GLAD 2.22.0
Philippe Hupe
| Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GLAD | | Last Changed Rev: 72060 / Revision: 74774 | | Last Changed Date: 2012-12-19 13:14:50 -0800 (Wed, 19 Dec 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | [ OK ] | OK |
* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/GLAD.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'GLAD/DESCRIPTION' ... OK
* this is package 'GLAD' version '2.22.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'GLAD' can be installed ... [15s/15s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
File 'GLAD/R/zzz.R':
.onLoad calls:
packageStartupMessage("\n")
packageStartupMessage("######################################################################################\n")
packageStartupMessage("\n")
packageStartupMessage("Have fun with GLAD\n")
packageStartupMessage("\n")
packageStartupMessage("For smoothing it is possible to use either\n")
packageStartupMessage("the AWS algorithm (Polzehl and Spokoiny, 2002)\n")
packageStartupMessage("or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008)\n")
packageStartupMessage("\n")
packageStartupMessage("If you use the package with AWS, please cite:\n")
packageStartupMessage("Hupe et al. (Bioinformatics, 2004) and Polzehl and Spokoiny (2002)\n")
packageStartupMessage("\n")
packageStartupMessage("If you use the package with HaarSeg, please cite:\n")
packageStartupMessage("Hupe et al. (Bioinformatics, 2004) and (Ben-Yaacov and Eldar, Bioinformatics, 2008)\n")
packageStartupMessage("\n")
packageStartupMessage("For fast computation it is recommanded to use\n")
packageStartupMessage("the daglad function with smoothfunc=haarseg\n")
packageStartupMessage("\n")
packageStartupMessage("######################################################################################\n")
packageStartupMessage("\n")
packageStartupMessage("New options are available in daglad: see help for details.")
packageStartupMessage("\n")
See section 'Good practice' in '?.onAttach'.
arrayPersp.arrayCGH: warning in layout(matrix(c(1, 2), 1, 2), width =
c(9, 1)): partial argument match of 'width' to 'widths'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.arrayCGH: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nc' to 'ncol'
arrayPersp.default: warning in layout(matrix(c(1, 2), 1, 2), width =
c(9, 1)): partial argument match of 'width' to 'widths'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nr' to 'nrow'
arrayPersp.default: warning in matrix("green", nr = nrow(z), nc =
ncol(z)): partial argument match of 'nc' to 'ncol'
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 arguments (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 arguments (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 compiled code ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/GLAD.Rcheck/GLAD/libs/i386/GLAD.so':
Found '__ZSt4cout', possibly from 'std::cout' (C++)
Object: 'glad-utils.o'
Found '_printf', possibly from 'printf' (C)
Object: 'chrBreakpoints.o'
Found '_puts', possibly from 'printf' (C), 'puts' (C)
Objects: 'OutliersGNL.o', 'chrBreakpoints.o', 'findCluster.o',
'glad-utils.o', 'hclust.o'
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [6s/6s] 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
NOTE: There were 2 notes.
See
'/Users/biocbuild/bbs-2.12-bioc/meat/GLAD.Rcheck/00check.log'
for details.
* 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: 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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -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-2.12-bioc/meat/GLAD.Rcheck/GLAD/libs/i386
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'GLAD.Rnw'
** testing if installed package can be loaded
* DONE (GLAD)