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Package 202/472HostnameOS / ArchBUILDCHECKBUILD BIN
GLAD 2.15.1
Philippe Hupe
Snapshot Date: 2011-06-21 19:21:48 -0700 (Tue, 21 Jun 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GLAD
Last Changed Rev: 56197 / Revision: 56351
Last Changed Date: 2011-06-15 03:25:00 -0700 (Wed, 15 Jun 2011)
wilson2 Linux (openSUSE 11.4) / 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 
moscato1 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: GLAD
Version: 2.15.1
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch GLAD_2.15.1.tar.gz
StartedAt: 2011-06-22 03:22:48 -0700 (Wed, 22 Jun 2011)
EndedAt: 2011-06-22 03:23:45 -0700 (Wed, 22 Jun 2011)
EllapsedTime: 57.3 seconds
RetCode: 0
Status:  OK 
CheckDir: GLAD.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/GLAD.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56037)
* 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 ‘2.15.1’
* 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 installed package size ... 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 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 sizes of PDF files under ‘inst/doc’ ... 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

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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c BkpInfo.cpp -o BkpInfo.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c HaarSeg.cpp -o HaarSeg.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c MoveBkp.cpp -o MoveBkp.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c OutliersGNL.cpp -o OutliersGNL.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c chrBreakpoints.cpp -o chrBreakpoints.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c cutree.cpp -o cutree.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c daglad.cpp -o daglad.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c distance.cpp -o distance.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c filterBkp.cpp -o filterBkp.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c findCluster.cpp -o findCluster.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/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++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c hclust.cpp -o hclust.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -pedantic -c laws.c -o laws.o
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386 -DIS_MAC_OS -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c loopRemove.cpp -o loopRemove.o
g++-4.2 -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-2.9-bioc/meat/GLAD.Rcheck/GLAD/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘GLAD.Rnw’ 
** testing if installed package can be loaded

* DONE (GLAD)

GLAD.Rcheck/GLAD-Ex.timings:

nameusersystemelapsed
ChrNumeric0.0010.0000.001
ColorBar0.0190.0010.020
arrayCGH0.0720.0050.077
arrayPersp0.1420.0120.156
arrayPlot0.2510.0200.273
as.data.frame.profileCGH0.8560.1311.006
as.profileCGH0.1400.0050.146
bladder0.0510.0030.053
cytoband0.0440.0140.061
daglad1.2310.1051.347
glad1.1890.1491.363
hclust0.0250.0030.028
myPalette0.0110.0010.012
plotProfile1.3250.1651.530
profileCGH0.1460.0040.153
snijders0.1340.0030.138
tkdaglad0.1500.0060.157
veltman0.2760.0660.343