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Package 183/436HostnameOS / ArchBUILDCHECKBUILD BIN
GLAD 2.13.5
Philippe Hupe
Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GLAD
Last Changed Rev: 52474 / Revision: 53255
Last Changed Date: 2011-02-04 15:33:08 -0800 (Fri, 04 Feb 2011)
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 
petty Mac OS X Snow Leopard (10.6.4) / i386  OK  OK  OK 

Summary

Package: GLAD
Version: 2.13.5
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GLAD_2.13.5.tar.gz
StartedAt: 2011-02-24 19:35:04 -0800 (Thu, 24 Feb 2011)
EndedAt: 2011-02-24 19:35:59 -0800 (Thu, 24 Feb 2011)
EllapsedTime: 55.0 seconds
RetCode: 0
Status:  OK 
CheckDir: GLAD.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/GLAD.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.13.5’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘GLAD’ 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
chrBreakpoints.profileCGH: no visible global function definition for
  ‘laws’
chrBreakpoints.profileCGH: possible error in aws(y =
  subsetdata[["LogRatio"]], x = x, hinit = hinit, hmax = hmax, sigma2 =
  sigma, NN = FALSE, symmetric = TRUE, ...): unused argument(s) (x = x,
  hinit = hinit, NN = FALSE, symmetric = TRUE)
chrBreakpoints.profileCGH: possible error in aws(y =
  subsetdata[["LogRatio"]], hinit = hinit, hmax = hmax, sigma2 = sigma,
  symmetric = TRUE, ...): unused argument(s) (hinit = hinit, symmetric
  = TRUE)
* 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 ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

GLAD.Rcheck/00install.out:

* installing *source* package ‘GLAD’ ...
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for GSL... yes
GSL has been found on the operating system
operating system: Darwin
configure: creating ./config.status
config.status: creating src/Makevars

src/Makevars file

PKG_LIBS = -L/usr/local/lib -lgsl -lgslcblas -lm  
PKG_CPPFLAGS += -DIS_MAC_OS

** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c BkpInfo.cpp -o BkpInfo.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c HaarSeg.cpp -o HaarSeg.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c MoveBkp.cpp -o MoveBkp.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c OutliersGNL.cpp -o OutliersGNL.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c chrBreakpoints.cpp -o chrBreakpoints.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c cutree.cpp -o cutree.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c daglad.cpp -o daglad.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c distance.cpp -o distance.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c filterBkp.cpp -o filterBkp.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c findCluster.cpp -o findCluster.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c glad-utils.cpp -o glad-utils.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hclust.cpp -o hclust.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c laws.c -o laws.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c loopRemove.cpp -o loopRemove.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o GLAD.so BkpInfo.o HaarSeg.o MoveBkp.o OutliersGNL.o chrBreakpoints.o cutree.o daglad.o distance.o filterBkp.o findCluster.o glad-utils.o hclust.o laws.o loopRemove.o -L/usr/local/lib -lgsl -lgslcblas -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/GLAD.Rcheck/GLAD/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (GLAD)

GLAD.Rcheck/GLAD-Ex.timings:

nameusersystemelapsed
ChrNumeric0.0010.0000.001
ColorBar0.0180.0010.020
arrayCGH0.0650.0050.073
arrayPersp0.1430.0150.177
arrayPlot0.2030.0200.223
as.data.frame.profileCGH0.8790.1331.018
as.profileCGH0.1580.0050.163
bladder0.0480.0030.051
cytoband0.0450.0140.059
daglad1.2160.1091.331
glad1.2900.1541.451
hclust0.0210.0020.044
myPalette0.0120.0010.012
plotProfile1.3540.1651.531
profileCGH0.1440.0040.149
snijders0.1300.0020.139
tkdaglad0.1650.0050.171
veltman0.2700.0630.335