GLAD 2.35.1
Philippe Hupe
| Snapshot Date: 2016-04-20 17:20:35 -0700 (Wed, 20 Apr 2016) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/GLAD | | Last Changed Rev: 113834 / Revision: 116626 | | Last Changed Date: 2016-02-21 09:40:33 -0800 (Sun, 21 Feb 2016) |
| zin2 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| morelia | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | [ OK ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GLAD_2.35.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/GLAD.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.35.1’
* 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 ... [10s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘aws’ ‘tcltk’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 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 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'
ColorBar: no visible global function definition for ‘heat.colors’
ColorBar: no visible global function definition for ‘image’
ColorBar: no visible global function definition for ‘axis’
ColorBar: no visible global function definition for ‘par’
ColorBar: no visible global function definition for ‘box’
FDRThres: no visible global function definition for ‘pnorm’
HaarSeg: no visible global function definition for ‘median’
HaarSegGLAD: no visible global function definition for ‘median’
OptimBkpFindCluster: no visible global function definition for ‘qnorm’
OutliersGNL.profileCGH: no visible global function definition for
‘qnorm’
RecomputeGNL: no visible global function definition for ‘qnorm’
affectationGNL.profileCGH: no visible global function definition for
‘aggregate’
affectationGNL.profileCGH: no visible binding for global variable
‘median’
affectationGNL.profileCGH: no visible binding for global variable ‘var’
affectationGNL.profileCGH: no visible global function definition for
‘qnorm’
arrayPersp.arrayCGH: no visible global function definition for ‘median’
arrayPersp.arrayCGH: no visible global function definition for
‘na.omit’
arrayPersp.arrayCGH: no visible global function definition for ‘par’
arrayPersp.arrayCGH: no visible global function definition for ‘layout’
arrayPersp.arrayCGH: no visible global function definition for
‘dev.cur’
arrayPersp.arrayCGH: no visible global function definition for ‘persp’
arrayPersp.default: no visible global function definition for ‘median’
arrayPersp.default: no visible global function definition for ‘na.omit’
arrayPersp.default: no visible global function definition for ‘par’
arrayPersp.default: no visible global function definition for ‘layout’
arrayPersp.default: no visible global function definition for ‘dev.cur’
arrayPersp.default: no visible global function definition for ‘persp’
arrayPlot.arrayCGH: no visible global function definition for ‘par’
arrayPlot.arrayCGH: no visible global function definition for ‘median’
arrayPlot.arrayCGH: no visible global function definition for ‘na.omit’
arrayPlot.arrayCGH: no visible global function definition for ‘image’
arrayPlot.arrayCGH: no visible global function definition for ‘box’
arrayPlot.arrayCGH: no visible global function definition for ‘abline’
as.profileCGH.data.frame: no visible global function definition for
‘na.omit’
chrBreakpoints.profileCGH : IQRdiff: no visible global function
definition for ‘IQR’
chrBreakpoints.profileCGH: no visible global function definition for
‘median’
chrBreakpoints.profileCGH: no visible global function definition for
‘laws’
chrBreakpoints.profileCGH: no visible global function definition for
‘aws’
clusterglad.hclust: no visible global function definition for ‘cutree’
daglad.profileCGH : IQRdiff: no visible global function definition for
‘IQR’
daglad.profileCGH: no visible global function definition for ‘median’
detectOutliers.profileChr: no visible global function definition for
‘qnorm’
dogenomestep: no visible global function definition for ‘median’
glad.profileCGH: no visible global function definition for ‘median’
glad.profileCGH : IQRdiff: no visible global function definition for
‘IQR’
glad.profileCGH: no visible global function definition for ‘aggregate’
glad.profileCGH: no visible binding for global variable ‘median’
hclustglad: no visible global function definition for ‘as.dist’
lawsglad: no visible global function definition for ‘qchisq’
loopRemove.profileChr: no visible global function definition for
‘qnorm’
myPalette: no visible global function definition for ‘col2rgb’
myPalette: no visible global function definition for ‘rgb’
plotCytoBand.default: no visible global function definition for
‘symbols’
plotCytoBand.default: no visible global function definition for
‘arrows’
plotCytoBand.default: no visible global function definition for ‘axis’
plotProfile.profileCGH: no visible global function definition for
‘na.omit’
plotProfile.profileCGH: no visible global function definition for
‘aggregate’
plotProfile.profileCGH: no visible global function definition for ‘par’
plotProfile.profileCGH: no visible global function definition for
‘layout’
plotProfile.profileCGH: no visible global function definition for
‘plot’
plotProfile.profileCGH: no visible global function definition for
‘lines’
plotProfile.profileCGH: no visible global function definition for
‘abline’
removeLevel.profileChr: no visible global function definition for
‘qnorm’
tkdaglad.default: no visible global function definition for
‘tktoplevel’
tkdaglad.default: no visible global function definition for ‘tkframe’
tkdaglad.default: no visible global function definition for
‘tkwm.title’
tkdaglad.default: no visible global function definition for ‘tkpack’
tkdaglad.default: no visible global function definition for ‘tklabel’
tkdaglad.default: no visible global function definition for ‘tclVar’
tkdaglad.default: no visible global function definition for
‘tkimage.create’
tkdaglad.default: no visible global function definition for
‘tkcheckbutton’
tkdaglad.default: no visible global function definition for
‘tkradiobutton’
tkdaglad.default: no visible global function definition for ‘tkentry’
tkdaglad.default : OnAnalysis: no visible global function definition
for ‘tclvalue’
