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Package 68/294HostnameOS / ArchBUILDCHECKBUILD BIN
cosmo 1.8.0
Oliver Bembom
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/cosmo
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 
Package: cosmo
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes cosmo_1.8.0.tar.gz
StartedAt: 2009-04-18 16:43:39 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 16:45:04 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 85.0 seconds
RetCode: 0
Status: OK
CheckDir: cosmo.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/cosmo.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ASCII
* checking for file 'cosmo/DESCRIPTION' ... OK
* this is package 'cosmo' 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 'cosmo' 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
.onUnload: no visible binding for global variable 'libpath'
* 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 compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating cosmo-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating cosmo-manual.tex ... OK
* checking cosmo-manual.tex using pdflatex ... OK

cosmo.Rcheck/00install.out:

* Installing *source* package 'cosmo' ...
** libs
** arch - i386
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c alloc.c -o alloc.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c back.c -o back.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c constraints.c -o constraints.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c cosmo.c -o cosmo.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c cregistration.c -o cregistration.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c donlp2.c -o donlp2.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c estarts.c -o estarts.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c eval.c -o eval.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c fit.c -o fit.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c free.c -o free.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c init.c -o init.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c io.c -o io.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c lstarts.c -o lstarts.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c matLib.c -o matLib.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c newx.c -o newx.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c optimize.c -o optimize.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c posterior.c -o posterior.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c precalc.c -o precalc.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c rio.c -o rio.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c theta.c -o theta.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c user_eval.c -o user_eval.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c xml.c -o xml.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=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 -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c alloc.c -o alloc.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c back.c -o back.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c constraints.c -o constraints.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c cosmo.c -o cosmo.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c cregistration.c -o cregistration.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c donlp2.c -o donlp2.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c estarts.c -o estarts.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c eval.c -o eval.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c fit.c -o fit.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c free.c -o free.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c init.c -o init.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c io.c -o io.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c lstarts.c -o lstarts.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c matLib.c -o matLib.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c newx.c -o newx.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c optimize.c -o optimize.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c posterior.c -o posterior.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c precalc.c -o precalc.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c rio.c -o rio.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c theta.c -o theta.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c user_eval.c -o user_eval.o
gcc -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 -IINCLUDE -I/usr/local/include    -fPIC  -g -O2 -c xml.c -o xml.o
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=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 -Wl,-framework -Wl,CoreFoundation
** 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 
Note: removing empty section \details in file 'addCon.Rd'
  addCon                            text    html    latex   example
Note: removing empty section \note in file 'align-class.Rd'
Note: removing empty section \references in file 'align-class.Rd'
Note: removing empty section \seealso in file 'align-class.Rd'
Note: removing empty section \examples in file 'align-class.Rd'
  align-class                       text    html    latex
Note: ignoring empty \keyword entries in file 'bfile2tmat.Rd'
Note: removing empty section \details in file 'bfile2tmat.Rd'
Note: removing empty section \note in file 'bfile2tmat.Rd'
Note: removing empty section \references in file 'bfile2tmat.Rd'
  bfile2tmat                        text    html    latex   example
Note: ignoring empty \keyword entries in file 'bgModel.Rd'
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Note: removing empty section \note in file 'bgModel.Rd'
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  bgModel                           text    html    latex   example
Note: removing empty section \references in file 'boundCon-class.Rd'
  boundCon-class                    text    html    latex   example
Note: removing empty section \note in file 'constraintSet-class.Rd'
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Note: removing empty section \examples in file 'constraintSet-class.Rd'
  constraintSet-class               text    html    latex
Note: removing empty section \note in file 'cosmo-class.Rd'
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  cosmo-class                       text    html    latex
Note: removing empty section \details in file 'cosmo.Rd'
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  cosmo                             text    html    latex   example
Note: removing empty section \note in file 'intInfo-class.Rd'
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Note: removing empty section \examples in file 'intInfo-class.Rd'
  intInfo-class                     text    html    latex
Note: removing empty section \details in file 'license.cosmo.Rd'
Note: removing empty section \arguments in file 'license.cosmo.Rd'
Note: removing empty section \seealso in file 'license.cosmo.Rd'
  license.cosmo                     text    html    latex   example
Note: removing empty section \details in file 'makeBoundCon.Rd'
  makeBoundCon                      text    html    latex   example
  makeConSet                        text    html    latex   example
Note: removing empty section \details in file 'makePalCon.Rd'
  makePalCon                        text    html    latex   example
Note: removing empty section \details in file 'makePosFreqCon.Rd'
  makePosFreqCon                    text    html    latex   example
Note: removing empty section \details in file 'makeShapeCon.Rd'
  makeShapeCon                      text    html    latex   example
Note: removing empty section \details in file 'makeShapeDiffCon.Rd'
  makeShapeDiffCon                  text    html    latex   example
Note: removing empty section \details in file 'makeSubMotifCon.Rd'
  makeSubMotifCon                   text    html    latex   example
Note: removing empty section \source in file 'motifPWM.Rd'
Note: removing empty section \details in file 'motifPWM.Rd'
Note: removing empty section \references in file 'motifPWM.Rd'
  motifPWM                          text    html    latex   example
Note: removing empty section \references in file 'palCon-class.Rd'
  palCon-class                      text    html    latex   example
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  posFreqCon-class                  text    html    latex   example
Note: removing empty section \note in file 'postProbs-class.Rd'
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Note: removing empty section \examples in file 'postProbs-class.Rd'
  postProbs-class                   text    html    latex
Note: removing empty section \details in file 'readConFile.Rd'
  readConFile                       text    html    latex   example
Note: removing empty section \details in file 'rseq.Rd'
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  rseq                              text    html    latex   example
Note: removing empty section \references in file 'shapeCon-class.Rd'
  shapeCon-class                    text    html    latex   example
Note: removing empty section \references in file 'shapeDiffCon-class.Rd'
  shapeDiffCon-class                text    html    latex   example
Note: removing empty section \details in file 'simScore.Rd'
Note: removing empty section \note in file 'simScore.Rd'
Note: removing empty section \references in file 'simScore.Rd'
  simScore                          text    html    latex   example
Note: removing empty section \note in file 'subMotifCon-class.Rd'
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  subMotifCon-class                 text    html    latex   example
Note: removing empty section \source in file 'transMats.Rd'
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  transMats                         text    html    latex   example
  writeConFile                      text    html    latex   example
** building package indices ...
* DONE (cosmo)