cosmo 1.12.0
Oliver Bembom
| Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/cosmo | | Last Changed Rev: 42684 / Revision: 43539 | | Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009) |
| 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 (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.5-bioc/meat/cosmo.Rcheck'
* using R version 2.10.0 Patched (2009-10-27 r50222)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'cosmo/DESCRIPTION' ... OK
* this is package 'cosmo' version '1.12.0'
* 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 ... NOTE
prepare_Rd: addCon.Rd:22-23: Dropping empty section \details
prepare_Rd: align-class.Rd:59: Dropping empty section \note
prepare_Rd: align-class.Rd:56: Dropping empty section \references
prepare_Rd: align-class.Rd:62-63: Dropping empty section \seealso
prepare_Rd: align-class.Rd:64-65: Dropping empty section \examples
prepare_Rd: bfile2tmat.Rd:40: Dropping empty section \keyword
prepare_Rd: bfile2tmat.Rd:14-16: Dropping empty section \details
prepare_Rd: bfile2tmat.Rd:27: Dropping empty section \note
prepare_Rd: bfile2tmat.Rd:25: Dropping empty section \references
prepare_Rd: bgModel.Rd:67: Dropping empty section \keyword
prepare_Rd: bgModel.Rd:33-35: Dropping empty section \details
prepare_Rd: bgModel.Rd:51: Dropping empty section \note
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prepare_Rd: constraintSet-class.Rd:82: Dropping empty section \note
prepare_Rd: constraintSet-class.Rd:78: Dropping empty section \references
prepare_Rd: constraintSet-class.Rd:88-89: Dropping empty section \examples
prepare_Rd: cosmo-class.Rd:60: Dropping empty section \note
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prepare_Rd: cosmo-class.Rd:65-66: Dropping empty section \examples
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prepare_Rd: intInfo-class.Rd:92-93: Dropping empty section \examples
prepare_Rd: license.cosmo.Rd:10-11: Dropping empty section \arguments
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prepare_Rd: license.cosmo.Rd:21-22: Dropping empty section \seealso
prepare_Rd: makeBoundCon.Rd:17-18: Dropping empty section \details
prepare_Rd: makePalCon.Rd:18-19: Dropping empty section \details
prepare_Rd: makePosFreqCon.Rd:24-25: Dropping empty section \details
prepare_Rd: makeShapeCon.Rd:28-29: Dropping empty section \details
prepare_Rd: makeShapeDiffCon.Rd:30-31: Dropping empty section \details
prepare_Rd: makeSubMotifCon.Rd:17-18: Dropping empty section \details
prepare_Rd: motifPWM.Rd:13-14: Dropping empty section \details
prepare_Rd: motifPWM.Rd:15-16: Dropping empty section \source
prepare_Rd: motifPWM.Rd:17-18: Dropping empty section \references
prepare_Rd: palCon-class.Rd:32: Dropping empty section \references
prepare_Rd: posFreqCon-class.Rd:32: Dropping empty section \references
prepare_Rd: postProbs-class.Rd:39: Dropping empty section \note
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prepare_Rd: simScore.Rd:28: Dropping empty section \note
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prepare_Rd: subMotifCon-class.Rd:33-34: Dropping empty section \note
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prepare_Rd: transMats.Rd:19-20: Dropping empty section \source
prepare_Rd: transMats.Rd:21-22: Dropping empty section \references
* checking Rd metadata ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package ‘cosmo’ ...
** libs
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/Resources/include -I/Library/Frameworks/R.framework/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/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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -std=gnu99 -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 -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: grid
** help
*** installing help indices
** building package indices ...
* DONE (cosmo)