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Package 179/419HostnameOS / ArchBUILDCHECKBUILD BIN
GLAD 2.12.0
Philippe Hupe
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/GLAD
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  WARNINGS 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ WARNINGS ] OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  WARNINGS  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  WARNINGS  OK 

Summary

Package: GLAD
Version: 2.12.0
Command: E:\biocbld\bbs-2.7-bioc\R\bin\R.exe CMD check --no-vignettes --timings GLAD_2.12.0.tar.gz
StartedAt: 2011-03-31 06:47:19 -0700 (Thu, 31 Mar 2011)
EndedAt: 2011-03-31 06:48:14 -0700 (Thu, 31 Mar 2011)
EllapsedTime: 54.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: GLAD.Rcheck
Warnings: 1

Command output

* using log directory 'E:/biocbld/bbs-2.7-bioc/meat/GLAD.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 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '2.12.0'
* checking package name space information ...Warning: unknown namespace directive: .onLoad()
 OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'GLAD' can be installed ... WARNING
Found the following significant warnings:
  Warning: unknown namespace directive: .onLoad()
  Warning: unknown namespace directive: .onLoad()
See 'E:/biocbld/bbs-2.7-bioc/meat/GLAD.Rcheck/00install.out' for details.
* 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
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) and $(LAPACK_LIBS) ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There was 1 warning, see
  'E:/biocbld/bbs-2.7-bioc/meat/GLAD.Rcheck/00check.log'
for details

GLAD.Rcheck/00install.out:

* installing *source* package 'GLAD' ...

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************


** libs
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c BkpInfo.cpp -o BkpInfo.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c HaarSeg.cpp -o HaarSeg.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c MoveBkp.cpp -o MoveBkp.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c OutliersGNL.cpp -o OutliersGNL.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c chrBreakpoints.cpp -o chrBreakpoints.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c cutree.cpp -o cutree.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c daglad.cpp -o daglad.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c distance.cpp -o distance.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c filterBkp.cpp -o filterBkp.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c findCluster.cpp -o findCluster.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c glad-utils.cpp -o glad-utils.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c hclust.cpp -o hclust.o
gcc -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O3 -Wall  -std=gnu99 -c laws.c -o laws.o
g++ -I"E:/biocbld/BBS-2˜1.7-B/R/include" -I/src/include -IC:/gsl/include        -O2 -Wall  -c loopRemove.cpp -o loopRemove.o
g++ -shared -s -static-libgcc -o GLAD.dll tmp.def 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 -LC:/gsl/bin -lgsl -lgslcblas -lm -LE:/biocbld/BBS-2˜1.7-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.7-bioc/meat/GLAD.Rcheck/GLAD/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
Warning: unknown namespace directive: .onLoad()
** help
*** installing help indices
** building package indices ...
Warning: unknown namespace directive: .onLoad()
** testing if installed package can be loaded

* DONE (GLAD)

GLAD.Rcheck/GLAD-Ex.timings:

nameusersystemelapsed
ChrNumeric000
ColorBar0.070.000.06
arrayCGH0.030.010.04
arrayPersp0.730.020.77
arrayPlot0.580.000.64
as.data.frame.profileCGH0.810.000.82
as.profileCGH0.090.010.11
bladder0.030.020.05
cytoband0.020.030.05
daglad1.360.001.39
glad1.490.001.50
hclust0.010.000.27
myPalette0.030.000.03
plotProfile1.820.001.83
profileCGH0.110.000.11
snijders0.090.010.11
tkdaglad0.160.000.15
veltman0.150.000.16