Sprocs0.500.010.51
clusterGenome8.640.058.72
colorectal1.360.001.36
fga.func1.180.001.17
find.hmm.states1.110.021.13
gainLoss2.220.042.26
heatmap1.360.021.38
impute.HMM1.830.001.82
impute.lowess0.250.000.25
mergeLevels0.180.000.19
plotFreqStat11.71 0.0011.78
plotGenome4.730.035.02
plotHmmStates1.140.001.20
plotSummaryProfile3.330.023.35
summarize.clones0.990.011.00
threshold.func0.70.00.7