GLAD 2.34.0
Philippe Hupe
| Snapshot Date: 2015-11-09 16:24:09 -0800 (Mon, 09 Nov 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/GLAD | | Last Changed Rev: 109589 / Revision: 110496 | | Last Changed Date: 2015-10-13 12:36:05 -0700 (Tue, 13 Oct 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | OK | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ OK ] | OK | |
| oaxaca | 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_2.34.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/GLAD.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GLAD/DESCRIPTION’ ... OK
* this is package ‘GLAD’ version ‘2.34.0’
* 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 ... [8s/9s] 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 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: no visible global function definition for
‘aws’
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 : 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 : 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’
* 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 ‘__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, 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-3.2-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
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c BkpInfo.cpp -o BkpInfo.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c HaarSeg.cpp -o HaarSeg.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c MoveBkp.cpp -o MoveBkp.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c OutliersGNL.cpp -o OutliersGNL.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c chrBreakpoints.cpp -o chrBreakpoints.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c cutree.cpp -o cutree.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c daglad.cpp -o daglad.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c distance.cpp -o distance.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c filterBkp.cpp -o filterBkp.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c findCluster.cpp -o findCluster.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c glad-utils.cpp -o glad-utils.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c hclust.cpp -o hclust.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c laws.c -o laws.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -DIS_MAC_OS -I/usr/local/include -fPIC -mtune=core2 -g -O2 -Wall -c loopRemove.cpp -o loopRemove.o
llvm-g++-4.2 -arch x86_64 -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 -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-3.2-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)