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Package 207/444HostnameOS / ArchBUILDCHECKBUILD BIN
HilbertVisGUI 1.9.0
Simon Anders
Snapshot Date: 2011-03-17 11:16:30 -0700 (Thu, 17 Mar 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/HilbertVisGUI
Last Changed Rev: 50295 / Revision: 53825
Last Changed Date: 2010-10-17 22:57:44 -0700 (Sun, 17 Oct 2010)
lamb1 Linux (openSUSE 11.3) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  WARNINGS  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64 N O T   S U P P O R T E D
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.6) / i386  OK [ ERROR ] OK 

Summary

Package: HilbertVisGUI
Version: 1.9.0
Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HilbertVisGUI_1.9.0.tar.gz
StartedAt: 2011-03-17 16:35:58 -0700 (Thu, 17 Mar 2011)
EndedAt: 2011-03-17 16:36:40 -0700 (Thu, 17 Mar 2011)
EllapsedTime: 42.8 seconds
RetCode: 1
Status:  ERROR 
CheckDir: HilbertVisGUI.Rcheck
Warnings: NA

Command output

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/HilbertVisGUI.Rcheck'
* using R version 2.13.0 Under development (unstable) (2011-03-06 r54683)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'HilbertVisGUI/DESCRIPTION' ... OK
* this is package 'HilbertVisGUI' version '1.9.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'HilbertVisGUI' can be installed ... OK
* checking installed package size ... 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 ... OK
* 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 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 ...sh: line 1: 53530 Segmentation fault      LANGUAGE=en '/Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R' --vanilla > 'HilbertVisGUI-Ex.Rout' 2>&1 < HilbertVisGUI-Ex.R
 ERROR
Running examples in 'HilbertVisGUI-Ex.R' failed
The error most likely occurred in:

> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hilbertDisplay
> ### Title: Hilbert curve visualization
> ### Aliases: hilbertDisplay
> 
> ### ** Examples
> 
> random <- c( as.integer( runif(100000)*30 ) ) 
> ramp <- c( as.integer( 0:19999/100 ) )
> try( hilbertDisplay( random, ramp ) )
R(53530,0xa03f8540) malloc: *** error for object 0xa110000: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug
R(53530,0xa03f8540) malloc: *** error for object 0xa310000: pointer being freed was not allocated
*** set a breakpoint in malloc_error_break to debug

 *** caught segfault ***
address 0x8e594d10, cause 'memory not mapped'

Traceback:
 1: .External(R_display_hilbert, function(data, info) try(plotFunc(data,     info)), names, as.integer(palettePos), as.integer(paletteNeg),     as.integer(naColor), maxPaletteValue, fullLengths, portrait,     ...)
 2: hilbertDisplay(random, ramp)
 3: doTryCatch(return(expr), name, parentenv, handler)
 4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 6: tryCatch(expr, error = function(e) {    call <- conditionCall(e)    if (!is.null(call)) {        if (identical(call[[1L]], quote(doTryCatch)))             call <- sys.call(-4L)        dcall <- deparse(call)[1L]        prefix <- paste("Error in", dcall, ": ")        LONG <- 75L        msg <- conditionMessage(e)        sm <- strsplit(msg, "\n")[[1L]]        w <- 14L + nchar(dcall, type = "w") + nchar(sm[1L], type = "w")        if (is.na(w))             w <- 14L + nchar(dcall, type = "b") + nchar(sm[1L],                 type = "b")        if (w > LONG)             prefix <- paste(prefix, "\n  ", sep = "")    }    else prefix <- "Error : "    msg <- paste(prefix, conditionMessage(e), "\n", sep = "")    .Internal(seterrmessage(msg[1L]))    if (!silent && identical(getOption("show.error.messages"),         TRUE)) {        cat(msg, file = stderr())        .Internal(printDeferredWarnings())    }    invisible(structure(msg, class = "try-error"))})
 7: try(hilbertDisplay(random, ramp))
aborting ...

HilbertVisGUI.Rcheck/00install.out:

* installing *source* package 'HilbertVisGUI' ...
-n Checking for pkg-config... 
/usr/local/bin/pkg-config
-n Checking for gtkmm-2.4... 
found: version 2.18.2
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include   `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -fPIC  -g -O2 -Wall -pedantic -c R_env_prot.c -o R_env_prot.o
R_env_prot.c: In function 'env_protect':
R_env_prot.c:49: warning: format '%p' expects type 'void *', but argument 6 has type 'SEXP'
R_env_prot.c: In function 'env_unprotect':
R_env_prot.c:75: warning: format '%p' expects type 'void *', but argument 6 has type 'SEXP'
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c R_interface.cc -o R_interface.o
R_interface.cc: In function 'SEXPREC* R_display_hilbert(SEXPREC*)':
R_interface.cc:510: warning: comparison between signed and unsigned integer expressions
R_interface.cc:509: warning: unused variable 'palette_level'
R_interface.cc: In member function 'void MainWindowForRForBidir::set_palette_level(double)':
R_interface.cc:702: warning: comparison between signed and unsigned integer expressions
R_interface.cc: In function 'RDataVector<double>* create_normal_or_Rle_RDataVector(SEXPREC*, long int, binning_mode)':
R_interface.cc:431: warning: control reaches end of non-void function
R_interface.cc: In member function 'double RDataVector<data_el_t>::get_bin_value(long int, long int) const [with data_el_t = int]':
R_interface.cc:119: warning: 'val' may be used uninitialized in this function
R_interface.cc: In member function 'double RDataVector<data_el_t>::get_bin_value(long int, long int) const [with data_el_t = double]':
R_interface.cc:180: warning: 'val' may be used uninitialized in this function
R_interface.cc: In function 'SEXPREC* R_display_hilbert(SEXPREC*)':
R_interface.cc:535: warning: 'datavec' may be used uninitialized in this function
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c colorizers.cc -o colorizers.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c display.cc -o display.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c ruler.cc -o ruler.o
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 `pkg-config gtkmm-2.4 --cflags` -DSO_NAME=HilbertVisGUI -DSO_NAME=HilbertVisGUI -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c window.cc -o window.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o HilbertVisGUI.so R_env_prot.o R_interface.o colorizers.o display.o ruler.o window.o -L/Library/Frameworks/GTK+.framework/Versions/2.14.X11/Resources/lib -lgtkmm-2.4 -lgiomm-2.4 -lgdkmm-2.4 -latkmm-1.6 -lgtk-x11-2.0 -lpangomm-1.4 -lcairomm-1.0 -lglibmm-2.4 -lsigc-2.0 -lgdk-x11-2.0 -latk-1.0 -lgio-2.0 -lpangoft2-1.0 -lgdk_pixbuf-2.0 -lpangocairo-1.0 -lcairo -lpango-1.0 -lfreetype -lz -lfontconfig -lgobject-2.0 -lgmodule-2.0 -lglib-2.0 -lintl -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/HilbertVisGUI.Rcheck/HilbertVisGUI/libs/i386
** R
** inst
** preparing package for lazy loading
Loading required package: grid
Loading required package: lattice
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (HilbertVisGUI)

HilbertVisGUI.Rcheck/HilbertVisGUI-Ex.timings:

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