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Package 96/354HostnameOS / ArchBUILDCHECKBUILD BIN
DNAcopy 1.21.0
Venkatraman E. Seshan
Bioconductor Changelog
Snapshot Date: 2009-12-07 11:32:00 -0800 (Mon, 07 Dec 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DNAcopy
Last Changed Rev: 42686 / Revision: 43434
Last Changed Date: 2009-10-27 16:45:24 -0700 (Tue, 27 Oct 2009)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 
Package: DNAcopy
Version: 1.21.0
Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes DNAcopy_1.21.0.tar.gz
StartedAt: 2009-12-07 17:06:35 -0800 (Mon, 07 Dec 2009)
EndedAt: 2009-12-07 17:07:13 -0800 (Mon, 07 Dec 2009)
EllapsedTime: 37.2 seconds
RetCode: 0
Status: OK
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/DNAcopy.Rcheck'
* using R version 2.11.0 Under development (unstable) (2009-11-30 r50622)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DNAcopy/DESCRIPTION' ... OK
* this is package 'DNAcopy' version '1.21.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'DNAcopy' can be installed ... 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 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 use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking tests ...
  Running ‘redundancy,20090610,segment.R’
 OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

DNAcopy.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package ‘DNAcopy’ ...
** libs
** arch - i386
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function ‘wtmaxo’:
cbsWtstats.f:17: warning: ‘tmaxj’ may be used uninitialized in this function
cbsWtstats.f:17: warning: ‘tmaxi’ may be used uninitialized in this function
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c cbststats.f -o cbststats.o
cbststats.f: In function ‘tmaxo’:
cbststats.f:11: warning: ‘sxmxi’ may be used uninitialized in this function
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c changepoints-wtd.f -o changepoints-wtd.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c changepoints.f -o changepoints.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c esegment.f -o esegment.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c flchoose.c -o flchoose.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c fphyper.c -o fphyper.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c fpnorm.c -o fpnorm.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c getbdry.f -o getbdry.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c prune.f -o prune.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rshared.c -o rshared.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c segmentp.f -o segmentp.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c smoothCNA.f -o smoothCNA.o
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c tailprobs.f -o tailprobs.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning __gfortrani_options has different visibility (1) in /usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortran.a(environ.o) and (2) in DNAcopy.so
ld: warning __gfortrani_compile_options has different visibility (1) in /usr/lib/gcc/i686-apple-darwin9/4.2.1/libgfortran.a(compile_options.o) and (2) in DNAcopy.so
** arch - ppc
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function ‘wtmaxo’:
cbsWtstats.f:17: warning: ‘tmaxj’ may be used uninitialized in this function
cbsWtstats.f:17: warning: ‘tmaxi’ may be used uninitialized in this function
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c cbststats.f -o cbststats.o
cbststats.f: In function ‘tmaxo’:
cbststats.f:11: warning: ‘sxmxi’ may be used uninitialized in this function
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c changepoints-wtd.f -o changepoints-wtd.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c changepoints.f -o changepoints.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c esegment.f -o esegment.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c flchoose.c -o flchoose.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c fphyper.c -o fphyper.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c fpnorm.c -o fpnorm.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c getbdry.f -o getbdry.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c prune.f -o prune.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -c rshared.c -o rshared.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c segmentp.f -o segmentp.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c smoothCNA.f -o smoothCNA.o
gfortran-4.2 -arch ppc   -fPIC  -g -O2 -Wall -c tailprobs.f -o tailprobs.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning __gfortrani_options has different visibility (1) in /usr/lib/gcc/powerpc-apple-darwin9/4.2.1/libgfortran.a(environ.o) and (2) in DNAcopy.so
ld: warning __gfortrani_compile_options has different visibility (1) in /usr/lib/gcc/powerpc-apple-darwin9/4.2.1/libgfortran.a(compile_options.o) and (2) in DNAcopy.so
** arch - x86_64
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c cbsWtstats.f -o cbsWtstats.o
cbsWtstats.f: In function ‘wtmaxo’:
cbsWtstats.f:17: warning: ‘tmaxj’ may be used uninitialized in this function
cbsWtstats.f:17: warning: ‘tmaxi’ may be used uninitialized in this function
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c cbststats.f -o cbststats.o
cbststats.f: In function ‘tmaxo’:
cbststats.f:11: warning: ‘sxmxi’ may be used uninitialized in this function
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c changepoints-wtd.f -o changepoints-wtd.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c changepoints.f -o changepoints.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c esegment.f -o esegment.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c flchoose.c -o flchoose.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c fphyper.c -o fphyper.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c fpnorm.c -o fpnorm.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c getbdry.f -o getbdry.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c prune.f -o prune.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c rshared.c -o rshared.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c segmentp.f -o segmentp.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c smoothCNA.f -o smoothCNA.o
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c tailprobs.f -o tailprobs.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DNAcopy.so cbsWtstats.o cbststats.o changepoints-wtd.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o smoothCNA.o tailprobs.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning __gfortrani_options has different visibility (1) in /usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64/libgfortran.a(environ.o) and (2) in DNAcopy.so
ld: warning __gfortrani_compile_options has different visibility (1) in /usr/lib/gcc/i686-apple-darwin9/4.2.1/x86_64/libgfortran.a(compile_options.o) and (2) in DNAcopy.so
** R
** data
**  moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
* DONE (DNAcopy)