tkdaglad.default : OnAnalysis: no visible global function definition
for ‘tkmessageBox’
tkdaglad.default : OnQuit: no visible global function definition for
‘tkdestroy’
tkdaglad.default : OnDefault: no visible global function definition for
‘tclvalue<-’
tkdaglad.default : OnPlot: no visible global function definition for
‘tclvalue’
tkdaglad.default : OnPlot: no visible global function definition for
‘tkget’
tkdaglad.default : OnPlot: no visible global function definition for
‘tkcurselection’
tkdaglad.default : OnPlot: no visible global function definition for
‘X11’
tkdaglad.default : OnLogo: no visible global function definition for
‘tkmessageBox’
tkdaglad.default: no visible global function definition for ‘tkbutton’
tkdaglad.default: no visible global function definition for
‘tkscrollbar’
tkdaglad.default : <anonymous>: no visible global function definition
for ‘tkyview’
tkdaglad.default: no visible global function definition for ‘tklistbox’
tkdaglad.default : <anonymous>: no visible global function definition
for ‘tkset’
tkdaglad.default : MakeListBox: no visible global function definition
for ‘tkdelete’
tkdaglad.default : MakeListBox: no visible global function definition
for ‘tksize’
tkdaglad.default : MakeListBox: no visible global function definition
for ‘tkinsert’
tkdaglad.default : MakeListBox: no visible global function definition
for ‘tkselection.set’
tkglad.default: no visible global function definition for ‘tktoplevel’
tkglad.default: no visible global function definition for ‘tkframe’
tkglad.default: no visible global function definition for ‘tkwm.title’
tkglad.default: no visible global function definition for ‘tkpack’
tkglad.default: no visible global function definition for ‘tklabel’
tkglad.default: no visible global function definition for ‘tclVar’
tkglad.default: no visible global function definition for
‘tkimage.create’
tkglad.default: no visible global function definition for
‘tkcheckbutton’
tkglad.default: no visible global function definition for
‘tkradiobutton’
tkglad.default: no visible global function definition for ‘tkentry’
tkglad.default : OnAnalysis: no visible global function definition for
‘tclvalue’
tkglad.default : OnAnalysis: no visible global function definition for
‘tkmessageBox’
tkglad.default : OnQuit: no visible global function definition for
‘tkdestroy’
tkglad.default : OnDefault: no visible global function definition for
‘tclvalue<-’
tkglad.default : OnPlot: no visible global function definition for
‘tclvalue’
tkglad.default : OnPlot: no visible global function definition for
‘tkget’
tkglad.default : OnPlot: no visible global function definition for
‘tkcurselection’
tkglad.default : OnPlot: no visible global function definition for
‘X11’
tkglad.default : OnLogo: no visible global function definition for
‘tkmessageBox’
tkglad.default: no visible global function definition for ‘tkbutton’
tkglad.default: no visible global function definition for ‘tkscrollbar’
tkglad.default : <anonymous>: no visible global function definition for
‘tkyview’
tkglad.default: no visible global function definition for ‘tklistbox’
tkglad.default : <anonymous>: no visible global function definition for
‘tkset’
tkglad.default : MakeListBox: no visible global function definition for
‘tkdelete’
tkglad.default : MakeListBox: no visible global function definition for
‘tksize’
tkglad.default : MakeListBox: no visible global function definition for
‘tkinsert’
tkglad.default : MakeListBox: no visible global function definition for
‘tkselection.set’
Undefined global functions or variables:
IQR X11 abline aggregate arrows as.dist aws axis box col2rgb cutree
dev.cur heat.colors image laws layout lines median na.omit par persp
plot pnorm qchisq qnorm rgb symbols tclVar tclvalue tclvalue<-
tkbutton tkcheckbutton tkcurselection tkdelete tkdestroy tkentry
tkframe tkget tkimage.create tkinsert tklabel tklistbox tkmessageBox
tkpack tkradiobutton tkscrollbar tkselection.set tkset tksize
tktoplevel tkwm.title tkyview var
Consider adding
importFrom("grDevices", "X11", "col2rgb", "dev.cur", "heat.colors",
"rgb")
importFrom("graphics", "abline", "arrows", "axis", "box", "image",
"layout", "lines", "par", "persp", "plot", "symbols")
importFrom("stats", "IQR", "aggregate", "as.dist", "cutree", "median",
"na.omit", "pnorm", "qchisq", "qnorm", "var")
to your NAMESPACE file.
* 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 compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘GLAD/libs/GLAD.so’:
Found ‘__ZNSt3__14coutE’, 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, nor the system RNG.
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 files in ‘vignettes’ ... OK
* checking examples ... [4s/4s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.3-bioc/meat/GLAD.Rcheck/00check.log’
for details.
* 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
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c BkpInfo.cpp -o BkpInfo.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c HaarSeg.cpp -o HaarSeg.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c MoveBkp.cpp -o MoveBkp.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c OutliersGNL.cpp -o OutliersGNL.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c chrBreakpoints.cpp -o chrBreakpoints.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c cutree.cpp -o cutree.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c daglad.cpp -o daglad.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c distance.cpp -o distance.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c filterBkp.cpp -o filterBkp.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c findCluster.cpp -o findCluster.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c glad-utils.cpp -o glad-utils.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c hclust.cpp -o hclust.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c laws.c -o laws.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c loopRemove.cpp -o loopRemove.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -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-3.3-bioc/meat/GLAD.Rcheck/GLAD/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (GLAD)