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Package 80/319HostnameOS / ArchBUILDCHECKBUILD BIN
DNAcopy 1.18.0
Venkatraman E. Seshan
Bioconductor Changelog
Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/DNAcopy
Last Changed Rev: 39013 / Revision: 42512
Last Changed Date: 2009-04-20 16:24:12 -0700 (Mon, 20 Apr 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: 1.18.0
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes DNAcopy_1.18.0.tar.gz
StartedAt: 2009-10-20 17:23:56 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 17:24:29 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 32.7 seconds
RetCode: 0
Status: OK
CheckDir: DNAcopy.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/DNAcopy.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'DNAcopy/DESCRIPTION' ... OK
* this is package 'DNAcopy' version '1.18.0'
* 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 name space 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 files against version 2 parser ... 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 package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

DNAcopy.Rcheck/00install.out:

* Installing *source* package ‘DNAcopy’ ...
** libs
** arch - i386
gfortran-4.2 -arch i386   -fPIC  -g -O2 -Wall -c cbsWtstats.f -o cbsWtstats.o
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-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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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 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 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 cbsWtstats.f -o cbsWtstats.o
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-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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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 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 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 cbsWtstats.f -o cbsWtstats.o
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-wtd.f -o changepoints-wtd.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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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 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 tailprobs.o -lgfortran -lSystemStubs -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gfortran-4.2 -arch x86_64   -fPIC  -g -O2 -Wall -c cbsWtstats.f -o cbsWtstats.o
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-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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/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 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 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
*** installing help indices
 >>> 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)