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Package 55/233HostnameOS / ArchBUILDCHECKBUILD BIN
cosmo 1.4.0
Oliver Bembom
Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/cosmo
Last Changed Rev: 27709 / Revision: 30966
Last Changed Date: 2007-10-02 17:41:09 -0700 (Tue, 02 Oct 2007)
lamb1 Linux (SUSE 10.1) / x86_64  OK  OK 
wilson2 Linux (openSUSE 10.3) / x86_64  OK  OK 
wellington Linux (openSUSE 10.3) / i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
lemming Windows Server 2003 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386 [ OK ] OK  OK 
Package: cosmo
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build cosmo
StartedAt: 2008-04-09 14:37:41 -0700 (Wed, 09 Apr 2008)
EndedAt: 2008-04-09 14:38:45 -0700 (Wed, 09 Apr 2008)
EllapsedTime: 63.9 seconds
RetCode: 0
Status: OK
PackageFile: cosmo_1.4.0.tar.gz
PackageFileSize: 813.5 KiB

Command output

* checking for file 'cosmo/DESCRIPTION' ... OK
* preparing 'cosmo':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running cleanup
rm: src/*.o: No such file or directory
rm: src/*.so: No such file or directory
rm: Makevars: No such file or directory
* installing the package to re-build vignettes
* Installing *source* package 'cosmo' ...
** libs
** arch - i386
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c alloc.c -o alloc.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c back.c -o back.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c constraints.c -o constraints.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c cosmo.c -o cosmo.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c cregistration.c -o cregistration.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c donlp2.c -o donlp2.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c estarts.c -o estarts.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c eval.c -o eval.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c fit.c -o fit.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c free.c -o free.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c init.c -o init.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c io.c -o io.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c lstarts.c -o lstarts.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c matLib.c -o matLib.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c newx.c -o newx.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c optimize.c -o optimize.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c posterior.c -o posterior.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c precalc.c -o precalc.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c rio.c -o rio.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c theta.c -o theta.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c user_eval.c -o user_eval.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -IINCLUDE -msse3    -fPIC  -g -O2 -march=nocona -c xml.c -o xml.o
gcc -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cosmo.so alloc.o back.o constraints.o cosmo.o cregistration.o donlp2.o estarts.o eval.o fit.o free.o init.o io.o lstarts.o matLib.o newx.o optimize.o posterior.o precalc.o rio.o theta.o user_eval.o xml.o   -F/Library/Frameworks/R.framework/.. -framework R 
** arch - ppc
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c alloc.c -o alloc.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c back.c -o back.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c constraints.c -o constraints.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c cosmo.c -o cosmo.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c cregistration.c -o cregistration.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c donlp2.c -o donlp2.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c estarts.c -o estarts.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c eval.c -o eval.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c fit.c -o fit.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c free.c -o free.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c init.c -o init.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c io.c -o io.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c lstarts.c -o lstarts.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c matLib.c -o matLib.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c newx.c -o newx.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c optimize.c -o optimize.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c posterior.c -o posterior.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c precalc.c -o precalc.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c rio.c -o rio.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c theta.c -o theta.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c user_eval.c -o user_eval.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c xml.c -o xml.o
gcc -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -mmacosx-version-min=10.4 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -Wl,-macosx_version_min -Wl,10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o cosmo.so alloc.o back.o constraints.o cosmo.o cregistration.o donlp2.o estarts.o eval.o fit.o free.o init.o io.o lstarts.o matLib.o newx.o optimize.o posterior.o precalc.o rio.o theta.o user_eval.o xml.o   -F/Library/Frameworks/R.framework/.. -framework R 
** R
** data
** inst
** preparing package for lazy loading
Loading required package: seqLogo
Loading required package: grid
** help
 >>> Building/Updating help pages for package 'cosmo'
     Formats: text html latex example 
  addCon                            text    html    latex   example
  align-class                       text    html    latex   example
  bfile2tmat                        text    html    latex   example
  bgModel                           text    html    latex   example
  boundCon-class                    text    html    latex   example
  constraintSet-class               text    html    latex   example
  cosmo-class                       text    html    latex   example
  cosmo                             text    html    latex   example
  intInfo-class                     text    html    latex   example
  license.cosmo                     text    html    latex   example
  makeBoundCon                      text    html    latex   example
  makeConSet                        text    html    latex   example
  makePalCon                        text    html    latex   example
  makePosFreqCon                    text    html    latex   example
  makeShapeCon                      text    html    latex   example
  makeShapeDiffCon                  text    html    latex   example
  makeSubMotifCon                   text    html    latex   example
  motifPWM                          text    html    latex   example
  palCon-class                      text    html    latex   example
  posFreqCon-class                  text    html    latex   example
  postProbs-class                   text    html    latex   example
  readConFile                       text    html    latex   example
  rseq                              text    html    latex   example
  shapeCon-class                    text    html    latex   example
  shapeDiffCon-class                text    html    latex   example
  simScore                          text    html    latex   example
  subMotifCon-class                 text    html    latex   example
  transMats                         text    html    latex   example
  writeConFile                      text    html    latex   example
** building package indices ...
* DONE (cosmo)
* creating vignettes ... OK
* cleaning src
* running cleanup
rm: src/*.o: No such file or directory
rm: src/*.so: No such file or directory
rm: Makevars: No such file or directory
* removing junk files
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building 'cosmo_1.4.0.tar.gz'