DNAcopy 1.16.0
Venkatraman E. Seshan
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/DNAcopy | | Last Changed Rev: 34811 / Revision: 38965 | | Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008) |
| wilson2 | 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 (10.5.6) / i386 | OK | [ OK ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/DNAcopy.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'DNAcopy/DESCRIPTION' ... OK
* this is package 'DNAcopy' version '1.16.0'
* 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 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 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
* creating DNAcopy-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating DNAcopy-manual.tex ... OK
* checking DNAcopy-manual.tex using pdflatex ... OK
* Installing *source* package 'DNAcopy' ...
** libs
** arch - i386
gfortran-4.2 -arch i386 -fPIC -g -O2 -Wall -c cbststats.f -o cbststats.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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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 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 cbststats.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o tailprobs.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gfortran-4.2 -arch ppc -fPIC -g -O2 -Wall -c cbststats.f -o cbststats.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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c flchoose.c -o flchoose.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c fphyper.c -o fphyper.o
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -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 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 cbststats.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o tailprobs.o -lgfortran -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gfortran-4.2 -arch ppc64 -fPIC -g -O2 -Wall -c cbststats.f -o cbststats.o
gfortran-4.2 -arch ppc64 -fPIC -g -O2 -Wall -c changepoints.f -o changepoints.o
gfortran-4.2 -arch ppc64 -fPIC -g -O2 -Wall -c esegment.f -o esegment.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c flchoose.c -o flchoose.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c fphyper.c -o fphyper.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c fpnorm.c -o fpnorm.o
gfortran-4.2 -arch ppc64 -fPIC -g -O2 -Wall -c getbdry.f -o getbdry.o
gfortran-4.2 -arch ppc64 -fPIC -g -O2 -Wall -c prune.f -o prune.o
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64 -I/usr/local/include -fPIC -g -O2 -Wall -c rshared.c -o rshared.o
gfortran-4.2 -arch ppc64 -fPIC -g -O2 -Wall -c segmentp.f -o segmentp.o
gfortran-4.2 -arch ppc64 -fPIC -g -O2 -Wall -c tailprobs.f -o tailprobs.o
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o DNAcopy.so cbststats.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o tailprobs.o -lgfortran -lSystemStubs -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gfortran-4.2 -arch x86_64 -fPIC -g -O2 -Wall -c cbststats.f -o cbststats.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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/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 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 cbststats.o changepoints.o esegment.o flchoose.o fphyper.o fpnorm.o getbdry.o prune.o rshared.o segmentp.o tailprobs.o -lgfortran -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'DNAcopy'
Formats: text html latex example
CNA text html latex example
DNAcopy-internal text html latex
DNAcopy text html latex
coriell text html latex
cytoBand text html latex
exon.segment text html latex example
getbdry text html latex
plot.DNAcopy text html latex example
segment text html latex example
segments.p text html latex example
segments.summary text html latex example
smooth.CNA text html latex example
subset.CNA text html latex example
subset.DNAcopy text html latex
** building package indices ...
* DONE (DNAcopy)