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Package 168/389HostnameOS / ArchBUILDCHECKBUILD BIN
GLAD 2.10.0
Philippe Hupe
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/GLAD
Last Changed Rev: 47149 / Revision: 49923
Last Changed Date: 2010-05-26 11:24:55 -0700 (Wed, 26 May 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: GLAD
Version: 2.10.0
Command: /home/biocbuild/bbs-2.6-bioc/R/bin/R CMD check --no-vignettes --timings GLAD_2.10.0.tar.gz
StartedAt: 2010-10-04 17:56:24 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 17:56:53 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 29.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GLAD.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.6-bioc/meat/GLAD.Rcheck'
* using R version 2.11.1 (2010-05-31)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '2.10.0'
* 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 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:

* install options are ' --no-html'

* installing *source* package 'GLAD' ...
checking for pkg-config... /usr/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: Linux
configure: creating ./config.status
config.status: creating src/Makevars

src/Makevars file

PKG_LIBS = -lgsl -lgslcblas -lm  
PKG_CPPFLAGS += 

** libs
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c BkpInfo.cpp -o BkpInfo.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c HaarSeg.cpp -o HaarSeg.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c MoveBkp.cpp -o MoveBkp.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c OutliersGNL.cpp -o OutliersGNL.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c chrBreakpoints.cpp -o chrBreakpoints.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c cutree.cpp -o cutree.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c daglad.cpp -o daglad.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c distance.cpp -o distance.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c filterBkp.cpp -o filterBkp.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c findCluster.cpp -o findCluster.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c glad-utils.cpp -o glad-utils.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c hclust.cpp -o hclust.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c laws.c -o laws.o
g++ -I/home/biocbuild/bbs-2.6-bioc/R/include  -I/usr/local/include    -fpic  -g -O2 -c loopRemove.cpp -o loopRemove.o
g++ -shared -L/usr/local/lib64 -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 -lgsl -lgslcblas -lm -L/home/biocbuild/bbs-2.6-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.6-bioc/meat/GLAD.Rcheck/GLAD/libs
** 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
ChrNumeric000
ColorBar0.0120.0000.013
arrayCGH0.0400.0000.039
arrayPersp0.0760.0080.085
arrayPlot0.1160.0160.133
as.data.frame.profileCGH0.8200.0000.821
as.profileCGH0.0720.0000.071
bladder0.0240.0000.024
cytoband0.0040.0080.015
daglad0.9400.0000.943
glad0.9640.0000.966
hclust0.0200.0000.017
myPalette0.0040.0040.008
plotProfile0.9720.0120.984
profileCGH0.1120.0000.113
snijders0.0640.0000.065
tkdaglad0.0680.0000.069
veltman0.0400.0200.061