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Package 257/319HostnameOS / ArchBUILDCHECKBUILD BIN
Ringo 1.8.0
J. Toedling
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/Ringo
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: Ringo
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.9/Resources/bin/R CMD check --no-vignettes Ringo_1.8.0.tar.gz
StartedAt: 2009-10-20 18:45:09 -0700 (Tue, 20 Oct 2009)
EndedAt: 2009-10-20 18:47:34 -0700 (Tue, 20 Oct 2009)
EllapsedTime: 144.4 seconds
RetCode: 0
Status: OK
CheckDir: Ringo.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.4-bioc/meat/Ringo.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49419)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'Ringo/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'Ringo' version '1.8.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'Ringo' 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 ... NOTE
oneChannelVSN: no visible global function definition for ‘vsnMatrix’
* 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 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

Ringo.Rcheck/00install.out:

* Installing *source* package ‘Ringo’ ...
** libs
** arch - i386
g++ -arch i386 -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  -mtune=core2 -g -O2 -c mmeansd.cpp -o mmeansd.o
g++ -arch i386 -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  -mtune=core2 -g -O2 -c mmedian.cpp -o mmedian.o
gcc -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  -mtune=core2 -g -O2 -c region_overlap.c -o region_overlap.o
gcc -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  -mtune=core2 -g -O2 -c ringo_init.c -o ringo_init.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
g++ -arch ppc -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 -c mmeansd.cpp -o mmeansd.o
g++ -arch ppc -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 -c mmedian.cpp -o mmedian.o
gcc -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 -c region_overlap.c -o region_overlap.o
gcc -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 -c ringo_init.c -o ringo_init.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Ringo.so mmeansd.o mmedian.o region_overlap.o ringo_init.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Loading required package: lattice

Attaching package: 'Matrix'


	The following object(s) are masked from package:stats :

	 contr.SAS,
	 contr.helmert,
	 contr.poly,
	 contr.sum,
	 contr.treatment,
	 xtabs 


	The following object(s) are masked from package:base :

	 rcond 

Creating a new generic function for "plot" in "Ringo"
Creating a new generic function for "get" in "Ringo"
Creating a new generic function for "ls" in "Ringo"
** help
*** installing help indices
 >>> Building/Updating help pages for package 'Ringo'
     Formats: text html latex example 
  Ringo-internal                    text    html    latex
  arrayImage                        text    html    latex   example
  asExprSet                         text    html    latex   example
  autocorr                          text    html    latex   example
  cherByThreshold                   text    html    latex   example
  cherClass                         text    html    latex   example
  chipAlongChrom                    text    html    latex   example
  computeRunningMedians             text    html    latex   example
  compute_gc                        text    html    latex   example
  compute_sliding_t                 text    html    latex   example
  corrPlot                          text    html    latex   example
  exportCherList                    text    html    latex   example
  extractProbeAnno                  text    html    latex
  features2Probes                   text    html    latex   example
  findChersOnSmoothed               text    html    latex   example
  ftr2xys                           text    html    latex   example
  getFeats                          text    html    latex
  newCER                            text    html    latex   example
  nimblegenNorm                     text    html    latex
  nonzero                           text    html    latex   example
  plotAutocorr                      text    html    latex   example
  plotBM                            text    html    latex   example
  plot_cher                         text    html    latex
  posToProbeAnnoEnvironment         text    html    latex   example
  preprocess                        text    html    latex   example
  probeAnnoClass                    text    html    latex   example
  readNimblegen                     text    html    latex   example
  regionoverlap                     text    html    latex   example
  relateCERs                        text    html    latex   example
  sliding_meansd                    text    html    latex   example
  sliding_quantile                  text    html    latex   example
  twoGaussiansNull                  text    html    latex   example
  upperBoundNull                    text    html    latex   example
  validProbeAnno                    text    html    latex   example
** building package indices ...
* DONE (Ringo)