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Package 2/389HostnameOS / ArchBUILDCHECKBUILD BIN
aCGH 1.26.0
Peter Dimitrov
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/aCGH
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / 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: 1.26.0
Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings aCGH_1.26.0.tar.gz
StartedAt: 2010-10-04 15:33:07 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 15:34:56 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 108.1 seconds
RetCode: 0
Status:  OK 
CheckDir: aCGH.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/aCGH.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* 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

aCGH.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package ‘aCGH’ ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -g3 -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hmm.cpp -o hmm.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/aCGH.Rcheck/aCGH/libs/i386
*** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -g3 -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hmm.cpp -o hmm.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/aCGH.Rcheck/aCGH/libs/ppc
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -g3 -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hmm.cpp -o hmm.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/aCGH.Rcheck/aCGH/libs/x86_64
** 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
aCGH5.4840.2605.801
aCGH.process0.1570.0070.164
aCGH.read.Sprocs0.6870.0250.712
clusterGenome2.4480.2492.723
colorectal1.0680.0481.181
fga.func1.2250.0611.294
find.hmm.states1.4100.0661.493
gainLoss2.4670.1412.634
heatmap1.2820.0521.374
impute.HMM1.1420.0171.168
impute.lowess0.2970.0310.335
mergeLevels0.1830.0050.188
plotFreqStat12.001 0.14712.209
plotGenome1.9040.1772.110
plotHmmStates0.8980.0481.013
plotSummaryProfile3.0100.1213.151
summarize.clones1.1680.0561.238
threshold.func0.8300.0560.899